From 67fec603ecbf2759064cd36566d23b4f6aaed4ff Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 20 Dec 2022 18:53:25 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.graphql | 2 +- biolink-model.owl.ttl | 1092 ++++++++--------- biolink-model.proto | 2 +- biolink-model.shexj | 2 +- biolink-model.ttl | 600 ++++----- biolink-modeln.shex | 2 +- biolink-modeln.shexj | 2 +- biolink/model.py | 4 +- biolink/pydanticmodel.py | 2 +- context.jsonld | 2 +- contextn.jsonld | 2 +- golr-views/RNA_product_config.yaml | 2 +- golr-views/RNA_product_isoform_config.yaml | 2 +- golr-views/activity_config.yaml | 2 +- golr-views/agent_config.yaml | 2 +- golr-views/anatomical_entity_config.yaml | 2 +- ...l_entity_ontogenic_association_config.yaml | 2 +- ...cal_entity_part_of_association_config.yaml | 2 +- golr-views/article_config.yaml | 2 +- golr-views/association_config.yaml | 2 +- golr-views/attribute_config.yaml | 2 +- golr-views/behavior_config.yaml | 2 +- ...behavioral_feature_association_config.yaml | 2 +- golr-views/behavioral_exposure_config.yaml | 2 +- golr-views/behavioral_feature_config.yaml | 2 +- golr-views/biological_process_config.yaml | 2 +- ...biological_process_or_activity_config.yaml | 2 +- golr-views/biological_sex_config.yaml | 2 +- golr-views/biotic_exposure_config.yaml | 2 +- golr-views/book_chapter_config.yaml | 2 +- golr-views/book_config.yaml | 2 +- golr-views/case_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/cell_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/cell_line_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/cellular_component_config.yaml | 2 +- golr-views/cellular_organism_config.yaml | 2 +- ...mical_affects_gene_association_config.yaml | 2 +- ...sesses_named_thing_association_config.yaml | 2 +- golr-views/chemical_entity_config.yaml | 2 +- ...uct_regulates_gene_association_config.yaml | 2 +- golr-views/chemical_exposure_config.yaml | 2 +- ...l_gene_interaction_association_config.yaml | 2 +- golr-views/chemical_mixture_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/chemical_role_config.yaml | 2 +- ...emical_to_chemical_association_config.yaml | 2 +- ...hemical_derivation_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...hemical_to_pathway_association_config.yaml | 2 +- .../chi_squared_analysis_result_config.yaml | 2 +- golr-views/clinical_attribute_config.yaml | 2 +- golr-views/clinical_course_config.yaml | 2 +- golr-views/clinical_entity_config.yaml | 2 +- golr-views/clinical_finding_config.yaml | 2 +- golr-views/clinical_intervention_config.yaml | 2 +- golr-views/clinical_measurement_config.yaml | 2 +- golr-views/clinical_modifier_config.yaml | 2 +- golr-views/clinical_trial_config.yaml | 2 +- golr-views/coding_sequence_config.yaml | 2 +- golr-views/cohort_config.yaml | 2 +- golr-views/common_data_element_config.yaml | 2 +- .../complex_chemical_exposure_config.yaml | 2 +- .../complex_molecular_mixture_config.yaml | 2 +- .../concept_count_analysis_result_config.yaml | 2 +- golr-views/confidence_level_config.yaml | 2 +- .../contributor_association_config.yaml | 2 +- golr-views/dataset_config.yaml | 2 +- golr-views/dataset_distribution_config.yaml | 2 +- golr-views/dataset_summary_config.yaml | 2 +- golr-views/dataset_version_config.yaml | 2 +- golr-views/device_config.yaml | 2 +- golr-views/disease_config.yaml | 2 +- .../disease_or_phenotypic_feature_config.yaml | 2 +- ...or_phenotypic_feature_exposure_config.yaml | 2 +- ...enetic_inheritance_association_config.yaml | 2 +- ...eature_to_location_association_config.yaml | 2 +- ..._to_exposure_event_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/drug_config.yaml | 2 +- golr-views/drug_exposure_config.yaml | 2 +- .../drug_to_gene_association_config.yaml | 2 +- ...g_to_gene_interaction_exposure_config.yaml | 2 +- ...le_gene_to_disease_association_config.yaml | 2 +- .../entity_to_disease_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/environmental_exposure_config.yaml | 2 +- golr-views/environmental_feature_config.yaml | 2 +- ...environmental_food_contaminant_config.yaml | 2 +- golr-views/environmental_process_config.yaml | 2 +- golr-views/event_config.yaml | 2 +- golr-views/evidence_type_config.yaml | 2 +- golr-views/exon_config.yaml | 2 +- ...xon_to_transcript_relationship_config.yaml | 2 +- ...e_event_to_outcome_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/food_additive_config.yaml | 2 +- golr-views/food_config.yaml | 2 +- golr-views/functional_association_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/gene_config.yaml | 2 +- golr-views/gene_family_config.yaml | 2 +- ...ributes_to_disease_association_config.yaml | 2 +- .../gene_to_disease_association_config.yaml | 2 +- ...to_expression_site_association_config.yaml | 2 +- ..._gene_coexpression_association_config.yaml | 2 +- ...ene_to_gene_family_association_config.yaml | 2 +- ...e_to_gene_homology_association_config.yaml | 2 +- ...e_to_gene_product_relationship_config.yaml | 2 +- .../gene_to_go_term_association_config.yaml | 2 +- .../gene_to_pathway_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/genetic_inheritance_config.yaml | 2 +- golr-views/genome_config.yaml | 2 +- .../genomic_background_exposure_config.yaml | 2 +- .../genomic_sequence_localization_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- golr-views/genotype_config.yaml | 2 +- ...enotype_to_disease_association_config.yaml | 2 +- .../genotype_to_gene_association_config.yaml | 2 +- ...e_to_genotype_part_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...enotype_to_variant_association_config.yaml | 2 +- golr-views/genotypic_sex_config.yaml | 2 +- golr-views/geographic_exposure_config.yaml | 2 +- .../geographic_location_at_time_config.yaml | 2 +- golr-views/geographic_location_config.yaml | 2 +- .../gross_anatomical_structure_config.yaml | 2 +- golr-views/haplotype_config.yaml | 2 +- golr-views/hospitalization_config.yaml | 2 +- golr-views/individual_organism_config.yaml | 2 +- ...ity_to_named_thing_association_config.yaml | 2 +- golr-views/information_resource_config.yaml | 2 +- golr-views/life_stage_config.yaml | 2 +- golr-views/macromolecular_complex_config.yaml | 2 +- ...biological_process_association_config.yaml | 2 +- ...cellular_component_association_config.yaml | 2 +- ...molecular_activity_association_config.yaml | 2 +- golr-views/material_sample_config.yaml | 2 +- ..._sample_derivation_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- golr-views/microRNA_config.yaml | 2 +- golr-views/molecular_activity_config.yaml | 2 +- ...to_chemical_entity_association_config.yaml | 2 +- ...molecular_activity_association_config.yaml | 2 +- ...ctivity_to_pathway_association_config.yaml | 2 +- golr-views/molecular_entity_config.yaml | 2 +- golr-views/molecular_mixture_config.yaml | 2 +- ...ood_of_named_thing_association_config.yaml | 2 +- golr-views/named_thing_config.yaml | 2 +- golr-views/noncoding_RNA_product_config.yaml | 2 +- golr-views/nucleic_acid_entity_config.yaml | 2 +- .../nucleic_acid_sequence_motif_config.yaml | 2 +- .../nucleosome_modification_config.yaml | 2 +- ...cted_frequency_analysis_result_config.yaml | 2 +- golr-views/onset_config.yaml | 2 +- golr-views/organism_attribute_config.yaml | 2 +- golr-views/organism_taxon_config.yaml | 2 +- ..._to_organism_taxon_interaction_config.yaml | 2 +- ..._organism_taxon_specialization_config.yaml | 2 +- ...ganism_to_organism_association_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- ...rwise_gene_to_gene_interaction_config.yaml | 2 +- ...pairwise_molecular_interaction_config.yaml | 2 +- ...thological_anatomical_exposure_config.yaml | 2 +- ...hological_anatomical_structure_config.yaml | 2 +- golr-views/pathological_process_config.yaml | 2 +- .../pathological_process_exposure_config.yaml | 2 +- golr-views/pathway_config.yaml | 2 +- golr-views/phenomenon_config.yaml | 2 +- golr-views/phenotypic_feature_config.yaml | 2 +- golr-views/phenotypic_quality_config.yaml | 2 +- golr-views/phenotypic_sex_config.yaml | 2 +- golr-views/physical_entity_config.yaml | 2 +- golr-views/physiological_process_config.yaml | 2 +- golr-views/planetary_entity_config.yaml | 2 +- golr-views/polypeptide_config.yaml | 2 +- ...lation_of_individual_organisms_config.yaml | 2 +- ...tion_to_population_association_config.yaml | 2 +- ...posttranslational_modification_config.yaml | 2 +- golr-views/predicate_mapping_config.yaml | 2 +- golr-views/procedure_config.yaml | 2 +- golr-views/processed_material_config.yaml | 2 +- golr-views/protein_config.yaml | 2 +- golr-views/protein_domain_config.yaml | 2 +- golr-views/protein_family_config.yaml | 2 +- golr-views/protein_isoform_config.yaml | 2 +- golr-views/publication_config.yaml | 2 +- golr-views/quantity_value_config.yaml | 2 +- ...action_to_catalyst_association_config.yaml | 2 +- ...ion_to_participant_association_config.yaml | 2 +- golr-views/reagent_targeted_gene_config.yaml | 2 +- ...tive_frequency_analysis_result_config.yaml | 2 +- golr-views/sequence_association_config.yaml | 2 +- .../sequence_feature_relationship_config.yaml | 2 +- golr-views/sequence_variant_config.yaml | 2 +- golr-views/serial_config.yaml | 2 +- golr-views/severity_value_config.yaml | 2 +- golr-views/siRNA_config.yaml | 2 +- golr-views/small_molecule_config.yaml | 2 +- golr-views/snv_config.yaml | 2 +- .../socioeconomic_attribute_config.yaml | 2 +- golr-views/socioeconomic_exposure_config.yaml | 2 +- golr-views/study_config.yaml | 2 +- golr-views/study_population_config.yaml | 2 +- golr-views/study_variable_config.yaml | 2 +- .../taxon_to_taxon_association_config.yaml | 2 +- golr-views/text_mining_result_config.yaml | 2 +- golr-views/transcript_config.yaml | 2 +- ...ranscript_to_gene_relationship_config.yaml | 2 +- golr-views/treatment_config.yaml | 2 +- ...a_model_of_disease_association_config.yaml | 2 +- ...variant_to_disease_association_config.yaml | 2 +- .../variant_to_gene_association_config.yaml | 2 +- ...to_gene_expression_association_config.yaml | 2 +- ...phenotypic_feature_association_config.yaml | 2 +- ...iant_to_population_association_config.yaml | 2 +- golr-views/virus_config.yaml | 2 +- golr-views/zygosity_config.yaml | 2 +- json-schema/biolink-model.json | 2 +- 223 files changed, 1068 insertions(+), 1068 deletions(-) diff --git a/biolink-model.graphql b/biolink-model.graphql index c2aaabb2b1..510345fa18 100644 --- a/biolink-model.graphql +++ b/biolink-model.graphql @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.1.1 +# version: 3.1.2 type Activity implements ActivityAndBehavior { id: String! diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index c5383e6ff6..04e6807470 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -107,11 +107,11 @@ biolink:ThingWithTaxon, biolink:VariantToEntityAssociationMixin ; dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "3.1.1" ; - linkml:generation_date "2022-12-12T22:39:18" ; + pav:version "3.1.2" ; + linkml:generation_date "2022-12-20T18:46:15" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-12-12T22:38:08" ; + linkml:source_file_date "2022-12-20T18:45:00" ; linkml:source_file_size 334572 . biolink:Activity a owl:Class ; @@ -133,10 +133,6 @@ biolink:Activity a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -144,6 +140,10 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." . @@ -177,19 +177,19 @@ biolink:Article a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], biolink:Publication . biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BehavioralFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Behavior ; owl:onProperty rdf:subject ; @@ -197,35 +197,35 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:onClass biolink:BehavioralFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . @@ -275,35 +275,35 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -322,21 +322,21 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:CellLine ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -351,90 +351,90 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" . biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; @@ -465,49 +465,49 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; @@ -527,19 +527,19 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation ; skos:definition """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: @@ -640,20 +640,20 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:Agent ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:Agent ; - owl:onProperty rdf:object ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . @@ -708,28 +708,24 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -737,11 +733,15 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -775,9 +775,6 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -785,6 +782,9 @@ biolink:DruggableGeneToDiseaseAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, biolink:GeneToEntityAssociationMixin . @@ -837,26 +837,26 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Exon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Transcript ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Exon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" . biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], biolink:Association, biolink:EntityToOutcomeAssociationMixin ; skos:definition "An association between an exposure event and an outcome." . @@ -865,16 +865,12 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -884,21 +880,25 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:onClass biolink:ExposureEvent ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:ExposureEvent ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -927,21 +927,21 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:GeneToDiseaseAssociation . biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; @@ -1003,14 +1003,6 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1019,6 +1011,14 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" . @@ -1026,21 +1026,21 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; @@ -1070,11 +1070,11 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -1086,10 +1086,6 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1097,6 +1093,10 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onClass biolink:GeneProductMixin ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" . @@ -1117,13 +1117,13 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:GeneToEntityAssociationMixin ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." . @@ -1132,44 +1132,44 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -1194,19 +1194,19 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent, biolink:GeneGroupingMixin, @@ -1246,13 +1246,13 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; @@ -1265,43 +1265,43 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -1500,11 +1500,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" . @@ -1512,16 +1512,16 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; + owl:onClass biolink:MolecularActivity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." . @@ -1536,23 +1536,23 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "" . @@ -1603,11 +1603,11 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -1623,16 +1623,16 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . @@ -1652,14 +1652,6 @@ biolink:OrganismToOrganismAssociation a owl:Class ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1667,6 +1659,14 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1674,6 +1674,10 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], @@ -1685,10 +1689,6 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:object ; @@ -1915,13 +1915,13 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Treatment ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Treatment ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:note "An alternate way to model the same information could be via a qualifier" . @@ -1930,23 +1930,23 @@ biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty rdf:type ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], biolink:Publication ; skos:altLabel "journal" ; @@ -1997,16 +1997,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." . @@ -2037,11 +2037,11 @@ biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -2053,13 +2053,13 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Transcript ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Transcript ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" . @@ -2077,20 +2077,20 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; @@ -2103,40 +2103,40 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin . @@ -2150,27 +2150,27 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -3002,13 +3002,13 @@ biolink:ChemicalFormulaValue a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FDAIDAAdverseEventEnum ; + owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association, biolink:ChemicalToEntityAssociationMixin, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ; @@ -3117,28 +3117,28 @@ biolink:GeneFamily a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, @@ -3150,11 +3150,11 @@ biolink:GeographicLocation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -3210,20 +3210,20 @@ biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionDirectionEnum ; - owl:onProperty biolink:reaction_direction ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], + owl:onClass biolink:ReactionDirectionEnum ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:stoichiometry ], + owl:onClass biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], biolink:ChemicalToChemicalAssociation . biolink:SequenceAssociation a owl:Class ; @@ -3249,6 +3249,9 @@ biolink:SymbolType a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], @@ -3258,9 +3261,6 @@ biolink:Treatment a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -3274,13 +3274,9 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; @@ -3294,9 +3290,13 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -3305,13 +3305,13 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:VariantToEntityAssociationMixin ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" . @@ -5676,8 +5676,8 @@ biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -5688,8 +5688,8 @@ biolink:FrequencyQuantifier a owl:Class ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:RelationshipQuantifier, linkml:mixin . @@ -6574,11 +6574,11 @@ biolink:DatasetSummary a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty schema:logo ], + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:source_web_page ], + owl:onProperty schema:logo ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." . @@ -6630,30 +6630,26 @@ biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -6661,14 +6657,18 @@ biolink:GeneToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -6680,11 +6680,11 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; @@ -6748,31 +6748,10 @@ biolink:PredicateMapping a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -6780,19 +6759,22 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:AnatomicalContextQualifierEnum ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -6800,31 +6782,49 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalContextQualifierEnum ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ] ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ] ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." . biolink:Protein a owl:Class ; @@ -7148,13 +7148,13 @@ biolink:PhysicalEntity a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Unit ; owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_numeric_value ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" . @@ -7467,31 +7467,31 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NarrativeText ; owl:onProperty dct:description ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty rdf:type ], + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ] ; + owl:onClass linkml:String ; + owl:onProperty rdf:type ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . biolink:GeneToEntityAssociationMixin a owl:Class ; @@ -7669,13 +7669,6 @@ rdfs:label a owl:ObjectProperty ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalMixture ; owl:onProperty biolink:is_supplement ], @@ -7683,6 +7676,13 @@ biolink:ChemicalMixture a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -7744,13 +7744,13 @@ biolink:GeneProductMixin a owl:Class ; biolink:ModelToDiseaseAssociationMixin a owl:Class ; rdfs:label "model to disease association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], linkml:mixin ; skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" . @@ -8024,13 +8024,13 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -8038,11 +8038,11 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, biolink:FrequencyQuantifier, linkml:mixin . @@ -8338,6 +8338,10 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:onClass biolink:NucleicAcidEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -8348,24 +8352,20 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:PhaseEnum ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onClass biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:StrandEnum ; - owl:onProperty biolink:strand ], + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -8456,10 +8456,10 @@ biolink:MolecularActivity a owl:Class ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -8486,16 +8486,16 @@ biolink:has_biological_sequence a owl:ObjectProperty ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:affiliation ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; @@ -8519,10 +8519,10 @@ biolink:BiologicalProcessOrActivity a owl:Class ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:Occurrent ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:Occurrent ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass ; @@ -8559,12 +8559,12 @@ biolink:timepoint a owl:ObjectProperty ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], biolink:GenomicEntity, biolink:MolecularEntity, biolink:OntologyClass, @@ -8665,14 +8665,14 @@ biolink:InformationContentEntity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8699,33 +8699,33 @@ biolink:InformationContentEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:summary ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty dct:type ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:keywords ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], biolink:InformationContentEntity ; skos:definition "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; skos:exactMatch IAO:0000311 ; @@ -8747,20 +8747,20 @@ biolink:BiologicalEntity a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NamedThing ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], biolink:NamedThing, biolink:OntologyClass ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -8791,16 +8791,16 @@ biolink:AnatomicalEntity a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -8818,16 +8818,16 @@ biolink:SequenceVariant a owl:Class ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; owl:allValuesFrom biolink:LabelType ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -8845,23 +8845,23 @@ biolink:Gene a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:is_toxic ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], + owl:onClass linkml:Boolean ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty biolink:trade_name ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -8989,64 +8989,64 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:InformationResource ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:InformationResource ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:InformationResource ; owl:onProperty biolink:aggregator_knowledge_source ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty rdf:type ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Boolean ; owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:InformationResource ; + owl:onProperty biolink:knowledge_source ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -9056,18 +9056,18 @@ biolink:Association a owl:Class ; biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:provided_by ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ] [ a owl:Restriction ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:CategoryType ] ) ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:provided_by ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, diff --git a/biolink-model.proto b/biolink-model.proto index 568945e62e..a0eb3af5b2 100644 --- a/biolink-model.proto +++ b/biolink-model.proto @@ -1,7 +1,7 @@ syntax="proto3"; package // metamodel_version: 1.7.0 -// version: 3.1.1 +// version: 3.1.2 // An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. message Activity { diff --git a/biolink-model.shexj b/biolink-model.shexj index 9c2d01fa8f..92bc5c25f4 100644 --- a/biolink-model.shexj +++ b/biolink-model.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.1.1 +# version: 3.1.2 { "type": "Schema", "@context": [ diff --git a/biolink-model.ttl b/biolink-model.ttl index 9dff7dd4ca..609d9e74ba 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -12,7 +12,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "3.1.1" ; + pav:version "3.1.2" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -326,256 +326,256 @@ , , ; - linkml:generation_date "2022-12-12T22:39:26"^^xsd:dateTime ; + linkml:generation_date "2022-12-20T18:46:23"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "OMIM.PS" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "NDDF" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PomBase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYECO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBbt" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DOID-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "ECTO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcid" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ComplexPortal" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.food" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.bioplanet" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "RXNORM" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.DISEASE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "AspGD" ; linkml:prefix_reference ], [ linkml:prefix_prefix "gtpo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.RCLASS" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "orphanet" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SPDI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBbt" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ncats.drug" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.food" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "NLMID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AGRKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ChemBank" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "mmmp.biomaps" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.DISEASE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "REPODB" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; 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+ linkml:prefix_reference ] ; linkml:slots , , , @@ -1241,7 +1241,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-12-12T22:38:08"^^xsd:dateTime ; + linkml:source_file_date "2022-12-20T18:45:00"^^xsd:dateTime ; linkml:source_file_size 334572 ; linkml:subsets , , @@ -2039,9 +2039,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "cerebral cortext" ], + skos:example "blood" ], [ a linkml:Example ; - skos:example "blood" ] ; + skos:example "cerebral cortext" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -2200,9 +2200,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "zebrafish" ], + skos:example "human" ], [ a linkml:Example ; - skos:example "human" ] ; + skos:example "zebrafish" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -2480,9 +2480,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "blood" ], + skos:example "cerebral cortext" ], [ a linkml:Example ; - skos:example "cerebral cortext" ] ; + skos:example "blood" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3056,11 +3056,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ], - [ a linkml:Example ; skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ] ; + skos:example "MONDO:0017314" ], + [ a linkml:Example ; + skos:definition "abnormal brain ventricle size" ; + skos:example "MP:0013229" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; @@ -3438,14 +3438,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ], + [ a linkml:Example ; skos:definition "axon morphology variant" ; skos:example "WBPhenotype:0000180" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ], - [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ] ; + skos:example "HP:0002487" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -8094,11 +8094,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "CLINVAR:17681" ], - [ a linkml:Example ; skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; + skos:example "ZFIN:ZDB-ALT-980203-1091" ], + [ a linkml:Example ; + skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; + skos:example "CLINVAR:17681" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -9732,11 +9732,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "positively correlated with" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "positively correlated with" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -10770,11 +10770,11 @@ ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "narrow match" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "narrow match" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -11017,11 +11017,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "treats" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "treats" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11079,11 +11079,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "increases response to" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11241,11 +11241,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "prevents" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11418,11 +11418,11 @@ skos:inScheme ; skos:mappingRelation ; linkml:annotations [ a linkml:Annotation ; - skos:example "is excipient of" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "is excipient of" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11574,11 +11574,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has decreased amount" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11726,11 +11726,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "has completed" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has completed" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -11951,11 +11951,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "decreases response to" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "decreases response to" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12234,11 +12234,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "has part" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has part" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12564,11 +12564,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "prevents" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "prevents" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -14132,11 +14132,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "exacerbates" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "exacerbates" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -14155,12 +14155,12 @@ linkml:domain ; linkml:examples [ a linkml:Example ; skos:example "stability" ], - [ a linkml:Example ; - skos:example "abundance" ], [ a linkml:Example ; skos:example "exposure" ], [ a linkml:Example ; - skos:example "expression" ] ; + skos:example "expression" ], + [ a linkml:Example ; + skos:example "abundance" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -14264,11 +14264,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "prevents" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -14412,12 +14412,12 @@ linkml:domain ; linkml:examples [ a linkml:Example ; skos:example "chemical analog" ], + [ a linkml:Example ; + skos:example "late stage" ], [ a linkml:Example ; skos:example "mutation" ], [ a linkml:Example ; skos:example "transplant" ], - [ a linkml:Example ; - skos:example "late stage" ], [ a linkml:Example ; skos:example "severe" ] ; linkml:is_a ; @@ -18974,11 +18974,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "has input" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has input" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -19156,11 +19156,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has output" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -21244,11 +21244,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ], - [ a linkml:LocalName ; skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ; linkml:owner ; linkml:range ; linkml:required true ; diff --git a/biolink-modeln.shex b/biolink-modeln.shex index 2706f1b208..ba46bdb758 100644 --- a/biolink-modeln.shex +++ b/biolink-modeln.shex @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.1.1 +# version: 3.1.2 BASE PREFIX rdf: PREFIX xsd: diff --git a/biolink-modeln.shexj b/biolink-modeln.shexj index 81e15c5e25..98d9566f24 100644 --- a/biolink-modeln.shexj +++ b/biolink-modeln.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.1.1 +# version: 3.1.2 { "type": "Schema", "@context": [ diff --git a/biolink/model.py b/biolink/model.py index ad14100a6d..99d552995e 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-12T22:39:35 +# Generation date: 2022-12-20T18:46:33 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -26,7 +26,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDate, XSDTime metamodel_version = "1.7.0" -version = "3.1.1" +version = "3.1.2" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py index 356eb2a137..c6f17e2ceb 100644 --- a/biolink/pydanticmodel.py +++ b/biolink/pydanticmodel.py @@ -5,7 +5,7 @@ from pydantic import BaseModel as BaseModel, Field metamodel_version = "None" -version = "3.1.1" +version = "3.1.2" class WeakRefShimBaseModel(BaseModel): __slots__ = '__weakref__' diff --git a/context.jsonld b/context.jsonld index c756a3f404..a474e8a226 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-12T22:39:01\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.1.1\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-20T18:45:59\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.1.2\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "AGRKB": "https://www.alliancegenome.org/", "APO": { diff --git a/contextn.jsonld b/contextn.jsonld index f791053786..d9872556df 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-12T22:39:06\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.1.1\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-20T18:46:03\n Schema: Biolink-Model\n metamodel version: 1.7.0\n model version: 3.1.2\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "AGRKB": "https://www.alliancegenome.org/", "APO": { diff --git a/golr-views/RNA_product_config.yaml b/golr-views/RNA_product_config.yaml index 307c24037f..e5d570cddf 100644 --- a/golr-views/RNA_product_config.yaml +++ b/golr-views/RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: RNA_product +# metamodel_version: 1.7.0# version: 3.1.2id: RNA_product schema_generating: true display_name: RNA product document_category: RNA product diff --git a/golr-views/RNA_product_isoform_config.yaml b/golr-views/RNA_product_isoform_config.yaml index bc3409694d..c2e2f6d616 100644 --- a/golr-views/RNA_product_isoform_config.yaml +++ b/golr-views/RNA_product_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: RNA_product_isoform +# metamodel_version: 1.7.0# version: 3.1.2id: RNA_product_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference RNA diff --git a/golr-views/activity_config.yaml b/golr-views/activity_config.yaml index a838128251..3d72370971 100644 --- a/golr-views/activity_config.yaml +++ b/golr-views/activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: activity +# metamodel_version: 1.7.0# version: 3.1.2id: activity schema_generating: true description: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, diff --git a/golr-views/agent_config.yaml b/golr-views/agent_config.yaml index a929c5ec2e..2d236bae89 100644 --- a/golr-views/agent_config.yaml +++ b/golr-views/agent_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: agent +# metamodel_version: 1.7.0# version: 3.1.2id: agent schema_generating: true description: person, group, organization or project that provides a piece of information (i.e. a knowledge association) diff --git a/golr-views/anatomical_entity_config.yaml b/golr-views/anatomical_entity_config.yaml index 1448c6c5f9..b9d6c1eec0 100644 --- a/golr-views/anatomical_entity_config.yaml +++ b/golr-views/anatomical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: anatomical_entity +# metamodel_version: 1.7.0# version: 3.1.2id: anatomical_entity schema_generating: true description: A subcellular location, cell type or gross anatomical part display_name: anatomical entity diff --git a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml index 7c9ce184e6..796146f4b7 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: anatomical_entity_to_anatomical_entity_ontogenic_association +# metamodel_version: 1.7.0# version: 3.1.2id: anatomical_entity_to_anatomical_entity_ontogenic_association schema_generating: true description: A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different diff --git a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml index 5bf73b3ee6..aa4f3f957d 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: anatomical_entity_to_anatomical_entity_part_of_association +# metamodel_version: 1.7.0# version: 3.1.2id: anatomical_entity_to_anatomical_entity_part_of_association schema_generating: true description: A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships diff --git a/golr-views/article_config.yaml b/golr-views/article_config.yaml index bdc709c942..aff66b9cb9 100644 --- a/golr-views/article_config.yaml +++ b/golr-views/article_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: article +# metamodel_version: 1.7.0# version: 3.1.2id: article schema_generating: true display_name: article document_category: article diff --git a/golr-views/association_config.yaml b/golr-views/association_config.yaml index d36234b74a..a066beb3f2 100644 --- a/golr-views/association_config.yaml +++ b/golr-views/association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: association +# metamodel_version: 1.7.0# version: 3.1.2id: association schema_generating: true description: A typed association between two entities, supported by evidence display_name: association diff --git a/golr-views/attribute_config.yaml b/golr-views/attribute_config.yaml index 6cdcfeb08f..359e750ce1 100644 --- a/golr-views/attribute_config.yaml +++ b/golr-views/attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: attribute +# metamodel_version: 1.7.0# version: 3.1.2id: attribute schema_generating: true description: A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may diff --git a/golr-views/behavior_config.yaml b/golr-views/behavior_config.yaml index 85400e80ed..429642951a 100644 --- a/golr-views/behavior_config.yaml +++ b/golr-views/behavior_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: behavior +# metamodel_version: 1.7.0# version: 3.1.2id: behavior schema_generating: true display_name: behavior document_category: behavior diff --git a/golr-views/behavior_to_behavioral_feature_association_config.yaml b/golr-views/behavior_to_behavioral_feature_association_config.yaml index 4cf0155ab1..0d354ccaec 100644 --- a/golr-views/behavior_to_behavioral_feature_association_config.yaml +++ b/golr-views/behavior_to_behavioral_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: behavior_to_behavioral_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: behavior_to_behavioral_feature_association schema_generating: true description: An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. diff --git a/golr-views/behavioral_exposure_config.yaml b/golr-views/behavioral_exposure_config.yaml index 5c14933a32..1f6247e146 100644 --- a/golr-views/behavioral_exposure_config.yaml +++ b/golr-views/behavioral_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: behavioral_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: behavioral_exposure schema_generating: true description: A behavioral exposure is a factor relating to behavior impacting an individual. display_name: behavioral exposure diff --git a/golr-views/behavioral_feature_config.yaml b/golr-views/behavioral_feature_config.yaml index 56e15329ac..54c004bba7 100644 --- a/golr-views/behavioral_feature_config.yaml +++ b/golr-views/behavioral_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: behavioral_feature +# metamodel_version: 1.7.0# version: 3.1.2id: behavioral_feature schema_generating: true description: A phenotypic feature which is behavioral in nature. display_name: behavioral feature diff --git a/golr-views/biological_process_config.yaml b/golr-views/biological_process_config.yaml index 43ea643996..43b7879f7b 100644 --- a/golr-views/biological_process_config.yaml +++ b/golr-views/biological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: biological_process +# metamodel_version: 1.7.0# version: 3.1.2id: biological_process schema_generating: true description: One or more causally connected executions of molecular functions display_name: biological process diff --git a/golr-views/biological_process_or_activity_config.yaml b/golr-views/biological_process_or_activity_config.yaml index 3b1b86a05b..58f0a55f49 100644 --- a/golr-views/biological_process_or_activity_config.yaml +++ b/golr-views/biological_process_or_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: biological_process_or_activity +# metamodel_version: 1.7.0# version: 3.1.2id: biological_process_or_activity schema_generating: true description: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. diff --git a/golr-views/biological_sex_config.yaml b/golr-views/biological_sex_config.yaml index 7265395f52..951837e962 100644 --- a/golr-views/biological_sex_config.yaml +++ b/golr-views/biological_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: biological_sex +# metamodel_version: 1.7.0# version: 3.1.2id: biological_sex schema_generating: true display_name: biological sex document_category: biological sex diff --git a/golr-views/biotic_exposure_config.yaml b/golr-views/biotic_exposure_config.yaml index 6b2b110aae..ec758f9378 100644 --- a/golr-views/biotic_exposure_config.yaml +++ b/golr-views/biotic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: biotic_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: biotic_exposure schema_generating: true description: An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). diff --git a/golr-views/book_chapter_config.yaml b/golr-views/book_chapter_config.yaml index a2a299b150..cb347fe05c 100644 --- a/golr-views/book_chapter_config.yaml +++ b/golr-views/book_chapter_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: book_chapter +# metamodel_version: 1.7.0# version: 3.1.2id: book_chapter schema_generating: true display_name: book chapter document_category: book chapter diff --git a/golr-views/book_config.yaml b/golr-views/book_config.yaml index 4579afadbc..4875df3d67 100644 --- a/golr-views/book_config.yaml +++ b/golr-views/book_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: book +# metamodel_version: 1.7.0# version: 3.1.2id: book schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. diff --git a/golr-views/case_config.yaml b/golr-views/case_config.yaml index 3e47da9890..96e437e984 100644 --- a/golr-views/case_config.yaml +++ b/golr-views/case_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: case +# metamodel_version: 1.7.0# version: 3.1.2id: case schema_generating: true description: An individual (human) organism that has a patient role in some clinical context. diff --git a/golr-views/case_to_phenotypic_feature_association_config.yaml b/golr-views/case_to_phenotypic_feature_association_config.yaml index a9eec66800..4ad8d82769 100644 --- a/golr-views/case_to_phenotypic_feature_association_config.yaml +++ b/golr-views/case_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: case_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: case_to_phenotypic_feature_association schema_generating: true description: An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. diff --git a/golr-views/cell_config.yaml b/golr-views/cell_config.yaml index 85bc177be7..26fe10cf17 100644 --- a/golr-views/cell_config.yaml +++ b/golr-views/cell_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cell +# metamodel_version: 1.7.0# version: 3.1.2id: cell schema_generating: true display_name: cell document_category: cell diff --git a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml index 793da0542f..1068a6f60f 100644 --- a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml +++ b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cell_line_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: cell_line_as_a_model_of_disease_association schema_generating: true display_name: cell line as a model of disease association document_category: cell line as a model of disease association diff --git a/golr-views/cell_line_config.yaml b/golr-views/cell_line_config.yaml index 309bc8f878..270676d40b 100644 --- a/golr-views/cell_line_config.yaml +++ b/golr-views/cell_line_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cell_line +# metamodel_version: 1.7.0# version: 3.1.2id: cell_line schema_generating: true display_name: cell line document_category: cell line diff --git a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml index 1b6734602d..5a7f749e36 100644 --- a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cell_line_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: cell_line_to_disease_or_phenotypic_feature_association schema_generating: true description: An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. diff --git a/golr-views/cellular_component_config.yaml b/golr-views/cellular_component_config.yaml index 6286b95211..0b5b359430 100644 --- a/golr-views/cellular_component_config.yaml +++ b/golr-views/cellular_component_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cellular_component +# metamodel_version: 1.7.0# version: 3.1.2id: cellular_component schema_generating: true description: A location in or around a cell display_name: cellular component diff --git a/golr-views/cellular_organism_config.yaml b/golr-views/cellular_organism_config.yaml index 977a9f9044..99b6e50ecd 100644 --- a/golr-views/cellular_organism_config.yaml +++ b/golr-views/cellular_organism_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cellular_organism +# metamodel_version: 1.7.0# version: 3.1.2id: cellular_organism schema_generating: true description: '' display_name: cellular organism diff --git a/golr-views/chemical_affects_gene_association_config.yaml b/golr-views/chemical_affects_gene_association_config.yaml index c93285404a..e96d6482fc 100644 --- a/golr-views/chemical_affects_gene_association_config.yaml +++ b/golr-views/chemical_affects_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_affects_gene_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_affects_gene_association schema_generating: true description: Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.) diff --git a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml index 5e739b4ac1..4e5be16da1 100644 --- a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml +++ b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_entity_assesses_named_thing_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_entity_assesses_named_thing_association schema_generating: true display_name: chemical entity assesses named thing association document_category: chemical entity assesses named thing association diff --git a/golr-views/chemical_entity_config.yaml b/golr-views/chemical_entity_config.yaml index fdc632d6cc..d32a33d2aa 100644 --- a/golr-views/chemical_entity_config.yaml +++ b/golr-views/chemical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_entity +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_entity schema_generating: true description: A chemical entity is a physical entity that pertains to chemistry or biochemistry. diff --git a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml index b706eb7b16..a5b13c4509 100644 --- a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml +++ b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_entity_or_gene_or_gene_product_regulates_gene_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_entity_or_gene_or_gene_product_regulates_gene_association schema_generating: true description: A regulatory relationship between two genes display_name: chemical entity or gene or gene product regulates gene association diff --git a/golr-views/chemical_exposure_config.yaml b/golr-views/chemical_exposure_config.yaml index 77052051a6..291f4c9281 100644 --- a/golr-views/chemical_exposure_config.yaml +++ b/golr-views/chemical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_exposure schema_generating: true description: A chemical exposure is an intake of a particular chemical entity. display_name: chemical exposure diff --git a/golr-views/chemical_gene_interaction_association_config.yaml b/golr-views/chemical_gene_interaction_association_config.yaml index c90d0fbe87..7b0175f47c 100644 --- a/golr-views/chemical_gene_interaction_association_config.yaml +++ b/golr-views/chemical_gene_interaction_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_gene_interaction_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_gene_interaction_association schema_generating: true description: describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction diff --git a/golr-views/chemical_mixture_config.yaml b/golr-views/chemical_mixture_config.yaml index 6b64ae9eb7..4227422e5d 100644 --- a/golr-views/chemical_mixture_config.yaml +++ b/golr-views/chemical_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_mixture +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_mixture schema_generating: true description: A chemical mixture is a chemical entity composed of two or more molecular entities. diff --git a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml index 1a22772739..8b72cafd49 100644 --- a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association schema_generating: true description: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic diff --git a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml index a0b10fbcfe..499f6501a0 100644 --- a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association schema_generating: true description: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic diff --git a/golr-views/chemical_role_config.yaml b/golr-views/chemical_role_config.yaml index 7d5b71bea8..3a9a46d27a 100644 --- a/golr-views/chemical_role_config.yaml +++ b/golr-views/chemical_role_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_role +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_role schema_generating: true description: "\tA role played by the molecular entity or part thereof within a chemical\ \ context." diff --git a/golr-views/chemical_to_chemical_association_config.yaml b/golr-views/chemical_to_chemical_association_config.yaml index 5a0cace5a8..0f5abb9a44 100644 --- a/golr-views/chemical_to_chemical_association_config.yaml +++ b/golr-views/chemical_to_chemical_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_to_chemical_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_to_chemical_association schema_generating: true description: A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. diff --git a/golr-views/chemical_to_chemical_derivation_association_config.yaml b/golr-views/chemical_to_chemical_derivation_association_config.yaml index bc0c979364..81f4be1829 100644 --- a/golr-views/chemical_to_chemical_derivation_association_config.yaml +++ b/golr-views/chemical_to_chemical_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_to_chemical_derivation_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_to_chemical_derivation_association schema_generating: true description: "A causal relationship between two chemical entities, where the subject\ \ represents the upstream entity and the object represents the downstream. For any\ diff --git a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml index e9d4da4c8c..5470da5c73 100644 --- a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_to_disease_or_phenotypic_feature_association schema_generating: true description: An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. diff --git a/golr-views/chemical_to_pathway_association_config.yaml b/golr-views/chemical_to_pathway_association_config.yaml index 938032ecfa..69b739595d 100644 --- a/golr-views/chemical_to_pathway_association_config.yaml +++ b/golr-views/chemical_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chemical_to_pathway_association +# metamodel_version: 1.7.0# version: 3.1.2id: chemical_to_pathway_association schema_generating: true description: An interaction between a chemical entity and a biological process or pathway. diff --git a/golr-views/chi_squared_analysis_result_config.yaml b/golr-views/chi_squared_analysis_result_config.yaml index 5eae97803c..946e84297c 100644 --- a/golr-views/chi_squared_analysis_result_config.yaml +++ b/golr-views/chi_squared_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: chi_squared_analysis_result +# metamodel_version: 1.7.0# version: 3.1.2id: chi_squared_analysis_result schema_generating: true description: A result of a chi squared analysis. display_name: chi squared analysis result diff --git a/golr-views/clinical_attribute_config.yaml b/golr-views/clinical_attribute_config.yaml index 87463888b3..3f69d41fab 100644 --- a/golr-views/clinical_attribute_config.yaml +++ b/golr-views/clinical_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_attribute +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_attribute schema_generating: true description: Attributes relating to a clinical manifestation display_name: clinical attribute diff --git a/golr-views/clinical_course_config.yaml b/golr-views/clinical_course_config.yaml index bb24185a50..1ff1d9049a 100644 --- a/golr-views/clinical_course_config.yaml +++ b/golr-views/clinical_course_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_course +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_course schema_generating: true description: The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual diff --git a/golr-views/clinical_entity_config.yaml b/golr-views/clinical_entity_config.yaml index b569fcf8ae..a08fcaf6a1 100644 --- a/golr-views/clinical_entity_config.yaml +++ b/golr-views/clinical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_entity +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_entity schema_generating: true description: Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities diff --git a/golr-views/clinical_finding_config.yaml b/golr-views/clinical_finding_config.yaml index b139e36b4b..f1df11c74d 100644 --- a/golr-views/clinical_finding_config.yaml +++ b/golr-views/clinical_finding_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_finding +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_finding schema_generating: true description: this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some diff --git a/golr-views/clinical_intervention_config.yaml b/golr-views/clinical_intervention_config.yaml index 47ce3f113a..b48562f087 100644 --- a/golr-views/clinical_intervention_config.yaml +++ b/golr-views/clinical_intervention_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_intervention +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_intervention schema_generating: true display_name: clinical intervention document_category: clinical intervention diff --git a/golr-views/clinical_measurement_config.yaml b/golr-views/clinical_measurement_config.yaml index 4d6a26fe5a..57761864bf 100644 --- a/golr-views/clinical_measurement_config.yaml +++ b/golr-views/clinical_measurement_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_measurement +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_measurement schema_generating: true description: A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be diff --git a/golr-views/clinical_modifier_config.yaml b/golr-views/clinical_modifier_config.yaml index 5f09fafb12..cfe8b91ef6 100644 --- a/golr-views/clinical_modifier_config.yaml +++ b/golr-views/clinical_modifier_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_modifier +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_modifier schema_generating: true description: Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, diff --git a/golr-views/clinical_trial_config.yaml b/golr-views/clinical_trial_config.yaml index 1e4bc75263..a75aa7ed23 100644 --- a/golr-views/clinical_trial_config.yaml +++ b/golr-views/clinical_trial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: clinical_trial +# metamodel_version: 1.7.0# version: 3.1.2id: clinical_trial schema_generating: true display_name: clinical trial document_category: clinical trial diff --git a/golr-views/coding_sequence_config.yaml b/golr-views/coding_sequence_config.yaml index 114fc5a7a5..9802456eda 100644 --- a/golr-views/coding_sequence_config.yaml +++ b/golr-views/coding_sequence_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: coding_sequence +# metamodel_version: 1.7.0# version: 3.1.2id: coding_sequence schema_generating: true display_name: coding sequence document_category: coding sequence diff --git a/golr-views/cohort_config.yaml b/golr-views/cohort_config.yaml index 32c04eb69e..c8601711d7 100644 --- a/golr-views/cohort_config.yaml +++ b/golr-views/cohort_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: cohort +# metamodel_version: 1.7.0# version: 3.1.2id: cohort schema_generating: true description: A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that diff --git a/golr-views/common_data_element_config.yaml b/golr-views/common_data_element_config.yaml index e69046b467..eaf030bd77 100644 --- a/golr-views/common_data_element_config.yaml +++ b/golr-views/common_data_element_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: common_data_element +# metamodel_version: 1.7.0# version: 3.1.2id: common_data_element schema_generating: true description: A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different diff --git a/golr-views/complex_chemical_exposure_config.yaml b/golr-views/complex_chemical_exposure_config.yaml index e15e580de6..fdd51409bd 100644 --- a/golr-views/complex_chemical_exposure_config.yaml +++ b/golr-views/complex_chemical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: complex_chemical_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: complex_chemical_exposure schema_generating: true description: A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. diff --git a/golr-views/complex_molecular_mixture_config.yaml b/golr-views/complex_molecular_mixture_config.yaml index 3c01ca9f23..83a16cef24 100644 --- a/golr-views/complex_molecular_mixture_config.yaml +++ b/golr-views/complex_molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: complex_molecular_mixture +# metamodel_version: 1.7.0# version: 3.1.2id: complex_molecular_mixture schema_generating: true description: A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. diff --git a/golr-views/concept_count_analysis_result_config.yaml b/golr-views/concept_count_analysis_result_config.yaml index 4b8036baec..c03ad667e3 100644 --- a/golr-views/concept_count_analysis_result_config.yaml +++ b/golr-views/concept_count_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: concept_count_analysis_result +# metamodel_version: 1.7.0# version: 3.1.2id: concept_count_analysis_result schema_generating: true description: A result of a concept count analysis. display_name: concept count analysis result diff --git a/golr-views/confidence_level_config.yaml b/golr-views/confidence_level_config.yaml index c3e1e5077f..8694c57a57 100644 --- a/golr-views/confidence_level_config.yaml +++ b/golr-views/confidence_level_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: confidence_level +# metamodel_version: 1.7.0# version: 3.1.2id: confidence_level schema_generating: true description: Level of confidence in a statement display_name: confidence level diff --git a/golr-views/contributor_association_config.yaml b/golr-views/contributor_association_config.yaml index 451eb29b00..03e940424f 100644 --- a/golr-views/contributor_association_config.yaml +++ b/golr-views/contributor_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: contributor_association +# metamodel_version: 1.7.0# version: 3.1.2id: contributor_association schema_generating: true description: Any association between an entity (such as a publication) and various agents that contribute to its realisation diff --git a/golr-views/dataset_config.yaml b/golr-views/dataset_config.yaml index ba69635af6..78dc150d72 100644 --- a/golr-views/dataset_config.yaml +++ b/golr-views/dataset_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: dataset +# metamodel_version: 1.7.0# version: 3.1.2id: dataset schema_generating: true description: an item that refers to a collection of data from a data source. display_name: dataset diff --git a/golr-views/dataset_distribution_config.yaml b/golr-views/dataset_distribution_config.yaml index cd2382e814..4b7d22789d 100644 --- a/golr-views/dataset_distribution_config.yaml +++ b/golr-views/dataset_distribution_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: dataset_distribution +# metamodel_version: 1.7.0# version: 3.1.2id: dataset_distribution schema_generating: true description: an item that holds distribution level information about a dataset. display_name: dataset distribution diff --git a/golr-views/dataset_summary_config.yaml b/golr-views/dataset_summary_config.yaml index d0a69c4a7a..267bbef52b 100644 --- a/golr-views/dataset_summary_config.yaml +++ b/golr-views/dataset_summary_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: dataset_summary +# metamodel_version: 1.7.0# version: 3.1.2id: dataset_summary schema_generating: true description: an item that holds summary level information about a dataset. display_name: dataset summary diff --git a/golr-views/dataset_version_config.yaml b/golr-views/dataset_version_config.yaml index 8f897e0daa..56262c255d 100644 --- a/golr-views/dataset_version_config.yaml +++ b/golr-views/dataset_version_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: dataset_version +# metamodel_version: 1.7.0# version: 3.1.2id: dataset_version schema_generating: true description: an item that holds version level information about a dataset. display_name: dataset version diff --git a/golr-views/device_config.yaml b/golr-views/device_config.yaml index 4a77fd9fed..03a4871c5d 100644 --- a/golr-views/device_config.yaml +++ b/golr-views/device_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: device +# metamodel_version: 1.7.0# version: 3.1.2id: device schema_generating: true description: A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment diff --git a/golr-views/disease_config.yaml b/golr-views/disease_config.yaml index df3d4c4a1d..ee3431bec8 100644 --- a/golr-views/disease_config.yaml +++ b/golr-views/disease_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease +# metamodel_version: 1.7.0# version: 3.1.2id: disease schema_generating: true description: A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct diff --git a/golr-views/disease_or_phenotypic_feature_config.yaml b/golr-views/disease_or_phenotypic_feature_config.yaml index 8b3ca094be..429701ed42 100644 --- a/golr-views/disease_or_phenotypic_feature_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_or_phenotypic_feature +# metamodel_version: 1.7.0# version: 3.1.2id: disease_or_phenotypic_feature schema_generating: true description: Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please diff --git a/golr-views/disease_or_phenotypic_feature_exposure_config.yaml b/golr-views/disease_or_phenotypic_feature_exposure_config.yaml index 495ed7087a..af12147fb6 100644 --- a/golr-views/disease_or_phenotypic_feature_exposure_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_or_phenotypic_feature_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: disease_or_phenotypic_feature_exposure schema_generating: true description: A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an diff --git a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml index d2f6a409bf..27b027ba78 100644 --- a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_or_phenotypic_feature_to_genetic_inheritance_association +# metamodel_version: 1.7.0# version: 3.1.2id: disease_or_phenotypic_feature_to_genetic_inheritance_association schema_generating: true description: An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. diff --git a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml index 9a64ac2645..3a57b695a0 100644 --- a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_or_phenotypic_feature_to_location_association +# metamodel_version: 1.7.0# version: 3.1.2id: disease_or_phenotypic_feature_to_location_association schema_generating: true description: An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. diff --git a/golr-views/disease_to_exposure_event_association_config.yaml b/golr-views/disease_to_exposure_event_association_config.yaml index 5eed5ac0e4..3f85d71e2a 100644 --- a/golr-views/disease_to_exposure_event_association_config.yaml +++ b/golr-views/disease_to_exposure_event_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_to_exposure_event_association +# metamodel_version: 1.7.0# version: 3.1.2id: disease_to_exposure_event_association schema_generating: true description: An association between an exposure event and a disease. display_name: disease to exposure event association diff --git a/golr-views/disease_to_phenotypic_feature_association_config.yaml b/golr-views/disease_to_phenotypic_feature_association_config.yaml index 6c8015e742..b16cf9b2a0 100644 --- a/golr-views/disease_to_phenotypic_feature_association_config.yaml +++ b/golr-views/disease_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: disease_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: disease_to_phenotypic_feature_association schema_generating: true description: An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. diff --git a/golr-views/drug_config.yaml b/golr-views/drug_config.yaml index 51fd82abbe..29d6d6f6e0 100644 --- a/golr-views/drug_config.yaml +++ b/golr-views/drug_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: drug +# metamodel_version: 1.7.0# version: 3.1.2id: drug schema_generating: true description: A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease diff --git a/golr-views/drug_exposure_config.yaml b/golr-views/drug_exposure_config.yaml index 0ce13e8227..eb8d137a48 100644 --- a/golr-views/drug_exposure_config.yaml +++ b/golr-views/drug_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: drug_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: drug_exposure schema_generating: true description: A drug exposure is an intake of a particular drug. display_name: drug exposure diff --git a/golr-views/drug_to_gene_association_config.yaml b/golr-views/drug_to_gene_association_config.yaml index 1036c53c06..c96c1fca3c 100644 --- a/golr-views/drug_to_gene_association_config.yaml +++ b/golr-views/drug_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: drug_to_gene_association +# metamodel_version: 1.7.0# version: 3.1.2id: drug_to_gene_association schema_generating: true description: An interaction between a drug and a gene or gene product. display_name: drug to gene association diff --git a/golr-views/drug_to_gene_interaction_exposure_config.yaml b/golr-views/drug_to_gene_interaction_exposure_config.yaml index e851ba735b..03a8020efd 100644 --- a/golr-views/drug_to_gene_interaction_exposure_config.yaml +++ b/golr-views/drug_to_gene_interaction_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: drug_to_gene_interaction_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: drug_to_gene_interaction_exposure schema_generating: true description: drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, diff --git a/golr-views/druggable_gene_to_disease_association_config.yaml b/golr-views/druggable_gene_to_disease_association_config.yaml index 99c6feef3b..5f5a827c97 100644 --- a/golr-views/druggable_gene_to_disease_association_config.yaml +++ b/golr-views/druggable_gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: druggable_gene_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: druggable_gene_to_disease_association schema_generating: true display_name: druggable gene to disease association document_category: druggable gene to disease association diff --git a/golr-views/entity_to_disease_association_config.yaml b/golr-views/entity_to_disease_association_config.yaml index dd5939b709..0f9ae4ecc7 100644 --- a/golr-views/entity_to_disease_association_config.yaml +++ b/golr-views/entity_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: entity_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: entity_to_disease_association schema_generating: true display_name: entity to disease association document_category: entity to disease association diff --git a/golr-views/entity_to_phenotypic_feature_association_config.yaml b/golr-views/entity_to_phenotypic_feature_association_config.yaml index 23c4f9f322..6c606becc3 100644 --- a/golr-views/entity_to_phenotypic_feature_association_config.yaml +++ b/golr-views/entity_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: entity_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: entity_to_phenotypic_feature_association schema_generating: true display_name: entity to phenotypic feature association document_category: entity to phenotypic feature association diff --git a/golr-views/environmental_exposure_config.yaml b/golr-views/environmental_exposure_config.yaml index 3fc8da0a79..28717a8d1d 100644 --- a/golr-views/environmental_exposure_config.yaml +++ b/golr-views/environmental_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: environmental_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: environmental_exposure schema_generating: true description: A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) diff --git a/golr-views/environmental_feature_config.yaml b/golr-views/environmental_feature_config.yaml index d853891dcc..2796306f3a 100644 --- a/golr-views/environmental_feature_config.yaml +++ b/golr-views/environmental_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: environmental_feature +# metamodel_version: 1.7.0# version: 3.1.2id: environmental_feature schema_generating: true display_name: environmental feature document_category: environmental feature diff --git a/golr-views/environmental_food_contaminant_config.yaml b/golr-views/environmental_food_contaminant_config.yaml index 5f86ef1bc8..e77edbf8a1 100644 --- a/golr-views/environmental_food_contaminant_config.yaml +++ b/golr-views/environmental_food_contaminant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: environmental_food_contaminant +# metamodel_version: 1.7.0# version: 3.1.2id: environmental_food_contaminant schema_generating: true display_name: environmental food contaminant document_category: environmental food contaminant diff --git a/golr-views/environmental_process_config.yaml b/golr-views/environmental_process_config.yaml index 37ccc319fa..3f0ba050d3 100644 --- a/golr-views/environmental_process_config.yaml +++ b/golr-views/environmental_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: environmental_process +# metamodel_version: 1.7.0# version: 3.1.2id: environmental_process schema_generating: true display_name: environmental process document_category: environmental process diff --git a/golr-views/event_config.yaml b/golr-views/event_config.yaml index 3d6514ee0d..2f2bd7fcd9 100644 --- a/golr-views/event_config.yaml +++ b/golr-views/event_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: event +# metamodel_version: 1.7.0# version: 3.1.2id: event schema_generating: true description: Something that happens at a given place and time. display_name: event diff --git a/golr-views/evidence_type_config.yaml b/golr-views/evidence_type_config.yaml index 4365289578..e7f7e4af48 100644 --- a/golr-views/evidence_type_config.yaml +++ b/golr-views/evidence_type_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: evidence_type +# metamodel_version: 1.7.0# version: 3.1.2id: evidence_type schema_generating: true description: Class of evidence that supports an association display_name: evidence type diff --git a/golr-views/exon_config.yaml b/golr-views/exon_config.yaml index c106263a95..d4bdf0bfee 100644 --- a/golr-views/exon_config.yaml +++ b/golr-views/exon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: exon +# metamodel_version: 1.7.0# version: 3.1.2id: exon schema_generating: true description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. diff --git a/golr-views/exon_to_transcript_relationship_config.yaml b/golr-views/exon_to_transcript_relationship_config.yaml index 9c9b811c42..5b1eeb4d42 100644 --- a/golr-views/exon_to_transcript_relationship_config.yaml +++ b/golr-views/exon_to_transcript_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: exon_to_transcript_relationship +# metamodel_version: 1.7.0# version: 3.1.2id: exon_to_transcript_relationship schema_generating: true description: A transcript is formed from multiple exons display_name: exon to transcript relationship diff --git a/golr-views/exposure_event_to_outcome_association_config.yaml b/golr-views/exposure_event_to_outcome_association_config.yaml index c395b69206..cb8882c435 100644 --- a/golr-views/exposure_event_to_outcome_association_config.yaml +++ b/golr-views/exposure_event_to_outcome_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: exposure_event_to_outcome_association +# metamodel_version: 1.7.0# version: 3.1.2id: exposure_event_to_outcome_association schema_generating: true description: An association between an exposure event and an outcome. display_name: exposure event to outcome association diff --git a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml index 3696d89a4a..25d36bb38b 100644 --- a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml +++ b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: exposure_event_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: exposure_event_to_phenotypic_feature_association schema_generating: true description: Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. diff --git a/golr-views/food_additive_config.yaml b/golr-views/food_additive_config.yaml index fe881a6c4b..00e6dc4b3e 100644 --- a/golr-views/food_additive_config.yaml +++ b/golr-views/food_additive_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: food_additive +# metamodel_version: 1.7.0# version: 3.1.2id: food_additive schema_generating: true display_name: food additive document_category: food additive diff --git a/golr-views/food_config.yaml b/golr-views/food_config.yaml index 0fa47ff84c..4de807bc3d 100644 --- a/golr-views/food_config.yaml +++ b/golr-views/food_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: food +# metamodel_version: 1.7.0# version: 3.1.2id: food schema_generating: true description: A substance consumed by a living organism as a source of nutrition display_name: food diff --git a/golr-views/functional_association_config.yaml b/golr-views/functional_association_config.yaml index 86ca2b6fa0..d5148ed6af 100644 --- a/golr-views/functional_association_config.yaml +++ b/golr-views/functional_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: functional_association +# metamodel_version: 1.7.0# version: 3.1.2id: functional_association schema_generating: true description: An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process diff --git a/golr-views/gene_as_a_model_of_disease_association_config.yaml b/golr-views/gene_as_a_model_of_disease_association_config.yaml index 84fde0c8d2..fef89014c6 100644 --- a/golr-views/gene_as_a_model_of_disease_association_config.yaml +++ b/golr-views/gene_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_as_a_model_of_disease_association schema_generating: true display_name: gene as a model of disease association document_category: gene as a model of disease association diff --git a/golr-views/gene_config.yaml b/golr-views/gene_config.yaml index fed8669cc9..c7ea5ea272 100644 --- a/golr-views/gene_config.yaml +++ b/golr-views/gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene +# metamodel_version: 1.7.0# version: 3.1.2id: gene schema_generating: true description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, diff --git a/golr-views/gene_family_config.yaml b/golr-views/gene_family_config.yaml index 4c674a6f2e..2d0e1c34c1 100644 --- a/golr-views/gene_family_config.yaml +++ b/golr-views/gene_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_family +# metamodel_version: 1.7.0# version: 3.1.2id: gene_family schema_generating: true description: any grouping of multiple genes or gene products related by common descent display_name: gene family diff --git a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml index 2f1574d216..d7eefc2dff 100644 --- a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml +++ b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_has_variant_that_contributes_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_has_variant_that_contributes_to_disease_association schema_generating: true display_name: gene has variant that contributes to disease association document_category: gene has variant that contributes to disease association diff --git a/golr-views/gene_to_disease_association_config.yaml b/golr-views/gene_to_disease_association_config.yaml index 7ebc17957b..adf04c1128 100644 --- a/golr-views/gene_to_disease_association_config.yaml +++ b/golr-views/gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_disease_association schema_generating: true display_name: gene to disease association document_category: gene to disease association diff --git a/golr-views/gene_to_expression_site_association_config.yaml b/golr-views/gene_to_expression_site_association_config.yaml index 0d09c0f6ca..e7bab0331c 100644 --- a/golr-views/gene_to_expression_site_association_config.yaml +++ b/golr-views/gene_to_expression_site_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_expression_site_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_expression_site_association schema_generating: true description: An association between a gene and a gene expression site, possibly qualified by stage/timing info. diff --git a/golr-views/gene_to_gene_coexpression_association_config.yaml b/golr-views/gene_to_gene_coexpression_association_config.yaml index ebf07f44ea..3d0f7f1029 100644 --- a/golr-views/gene_to_gene_coexpression_association_config.yaml +++ b/golr-views/gene_to_gene_coexpression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_gene_coexpression_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_gene_coexpression_association schema_generating: true description: Indicates that two genes are co-expressed, generally under the same conditions. display_name: gene to gene coexpression association diff --git a/golr-views/gene_to_gene_family_association_config.yaml b/golr-views/gene_to_gene_family_association_config.yaml index 8ab4455a4b..cc1b11140c 100644 --- a/golr-views/gene_to_gene_family_association_config.yaml +++ b/golr-views/gene_to_gene_family_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_gene_family_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_gene_family_association schema_generating: true description: Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally diff --git a/golr-views/gene_to_gene_homology_association_config.yaml b/golr-views/gene_to_gene_homology_association_config.yaml index 9b8f386d41..8de377ba5d 100644 --- a/golr-views/gene_to_gene_homology_association_config.yaml +++ b/golr-views/gene_to_gene_homology_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_gene_homology_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_gene_homology_association schema_generating: true description: A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case diff --git a/golr-views/gene_to_gene_product_relationship_config.yaml b/golr-views/gene_to_gene_product_relationship_config.yaml index 49557affdb..ff1b3287ea 100644 --- a/golr-views/gene_to_gene_product_relationship_config.yaml +++ b/golr-views/gene_to_gene_product_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_gene_product_relationship +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_gene_product_relationship schema_generating: true description: A gene is transcribed and potentially translated to a gene product display_name: gene to gene product relationship diff --git a/golr-views/gene_to_go_term_association_config.yaml b/golr-views/gene_to_go_term_association_config.yaml index 6a6490b964..ad9f58e6b5 100644 --- a/golr-views/gene_to_go_term_association_config.yaml +++ b/golr-views/gene_to_go_term_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_go_term_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_go_term_association schema_generating: true display_name: gene to go term association document_category: gene to go term association diff --git a/golr-views/gene_to_pathway_association_config.yaml b/golr-views/gene_to_pathway_association_config.yaml index a5509cddce..06cfbf8ee0 100644 --- a/golr-views/gene_to_pathway_association_config.yaml +++ b/golr-views/gene_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_pathway_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_pathway_association schema_generating: true description: An interaction between a gene or gene product and a biological process or pathway. diff --git a/golr-views/gene_to_phenotypic_feature_association_config.yaml b/golr-views/gene_to_phenotypic_feature_association_config.yaml index 4d821b035b..f746a17a69 100644 --- a/golr-views/gene_to_phenotypic_feature_association_config.yaml +++ b/golr-views/gene_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gene_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: gene_to_phenotypic_feature_association schema_generating: true display_name: gene to phenotypic feature association document_category: gene to phenotypic feature association diff --git a/golr-views/genetic_inheritance_config.yaml b/golr-views/genetic_inheritance_config.yaml index abe1e5a890..9c7cfc0cee 100644 --- a/golr-views/genetic_inheritance_config.yaml +++ b/golr-views/genetic_inheritance_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genetic_inheritance +# metamodel_version: 1.7.0# version: 3.1.2id: genetic_inheritance schema_generating: true description: The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, diff --git a/golr-views/genome_config.yaml b/golr-views/genome_config.yaml index cb01e9ed80..edb4583d30 100644 --- a/golr-views/genome_config.yaml +++ b/golr-views/genome_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genome +# metamodel_version: 1.7.0# version: 3.1.2id: genome schema_generating: true description: A genome is the sum of genetic material within a cell or virion. display_name: genome diff --git a/golr-views/genomic_background_exposure_config.yaml b/golr-views/genomic_background_exposure_config.yaml index 9ef039b5ea..3e9138c551 100644 --- a/golr-views/genomic_background_exposure_config.yaml +++ b/golr-views/genomic_background_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genomic_background_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: genomic_background_exposure schema_generating: true description: A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions diff --git a/golr-views/genomic_sequence_localization_config.yaml b/golr-views/genomic_sequence_localization_config.yaml index e490198dc9..aa93ab56d4 100644 --- a/golr-views/genomic_sequence_localization_config.yaml +++ b/golr-views/genomic_sequence_localization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genomic_sequence_localization +# metamodel_version: 1.7.0# version: 3.1.2id: genomic_sequence_localization schema_generating: true description: A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or diff --git a/golr-views/genotype_as_a_model_of_disease_association_config.yaml b/golr-views/genotype_as_a_model_of_disease_association_config.yaml index 4ed9657dfc..6454501c15 100644 --- a/golr-views/genotype_as_a_model_of_disease_association_config.yaml +++ b/golr-views/genotype_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_as_a_model_of_disease_association schema_generating: true display_name: genotype as a model of disease association document_category: genotype as a model of disease association diff --git a/golr-views/genotype_config.yaml b/golr-views/genotype_config.yaml index a91f8464ee..be7d95a532 100644 --- a/golr-views/genotype_config.yaml +++ b/golr-views/genotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype +# metamodel_version: 1.7.0# version: 3.1.2id: genotype schema_generating: true description: An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established diff --git a/golr-views/genotype_to_disease_association_config.yaml b/golr-views/genotype_to_disease_association_config.yaml index d21528975c..d2762d204d 100644 --- a/golr-views/genotype_to_disease_association_config.yaml +++ b/golr-views/genotype_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_to_disease_association schema_generating: true display_name: genotype to disease association document_category: genotype to disease association diff --git a/golr-views/genotype_to_gene_association_config.yaml b/golr-views/genotype_to_gene_association_config.yaml index 4f50e91267..836048a619 100644 --- a/golr-views/genotype_to_gene_association_config.yaml +++ b/golr-views/genotype_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_to_gene_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_to_gene_association schema_generating: true description: Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality diff --git a/golr-views/genotype_to_genotype_part_association_config.yaml b/golr-views/genotype_to_genotype_part_association_config.yaml index 407a95ce1d..d0ae87a1d8 100644 --- a/golr-views/genotype_to_genotype_part_association_config.yaml +++ b/golr-views/genotype_to_genotype_part_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_to_genotype_part_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_to_genotype_part_association schema_generating: true description: Any association between one genotype and a genotypic entity that is a sub-component of it diff --git a/golr-views/genotype_to_phenotypic_feature_association_config.yaml b/golr-views/genotype_to_phenotypic_feature_association_config.yaml index dd5449a98e..741a22a2f4 100644 --- a/golr-views/genotype_to_phenotypic_feature_association_config.yaml +++ b/golr-views/genotype_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_to_phenotypic_feature_association schema_generating: true description: Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment diff --git a/golr-views/genotype_to_variant_association_config.yaml b/golr-views/genotype_to_variant_association_config.yaml index 92c5afe279..8c05cf5cf7 100644 --- a/golr-views/genotype_to_variant_association_config.yaml +++ b/golr-views/genotype_to_variant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotype_to_variant_association +# metamodel_version: 1.7.0# version: 3.1.2id: genotype_to_variant_association schema_generating: true description: Any association between a genotype and a sequence variant. display_name: genotype to variant association diff --git a/golr-views/genotypic_sex_config.yaml b/golr-views/genotypic_sex_config.yaml index 2b63e5905f..682cf9b190 100644 --- a/golr-views/genotypic_sex_config.yaml +++ b/golr-views/genotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: genotypic_sex +# metamodel_version: 1.7.0# version: 3.1.2id: genotypic_sex schema_generating: true description: An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. diff --git a/golr-views/geographic_exposure_config.yaml b/golr-views/geographic_exposure_config.yaml index 092b26f434..6bc1e67833 100644 --- a/golr-views/geographic_exposure_config.yaml +++ b/golr-views/geographic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: geographic_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: geographic_exposure schema_generating: true description: A geographic exposure is a factor relating to geographic proximity to some impactful entity. diff --git a/golr-views/geographic_location_at_time_config.yaml b/golr-views/geographic_location_at_time_config.yaml index 149c4cd6f2..84298fdd58 100644 --- a/golr-views/geographic_location_at_time_config.yaml +++ b/golr-views/geographic_location_at_time_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: geographic_location_at_time +# metamodel_version: 1.7.0# version: 3.1.2id: geographic_location_at_time schema_generating: true description: a location that can be described in lat/long coordinates, for a particular time diff --git a/golr-views/geographic_location_config.yaml b/golr-views/geographic_location_config.yaml index b005187f31..a895b246ca 100644 --- a/golr-views/geographic_location_config.yaml +++ b/golr-views/geographic_location_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: geographic_location +# metamodel_version: 1.7.0# version: 3.1.2id: geographic_location schema_generating: true description: a location that can be described in lat/long coordinates display_name: geographic location diff --git a/golr-views/gross_anatomical_structure_config.yaml b/golr-views/gross_anatomical_structure_config.yaml index e2cec1916c..4e79a7cfd1 100644 --- a/golr-views/gross_anatomical_structure_config.yaml +++ b/golr-views/gross_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: gross_anatomical_structure +# metamodel_version: 1.7.0# version: 3.1.2id: gross_anatomical_structure schema_generating: true display_name: gross anatomical structure document_category: gross anatomical structure diff --git a/golr-views/haplotype_config.yaml b/golr-views/haplotype_config.yaml index 8f5b3b7e6c..945ea45bc6 100644 --- a/golr-views/haplotype_config.yaml +++ b/golr-views/haplotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: haplotype +# metamodel_version: 1.7.0# version: 3.1.2id: haplotype schema_generating: true description: A set of zero or more Alleles on a single instance of a Sequence[VMC] display_name: haplotype diff --git a/golr-views/hospitalization_config.yaml b/golr-views/hospitalization_config.yaml index c56ebeaed6..db4a0bf4cb 100644 --- a/golr-views/hospitalization_config.yaml +++ b/golr-views/hospitalization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: hospitalization +# metamodel_version: 1.7.0# version: 3.1.2id: hospitalization schema_generating: true display_name: hospitalization document_category: hospitalization diff --git a/golr-views/individual_organism_config.yaml b/golr-views/individual_organism_config.yaml index 0087b1f6b1..e1983f9f30 100644 --- a/golr-views/individual_organism_config.yaml +++ b/golr-views/individual_organism_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: individual_organism +# metamodel_version: 1.7.0# version: 3.1.2id: individual_organism schema_generating: true description: 'An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576' diff --git a/golr-views/information_content_entity_to_named_thing_association_config.yaml b/golr-views/information_content_entity_to_named_thing_association_config.yaml index 04b51c3b3a..11128a2f70 100644 --- a/golr-views/information_content_entity_to_named_thing_association_config.yaml +++ b/golr-views/information_content_entity_to_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: information_content_entity_to_named_thing_association +# metamodel_version: 1.7.0# version: 3.1.2id: information_content_entity_to_named_thing_association schema_generating: true description: association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication diff --git a/golr-views/information_resource_config.yaml b/golr-views/information_resource_config.yaml index 315f61e5e4..f2fdea8549 100644 --- a/golr-views/information_resource_config.yaml +++ b/golr-views/information_resource_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: information_resource +# metamodel_version: 1.7.0# version: 3.1.2id: information_resource schema_generating: true description: A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, diff --git a/golr-views/life_stage_config.yaml b/golr-views/life_stage_config.yaml index 36ea8e6a11..dfd0d8e28f 100644 --- a/golr-views/life_stage_config.yaml +++ b/golr-views/life_stage_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: life_stage +# metamodel_version: 1.7.0# version: 3.1.2id: life_stage schema_generating: true description: A stage of development or growth of an organism, including post-natal adult stages diff --git a/golr-views/macromolecular_complex_config.yaml b/golr-views/macromolecular_complex_config.yaml index 5ebe107c8c..0baf43f5f1 100644 --- a/golr-views/macromolecular_complex_config.yaml +++ b/golr-views/macromolecular_complex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: macromolecular_complex +# metamodel_version: 1.7.0# version: 3.1.2id: macromolecular_complex schema_generating: true description: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and diff --git a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml index 684f540344..34ed1c14cb 100644 --- a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml +++ b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: macromolecular_machine_to_biological_process_association +# metamodel_version: 1.7.0# version: 3.1.2id: macromolecular_machine_to_biological_process_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO diff --git a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml index 6b835612a8..e32dc6b838 100644 --- a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml +++ b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: macromolecular_machine_to_cellular_component_association +# metamodel_version: 1.7.0# version: 3.1.2id: macromolecular_machine_to_cellular_component_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular diff --git a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml index e317510d4a..a0007c9f55 100644 --- a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml +++ b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: macromolecular_machine_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 3.1.2id: macromolecular_machine_to_molecular_activity_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular diff --git a/golr-views/material_sample_config.yaml b/golr-views/material_sample_config.yaml index da664647b7..ebb04264fa 100644 --- a/golr-views/material_sample_config.yaml +++ b/golr-views/material_sample_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: material_sample +# metamodel_version: 1.7.0# version: 3.1.2id: material_sample schema_generating: true description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, diff --git a/golr-views/material_sample_derivation_association_config.yaml b/golr-views/material_sample_derivation_association_config.yaml index e43f9c6456..f07166695d 100644 --- a/golr-views/material_sample_derivation_association_config.yaml +++ b/golr-views/material_sample_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: material_sample_derivation_association +# metamodel_version: 1.7.0# version: 3.1.2id: material_sample_derivation_association schema_generating: true description: An association between a material sample and the material entity from which it is derived. diff --git a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml index 704ef9f2d8..af0d09c767 100644 --- a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: material_sample_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: material_sample_to_disease_or_phenotypic_feature_association schema_generating: true description: An association between a material sample and a disease or phenotype. display_name: material sample to disease or phenotypic feature association diff --git a/golr-views/microRNA_config.yaml b/golr-views/microRNA_config.yaml index 80852cfffb..967d284dda 100644 --- a/golr-views/microRNA_config.yaml +++ b/golr-views/microRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: microRNA +# metamodel_version: 1.7.0# version: 3.1.2id: microRNA schema_generating: true display_name: microRNA document_category: microRNA diff --git a/golr-views/molecular_activity_config.yaml b/golr-views/molecular_activity_config.yaml index fbcb6618c5..2780788caf 100644 --- a/golr-views/molecular_activity_config.yaml +++ b/golr-views/molecular_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_activity +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_activity schema_generating: true description: An execution of a molecular function carried out by a gene product or macromolecular complex. diff --git a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml index 16a6ded6c4..08819ac6d2 100644 --- a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml +++ b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_activity_to_chemical_entity_association +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_activity_to_chemical_entity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml index 82416f062c..068c839ed1 100644 --- a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml +++ b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_activity_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_activity_to_molecular_activity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_activity_to_pathway_association_config.yaml b/golr-views/molecular_activity_to_pathway_association_config.yaml index 27650b5f37..217bf0df10 100644 --- a/golr-views/molecular_activity_to_pathway_association_config.yaml +++ b/golr-views/molecular_activity_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_activity_to_pathway_association +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_activity_to_pathway_association schema_generating: true description: Association that holds the relationship between a reaction and the pathway it participates in. diff --git a/golr-views/molecular_entity_config.yaml b/golr-views/molecular_entity_config.yaml index f35f0cc356..a5c5aed97e 100644 --- a/golr-views/molecular_entity_config.yaml +++ b/golr-views/molecular_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_entity +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_entity schema_generating: true description: A molecular entity is a chemical entity composed of individual or covalently bonded atoms. diff --git a/golr-views/molecular_mixture_config.yaml b/golr-views/molecular_mixture_config.yaml index d24ff863bc..d9cb38fcc9 100644 --- a/golr-views/molecular_mixture_config.yaml +++ b/golr-views/molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: molecular_mixture +# metamodel_version: 1.7.0# version: 3.1.2id: molecular_mixture schema_generating: true description: A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. diff --git a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml index 9cf815e111..4caae05633 100644 --- a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml +++ b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: named_thing_associated_with_likelihood_of_named_thing_association +# metamodel_version: 1.7.0# version: 3.1.2id: named_thing_associated_with_likelihood_of_named_thing_association schema_generating: true description: '' display_name: named thing associated with likelihood of named thing association diff --git a/golr-views/named_thing_config.yaml b/golr-views/named_thing_config.yaml index 89ca24c334..0f6f458c8c 100644 --- a/golr-views/named_thing_config.yaml +++ b/golr-views/named_thing_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: named_thing +# metamodel_version: 1.7.0# version: 3.1.2id: named_thing schema_generating: true description: a databased entity or concept/class display_name: named thing diff --git a/golr-views/noncoding_RNA_product_config.yaml b/golr-views/noncoding_RNA_product_config.yaml index fb92c66fb9..4b00dceb8b 100644 --- a/golr-views/noncoding_RNA_product_config.yaml +++ b/golr-views/noncoding_RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: noncoding_RNA_product +# metamodel_version: 1.7.0# version: 3.1.2id: noncoding_RNA_product schema_generating: true display_name: noncoding RNA product document_category: noncoding RNA product diff --git a/golr-views/nucleic_acid_entity_config.yaml b/golr-views/nucleic_acid_entity_config.yaml index 813b3c85f5..9387f95fc2 100644 --- a/golr-views/nucleic_acid_entity_config.yaml +++ b/golr-views/nucleic_acid_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: nucleic_acid_entity +# metamodel_version: 1.7.0# version: 3.1.2id: nucleic_acid_entity schema_generating: true description: A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; diff --git a/golr-views/nucleic_acid_sequence_motif_config.yaml b/golr-views/nucleic_acid_sequence_motif_config.yaml index 05309f98a5..f638ee85c6 100644 --- a/golr-views/nucleic_acid_sequence_motif_config.yaml +++ b/golr-views/nucleic_acid_sequence_motif_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: nucleic_acid_sequence_motif +# metamodel_version: 1.7.0# version: 3.1.2id: nucleic_acid_sequence_motif schema_generating: true description: A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, diff --git a/golr-views/nucleosome_modification_config.yaml b/golr-views/nucleosome_modification_config.yaml index 409e20e323..114726b26d 100644 --- a/golr-views/nucleosome_modification_config.yaml +++ b/golr-views/nucleosome_modification_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: nucleosome_modification +# metamodel_version: 1.7.0# version: 3.1.2id: nucleosome_modification schema_generating: true description: A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine diff --git a/golr-views/observed_expected_frequency_analysis_result_config.yaml b/golr-views/observed_expected_frequency_analysis_result_config.yaml index 20b73333be..20371b3ae0 100644 --- a/golr-views/observed_expected_frequency_analysis_result_config.yaml +++ b/golr-views/observed_expected_frequency_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: observed_expected_frequency_analysis_result +# metamodel_version: 1.7.0# version: 3.1.2id: observed_expected_frequency_analysis_result schema_generating: true description: A result of a observed expected frequency analysis. display_name: observed expected frequency analysis result diff --git a/golr-views/onset_config.yaml b/golr-views/onset_config.yaml index 4af170873e..6047ca2fb1 100644 --- a/golr-views/onset_config.yaml +++ b/golr-views/onset_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: onset +# metamodel_version: 1.7.0# version: 3.1.2id: onset schema_generating: true description: The age group in which (disease) symptom manifestations appear display_name: onset diff --git a/golr-views/organism_attribute_config.yaml b/golr-views/organism_attribute_config.yaml index 9e1f05ff45..5907a4650b 100644 --- a/golr-views/organism_attribute_config.yaml +++ b/golr-views/organism_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organism_attribute +# metamodel_version: 1.7.0# version: 3.1.2id: organism_attribute schema_generating: true description: describes a characteristic of an organismal entity. display_name: organism attribute diff --git a/golr-views/organism_taxon_config.yaml b/golr-views/organism_taxon_config.yaml index 000e202acd..3bfdda7734 100644 --- a/golr-views/organism_taxon_config.yaml +++ b/golr-views/organism_taxon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organism_taxon +# metamodel_version: 1.7.0# version: 3.1.2id: organism_taxon schema_generating: true description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or diff --git a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml index aa5e4f6ab2..65681fa96c 100644 --- a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organism_taxon_to_organism_taxon_interaction +# metamodel_version: 1.7.0# version: 3.1.2id: organism_taxon_to_organism_taxon_interaction schema_generating: true description: 'An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. diff --git a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml index 4af51b36be..80ead86186 100644 --- a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organism_taxon_to_organism_taxon_specialization +# metamodel_version: 1.7.0# version: 3.1.2id: organism_taxon_to_organism_taxon_specialization schema_generating: true description: 'A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo' diff --git a/golr-views/organism_to_organism_association_config.yaml b/golr-views/organism_to_organism_association_config.yaml index 5a91625e5c..7beb10ea5e 100644 --- a/golr-views/organism_to_organism_association_config.yaml +++ b/golr-views/organism_to_organism_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organism_to_organism_association +# metamodel_version: 1.7.0# version: 3.1.2id: organism_to_organism_association schema_generating: true display_name: organism to organism association document_category: organism to organism association diff --git a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml index ab9951c899..dd09688ccf 100644 --- a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml +++ b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: organismal_entity_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: organismal_entity_as_a_model_of_disease_association schema_generating: true display_name: organismal entity as a model of disease association document_category: organismal entity as a model of disease association diff --git a/golr-views/pairwise_gene_to_gene_interaction_config.yaml b/golr-views/pairwise_gene_to_gene_interaction_config.yaml index b158d027fb..9afec5b7d3 100644 --- a/golr-views/pairwise_gene_to_gene_interaction_config.yaml +++ b/golr-views/pairwise_gene_to_gene_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pairwise_gene_to_gene_interaction +# metamodel_version: 1.7.0# version: 3.1.2id: pairwise_gene_to_gene_interaction schema_generating: true description: An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein diff --git a/golr-views/pairwise_molecular_interaction_config.yaml b/golr-views/pairwise_molecular_interaction_config.yaml index 134a017850..37e1e7b2dd 100644 --- a/golr-views/pairwise_molecular_interaction_config.yaml +++ b/golr-views/pairwise_molecular_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pairwise_molecular_interaction +# metamodel_version: 1.7.0# version: 3.1.2id: pairwise_molecular_interaction schema_generating: true description: An interaction at the molecular level between two physical entities display_name: pairwise molecular interaction diff --git a/golr-views/pathological_anatomical_exposure_config.yaml b/golr-views/pathological_anatomical_exposure_config.yaml index e60da73a0a..fdd7c9168e 100644 --- a/golr-views/pathological_anatomical_exposure_config.yaml +++ b/golr-views/pathological_anatomical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pathological_anatomical_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: pathological_anatomical_exposure schema_generating: true description: An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to diff --git a/golr-views/pathological_anatomical_structure_config.yaml b/golr-views/pathological_anatomical_structure_config.yaml index dc3f348037..31d264ea1c 100644 --- a/golr-views/pathological_anatomical_structure_config.yaml +++ b/golr-views/pathological_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pathological_anatomical_structure +# metamodel_version: 1.7.0# version: 3.1.2id: pathological_anatomical_structure schema_generating: true description: An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathological_process_config.yaml b/golr-views/pathological_process_config.yaml index 468f48ee8a..315b7c078e 100644 --- a/golr-views/pathological_process_config.yaml +++ b/golr-views/pathological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pathological_process +# metamodel_version: 1.7.0# version: 3.1.2id: pathological_process schema_generating: true description: A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathological_process_exposure_config.yaml b/golr-views/pathological_process_exposure_config.yaml index edfe9acdff..0111535fe4 100644 --- a/golr-views/pathological_process_exposure_config.yaml +++ b/golr-views/pathological_process_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pathological_process_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: pathological_process_exposure schema_generating: true description: A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. diff --git a/golr-views/pathway_config.yaml b/golr-views/pathway_config.yaml index f2a2017119..d5363c3e41 100644 --- a/golr-views/pathway_config.yaml +++ b/golr-views/pathway_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: pathway +# metamodel_version: 1.7.0# version: 3.1.2id: pathway schema_generating: true display_name: pathway document_category: pathway diff --git a/golr-views/phenomenon_config.yaml b/golr-views/phenomenon_config.yaml index 4b581c7d21..e3e1068fe1 100644 --- a/golr-views/phenomenon_config.yaml +++ b/golr-views/phenomenon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: phenomenon +# metamodel_version: 1.7.0# version: 3.1.2id: phenomenon schema_generating: true description: a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question diff --git a/golr-views/phenotypic_feature_config.yaml b/golr-views/phenotypic_feature_config.yaml index a5bb592800..6fc104eb8f 100644 --- a/golr-views/phenotypic_feature_config.yaml +++ b/golr-views/phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: phenotypic_feature +# metamodel_version: 1.7.0# version: 3.1.2id: phenotypic_feature schema_generating: true description: A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of diff --git a/golr-views/phenotypic_quality_config.yaml b/golr-views/phenotypic_quality_config.yaml index 118fe5ffcc..ff7a37d373 100644 --- a/golr-views/phenotypic_quality_config.yaml +++ b/golr-views/phenotypic_quality_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: phenotypic_quality +# metamodel_version: 1.7.0# version: 3.1.2id: phenotypic_quality schema_generating: true description: A property of a phenotype display_name: phenotypic quality diff --git a/golr-views/phenotypic_sex_config.yaml b/golr-views/phenotypic_sex_config.yaml index 29508615a2..f0c6733de9 100644 --- a/golr-views/phenotypic_sex_config.yaml +++ b/golr-views/phenotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: phenotypic_sex +# metamodel_version: 1.7.0# version: 3.1.2id: phenotypic_sex schema_generating: true description: An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. diff --git a/golr-views/physical_entity_config.yaml b/golr-views/physical_entity_config.yaml index 69a557d00b..26ca19a114 100644 --- a/golr-views/physical_entity_config.yaml +++ b/golr-views/physical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: physical_entity +# metamodel_version: 1.7.0# version: 3.1.2id: physical_entity schema_generating: true description: An entity that has material reality (a.k.a. physical essence). display_name: physical entity diff --git a/golr-views/physiological_process_config.yaml b/golr-views/physiological_process_config.yaml index ee7bc95226..bf28624d3b 100644 --- a/golr-views/physiological_process_config.yaml +++ b/golr-views/physiological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: physiological_process +# metamodel_version: 1.7.0# version: 3.1.2id: physiological_process schema_generating: true display_name: physiological process document_category: physiological process diff --git a/golr-views/planetary_entity_config.yaml b/golr-views/planetary_entity_config.yaml index a73bbb1339..7d66ef5078 100644 --- a/golr-views/planetary_entity_config.yaml +++ b/golr-views/planetary_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: planetary_entity +# metamodel_version: 1.7.0# version: 3.1.2id: planetary_entity schema_generating: true description: Any entity or process that exists at the level of the whole planet display_name: planetary entity diff --git a/golr-views/polypeptide_config.yaml b/golr-views/polypeptide_config.yaml index 0e3832ad97..3eabafedf6 100644 --- a/golr-views/polypeptide_config.yaml +++ b/golr-views/polypeptide_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: polypeptide +# metamodel_version: 1.7.0# version: 3.1.2id: polypeptide schema_generating: true description: A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary diff --git a/golr-views/population_of_individual_organisms_config.yaml b/golr-views/population_of_individual_organisms_config.yaml index ea893ada51..041483abca 100644 --- a/golr-views/population_of_individual_organisms_config.yaml +++ b/golr-views/population_of_individual_organisms_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: population_of_individual_organisms +# metamodel_version: 1.7.0# version: 3.1.2id: population_of_individual_organisms schema_generating: true description: A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited diff --git a/golr-views/population_to_population_association_config.yaml b/golr-views/population_to_population_association_config.yaml index ddb2fbbe2f..4f28c4dc74 100644 --- a/golr-views/population_to_population_association_config.yaml +++ b/golr-views/population_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: population_to_population_association +# metamodel_version: 1.7.0# version: 3.1.2id: population_to_population_association schema_generating: true description: An association between a two populations display_name: population to population association diff --git a/golr-views/posttranslational_modification_config.yaml b/golr-views/posttranslational_modification_config.yaml index d80054f66f..5da93eecf1 100644 --- a/golr-views/posttranslational_modification_config.yaml +++ b/golr-views/posttranslational_modification_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: posttranslational_modification +# metamodel_version: 1.7.0# version: 3.1.2id: posttranslational_modification schema_generating: true description: A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or diff --git a/golr-views/predicate_mapping_config.yaml b/golr-views/predicate_mapping_config.yaml index 256ca9079f..9d317cacb2 100644 --- a/golr-views/predicate_mapping_config.yaml +++ b/golr-views/predicate_mapping_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: predicate_mapping +# metamodel_version: 1.7.0# version: 3.1.2id: predicate_mapping schema_generating: true description: A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement diff --git a/golr-views/procedure_config.yaml b/golr-views/procedure_config.yaml index d2682df266..e5c32d5461 100644 --- a/golr-views/procedure_config.yaml +++ b/golr-views/procedure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: procedure +# metamodel_version: 1.7.0# version: 3.1.2id: procedure schema_generating: true description: A series of actions conducted in a certain order or manner display_name: procedure diff --git a/golr-views/processed_material_config.yaml b/golr-views/processed_material_config.yaml index 7962f0282a..dabaaf3fed 100644 --- a/golr-views/processed_material_config.yaml +++ b/golr-views/processed_material_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: processed_material +# metamodel_version: 1.7.0# version: 3.1.2id: processed_material schema_generating: true description: A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during diff --git a/golr-views/protein_config.yaml b/golr-views/protein_config.yaml index 694518696d..98ae6b889f 100644 --- a/golr-views/protein_config.yaml +++ b/golr-views/protein_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: protein +# metamodel_version: 1.7.0# version: 3.1.2id: protein schema_generating: true description: A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA diff --git a/golr-views/protein_domain_config.yaml b/golr-views/protein_domain_config.yaml index 44e8e4a6c6..5d770d8a64 100644 --- a/golr-views/protein_domain_config.yaml +++ b/golr-views/protein_domain_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: protein_domain +# metamodel_version: 1.7.0# version: 3.1.2id: protein_domain schema_generating: true description: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein diff --git a/golr-views/protein_family_config.yaml b/golr-views/protein_family_config.yaml index 50db6d588f..f5d75254e7 100644 --- a/golr-views/protein_family_config.yaml +++ b/golr-views/protein_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: protein_family +# metamodel_version: 1.7.0# version: 3.1.2id: protein_family schema_generating: true display_name: protein family document_category: protein family diff --git a/golr-views/protein_isoform_config.yaml b/golr-views/protein_isoform_config.yaml index ddadf0445f..3dce90d383 100644 --- a/golr-views/protein_isoform_config.yaml +++ b/golr-views/protein_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: protein_isoform +# metamodel_version: 1.7.0# version: 3.1.2id: protein_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ diff --git a/golr-views/publication_config.yaml b/golr-views/publication_config.yaml index d32c56502a..607d7cdff5 100644 --- a/golr-views/publication_config.yaml +++ b/golr-views/publication_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: publication +# metamodel_version: 1.7.0# version: 3.1.2id: publication schema_generating: true description: Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, diff --git a/golr-views/quantity_value_config.yaml b/golr-views/quantity_value_config.yaml index 4a2021da1e..529cc6c44c 100644 --- a/golr-views/quantity_value_config.yaml +++ b/golr-views/quantity_value_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: quantity_value +# metamodel_version: 1.7.0# version: 3.1.2id: quantity_value schema_generating: true description: A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value diff --git a/golr-views/reaction_to_catalyst_association_config.yaml b/golr-views/reaction_to_catalyst_association_config.yaml index 4a61f12bd5..60445985e5 100644 --- a/golr-views/reaction_to_catalyst_association_config.yaml +++ b/golr-views/reaction_to_catalyst_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: reaction_to_catalyst_association +# metamodel_version: 1.7.0# version: 3.1.2id: reaction_to_catalyst_association schema_generating: true display_name: reaction to catalyst association document_category: reaction to catalyst association diff --git a/golr-views/reaction_to_participant_association_config.yaml b/golr-views/reaction_to_participant_association_config.yaml index cc1a9c9c38..ef45f34018 100644 --- a/golr-views/reaction_to_participant_association_config.yaml +++ b/golr-views/reaction_to_participant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: reaction_to_participant_association +# metamodel_version: 1.7.0# version: 3.1.2id: reaction_to_participant_association schema_generating: true display_name: reaction to participant association document_category: reaction to participant association diff --git a/golr-views/reagent_targeted_gene_config.yaml b/golr-views/reagent_targeted_gene_config.yaml index c193aa6d93..e07e6c663b 100644 --- a/golr-views/reagent_targeted_gene_config.yaml +++ b/golr-views/reagent_targeted_gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: reagent_targeted_gene +# metamodel_version: 1.7.0# version: 3.1.2id: reagent_targeted_gene schema_generating: true description: A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino diff --git a/golr-views/relative_frequency_analysis_result_config.yaml b/golr-views/relative_frequency_analysis_result_config.yaml index 38258c601e..e310076952 100644 --- a/golr-views/relative_frequency_analysis_result_config.yaml +++ b/golr-views/relative_frequency_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: relative_frequency_analysis_result +# metamodel_version: 1.7.0# version: 3.1.2id: relative_frequency_analysis_result schema_generating: true description: A result of a relative frequency analysis. display_name: relative frequency analysis result diff --git a/golr-views/sequence_association_config.yaml b/golr-views/sequence_association_config.yaml index b40188c4f0..3ad11e7762 100644 --- a/golr-views/sequence_association_config.yaml +++ b/golr-views/sequence_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: sequence_association +# metamodel_version: 1.7.0# version: 3.1.2id: sequence_association schema_generating: true description: An association between a sequence feature and a nucleic acid entity it is localized to. diff --git a/golr-views/sequence_feature_relationship_config.yaml b/golr-views/sequence_feature_relationship_config.yaml index 5611dd5e71..b4cc57f734 100644 --- a/golr-views/sequence_feature_relationship_config.yaml +++ b/golr-views/sequence_feature_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: sequence_feature_relationship +# metamodel_version: 1.7.0# version: 3.1.2id: sequence_feature_relationship schema_generating: true description: For example, a particular exon is part of a particular transcript or gene diff --git a/golr-views/sequence_variant_config.yaml b/golr-views/sequence_variant_config.yaml index 574205939a..cd57c6d520 100644 --- a/golr-views/sequence_variant_config.yaml +++ b/golr-views/sequence_variant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: sequence_variant +# metamodel_version: 1.7.0# version: 3.1.2id: sequence_variant schema_generating: true description: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. diff --git a/golr-views/serial_config.yaml b/golr-views/serial_config.yaml index c443be635a..e654fbfe1e 100644 --- a/golr-views/serial_config.yaml +++ b/golr-views/serial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: serial +# metamodel_version: 1.7.0# version: 3.1.2id: serial schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. diff --git a/golr-views/severity_value_config.yaml b/golr-views/severity_value_config.yaml index 0861bb2767..ab81910cf0 100644 --- a/golr-views/severity_value_config.yaml +++ b/golr-views/severity_value_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: severity_value +# metamodel_version: 1.7.0# version: 3.1.2id: severity_value schema_generating: true description: describes the severity of a phenotypic feature or disease display_name: severity value diff --git a/golr-views/siRNA_config.yaml b/golr-views/siRNA_config.yaml index 74877cebf7..7281b55d85 100644 --- a/golr-views/siRNA_config.yaml +++ b/golr-views/siRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: siRNA +# metamodel_version: 1.7.0# version: 3.1.2id: siRNA schema_generating: true description: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via diff --git a/golr-views/small_molecule_config.yaml b/golr-views/small_molecule_config.yaml index 8e463ba90c..67101f924c 100644 --- a/golr-views/small_molecule_config.yaml +++ b/golr-views/small_molecule_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: small_molecule +# metamodel_version: 1.7.0# version: 3.1.2id: small_molecule schema_generating: true description: A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation diff --git a/golr-views/snv_config.yaml b/golr-views/snv_config.yaml index a53b0fea36..817a268d47 100644 --- a/golr-views/snv_config.yaml +++ b/golr-views/snv_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: snv +# metamodel_version: 1.7.0# version: 3.1.2id: snv schema_generating: true description: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist diff --git a/golr-views/socioeconomic_attribute_config.yaml b/golr-views/socioeconomic_attribute_config.yaml index 9324949e1b..08386c24d7 100644 --- a/golr-views/socioeconomic_attribute_config.yaml +++ b/golr-views/socioeconomic_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: socioeconomic_attribute +# metamodel_version: 1.7.0# version: 3.1.2id: socioeconomic_attribute schema_generating: true description: Attributes relating to a socioeconomic manifestation display_name: socioeconomic attribute diff --git a/golr-views/socioeconomic_exposure_config.yaml b/golr-views/socioeconomic_exposure_config.yaml index fe3575339b..2e293d4c0a 100644 --- a/golr-views/socioeconomic_exposure_config.yaml +++ b/golr-views/socioeconomic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: socioeconomic_exposure +# metamodel_version: 1.7.0# version: 3.1.2id: socioeconomic_exposure schema_generating: true description: A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). diff --git a/golr-views/study_config.yaml b/golr-views/study_config.yaml index 97e9cce86b..ce15263eea 100644 --- a/golr-views/study_config.yaml +++ b/golr-views/study_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: study +# metamodel_version: 1.7.0# version: 3.1.2id: study schema_generating: true description: a detailed investigation and/or analysis display_name: study diff --git a/golr-views/study_population_config.yaml b/golr-views/study_population_config.yaml index 1414825133..be633ac5a8 100644 --- a/golr-views/study_population_config.yaml +++ b/golr-views/study_population_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: study_population +# metamodel_version: 1.7.0# version: 3.1.2id: study_population schema_generating: true description: A group of people banded together or treated as a group as participants in a research study. diff --git a/golr-views/study_variable_config.yaml b/golr-views/study_variable_config.yaml index 3521f0b57e..652eae1634 100644 --- a/golr-views/study_variable_config.yaml +++ b/golr-views/study_variable_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: study_variable +# metamodel_version: 1.7.0# version: 3.1.2id: study_variable schema_generating: true description: a variable that is used as a measure in the investigation of a study display_name: study variable diff --git a/golr-views/taxon_to_taxon_association_config.yaml b/golr-views/taxon_to_taxon_association_config.yaml index c088a575ae..4a972a6718 100644 --- a/golr-views/taxon_to_taxon_association_config.yaml +++ b/golr-views/taxon_to_taxon_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: taxon_to_taxon_association +# metamodel_version: 1.7.0# version: 3.1.2id: taxon_to_taxon_association schema_generating: true display_name: taxon to taxon association document_category: taxon to taxon association diff --git a/golr-views/text_mining_result_config.yaml b/golr-views/text_mining_result_config.yaml index 4e80eeeab4..9b93b00074 100644 --- a/golr-views/text_mining_result_config.yaml +++ b/golr-views/text_mining_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: text_mining_result +# metamodel_version: 1.7.0# version: 3.1.2id: text_mining_result schema_generating: true description: A result of text mining. display_name: text mining result diff --git a/golr-views/transcript_config.yaml b/golr-views/transcript_config.yaml index 564f459f7b..75d0186521 100644 --- a/golr-views/transcript_config.yaml +++ b/golr-views/transcript_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: transcript +# metamodel_version: 1.7.0# version: 3.1.2id: transcript schema_generating: true description: An RNA synthesized on a DNA or RNA template by an RNA polymerase. display_name: transcript diff --git a/golr-views/transcript_to_gene_relationship_config.yaml b/golr-views/transcript_to_gene_relationship_config.yaml index 6cfb65023c..23fc4f8dad 100644 --- a/golr-views/transcript_to_gene_relationship_config.yaml +++ b/golr-views/transcript_to_gene_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: transcript_to_gene_relationship +# metamodel_version: 1.7.0# version: 3.1.2id: transcript_to_gene_relationship schema_generating: true description: A gene is a collection of transcripts display_name: transcript to gene relationship diff --git a/golr-views/treatment_config.yaml b/golr-views/treatment_config.yaml index 18275bacbd..b72d7ee907 100644 --- a/golr-views/treatment_config.yaml +++ b/golr-views/treatment_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: treatment +# metamodel_version: 1.7.0# version: 3.1.2id: treatment schema_generating: true description: A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures diff --git a/golr-views/variant_as_a_model_of_disease_association_config.yaml b/golr-views/variant_as_a_model_of_disease_association_config.yaml index 00125ef63c..a2289bdb16 100644 --- a/golr-views/variant_as_a_model_of_disease_association_config.yaml +++ b/golr-views/variant_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_as_a_model_of_disease_association schema_generating: true display_name: variant as a model of disease association document_category: variant as a model of disease association diff --git a/golr-views/variant_to_disease_association_config.yaml b/golr-views/variant_to_disease_association_config.yaml index 06956c7b94..11cbfdddef 100644 --- a/golr-views/variant_to_disease_association_config.yaml +++ b/golr-views/variant_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_to_disease_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_to_disease_association schema_generating: true display_name: variant to disease association document_category: variant to disease association diff --git a/golr-views/variant_to_gene_association_config.yaml b/golr-views/variant_to_gene_association_config.yaml index 451bf2c41f..ad0b80556b 100644 --- a/golr-views/variant_to_gene_association_config.yaml +++ b/golr-views/variant_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_to_gene_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_to_gene_association schema_generating: true description: An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) diff --git a/golr-views/variant_to_gene_expression_association_config.yaml b/golr-views/variant_to_gene_expression_association_config.yaml index 51c173c7b5..ba5bc53f4a 100644 --- a/golr-views/variant_to_gene_expression_association_config.yaml +++ b/golr-views/variant_to_gene_expression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_to_gene_expression_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_to_gene_expression_association schema_generating: true description: An association between a variant and expression of a gene (i.e. e-QTL) display_name: variant to gene expression association diff --git a/golr-views/variant_to_phenotypic_feature_association_config.yaml b/golr-views/variant_to_phenotypic_feature_association_config.yaml index 0f47b2d785..76db9f462a 100644 --- a/golr-views/variant_to_phenotypic_feature_association_config.yaml +++ b/golr-views/variant_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_to_phenotypic_feature_association schema_generating: true display_name: variant to phenotypic feature association document_category: variant to phenotypic feature association diff --git a/golr-views/variant_to_population_association_config.yaml b/golr-views/variant_to_population_association_config.yaml index 37db3019df..7bf69ff8bd 100644 --- a/golr-views/variant_to_population_association_config.yaml +++ b/golr-views/variant_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: variant_to_population_association +# metamodel_version: 1.7.0# version: 3.1.2id: variant_to_population_association schema_generating: true description: An association between a variant and a population, where the variant has particular frequency in the population diff --git a/golr-views/virus_config.yaml b/golr-views/virus_config.yaml index ea88cb9550..c443e6f8a6 100644 --- a/golr-views/virus_config.yaml +++ b/golr-views/virus_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: virus +# metamodel_version: 1.7.0# version: 3.1.2id: virus schema_generating: true description: A virus is a microorganism that replicates itself as a microRNA and infects the host cell. diff --git a/golr-views/zygosity_config.yaml b/golr-views/zygosity_config.yaml index a21cc6f1fe..bced262c44 100644 --- a/golr-views/zygosity_config.yaml +++ b/golr-views/zygosity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.1.1id: zygosity +# metamodel_version: 1.7.0# version: 3.1.2id: zygosity schema_generating: true display_name: zygosity document_category: zygosity diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json index 5c6bbfccea..337027fa05 100644 --- a/json-schema/biolink-model.json +++ b/json-schema/biolink-model.json @@ -1 +1 @@ -{"$defs": {"Activity": {"additionalProperties": false, "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "person, group, organization or project that provides a piece of information (i.e. a knowledge association)", "properties": {"address": {"description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", "type": "string"}, "affiliation": {"description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Agent", "type": "object"}, "AnatomicalContextQualifierEnum": {"description": "", "enum": [], "title": "AnatomicalContextQualifierEnum", "type": "string"}, "AnatomicalEntity": {"additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AnatomicalEntity", "type": "object"}, "AnatomicalEntityToAnatomicalEntityOntogenicAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the structure at an earlier time", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the structure at a later time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityOntogenicAssociation", "type": "object"}, "AnatomicalEntityToAnatomicalEntityPartOfAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the whole", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the part", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityPartOfAssociation", "type": "object"}, "Article": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category", "type"], "title": "Article", "type": "object"}, "Association": {"additionalProperties": false, "description": "A typed association between two entities, supported by evidence", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "Association", "type": "object"}, "Attribute": {"additionalProperties": false, "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Attribute", "type": "object"}, "Behavior": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Behavior", "type": "object"}, "BehaviorToBehavioralFeatureAssociation": {"additionalProperties": false, "description": "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "behavioral feature that is the object of the association", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "behavior that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "BehaviorToBehavioralFeatureAssociation", "type": "object"}, "BehavioralExposure": {"additionalProperties": false, "description": "A behavioral exposure is a factor relating to behavior impacting an individual.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BehavioralExposure", "type": "object"}, "BehavioralFeature": {"additionalProperties": false, "description": "A phenotypic feature which is behavioral in nature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BehavioralFeature", "type": "object"}, "BehavioralOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of human behavior.", "title": "BehavioralOutcome", "type": "object"}, "BiologicalProcess": {"additionalProperties": false, "description": "One or more causally connected executions of molecular functions", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcess", "type": "object"}, "BiologicalProcessOrActivity": {"additionalProperties": false, "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcessOrActivity", "type": "object"}, "BiologicalSex": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BiologicalSex", "type": "object"}, "BioticExposure": {"additionalProperties": false, "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BioticExposure", "type": "object"}, "Book": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Books should have industry-standard identifier such as from ISBN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'book'.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Book", "type": "object"}, "BookChapter": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "chapter": {"description": "chapter of a book", "type": "string"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category", "type"], "title": "BookChapter", "type": "object"}, "Case": {"additionalProperties": false, "description": "An individual (human) organism that has a patient role in some clinical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Case", "type": "object"}, "CaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CaseToPhenotypicFeatureAssociation", "type": "object"}, "CausalMechanismQualifierEnum": {"description": "", "enum": ["binding", "inhibition", "antibody_inhibition", "antagonism", "molecular_channel_blockage", "inverse_agonism", "negative_allosteric_modulation", "agonism", "molecular_channel_opening", "positive_allosteric_modulation", "potentiation", "activation", "inducer", "transcriptional_regulation", "signaling_mediated_control", "stabilization", "stimulation", "releasing_activity"], "title": "CausalMechanismQualifierEnum", "type": "string"}, "Cell": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cell", "type": "object"}, "CellLine": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellLine", "type": "object"}, "CellLineAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineAsAModelOfDiseaseAssociation", "type": "object"}, "CellLineToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "CellularComponent": {"additionalProperties": false, "description": "A location in or around a cell", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularComponent", "type": "object"}, "CellularOrganism": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularOrganism", "type": "object"}, "ChemicalAffectsGeneAssociation": {"additionalProperties": false, "description": "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalAffectsGeneAssociation", "type": "object"}, "ChemicalEntity": {"additionalProperties": false, "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalEntity", "type": "object"}, "ChemicalEntityAssessesNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityAssessesNamedThingAssociation", "type": "object"}, "ChemicalEntityDerivativeEnum": {"description": "", "enum": ["metabolite"], "title": "ChemicalEntityDerivativeEnum", "type": "string"}, "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": {"additionalProperties": false, "description": "A regulatory relationship between two genes", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the direction is always from regulator to regulated", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", "type": "object"}, "ChemicalExposure": {"additionalProperties": false, "description": "A chemical exposure is an intake of a particular chemical entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalExposure", "type": "object"}, "ChemicalGeneInteractionAssociation": {"additionalProperties": false, "description": "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalGeneInteractionAssociation", "type": "object"}, "ChemicalMixture": {"additionalProperties": false, "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalMixture", "type": "object"}, "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrGeneOrGeneProductFormOrVariantEnum": {"description": "", "enum": ["genetic_variant_form", "modified_form", "loss_of_function_variant_form", "gain_of_function_variant_form", "polymorphic_form", "snp_form", "analog_form"], "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", "type": "string"}, "ChemicalRole": {"additionalProperties": false, "description": "A role played by the molecular entity or part thereof within a chemical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalRole", "type": "object"}, "ChemicalToChemicalAssociation": {"additionalProperties": false, "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the chemical element that is the target of the statement", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalAssociation", "type": "object"}, "ChemicalToChemicalDerivationAssociation": {"additionalProperties": false, "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "catalyst_qualifier": {"description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the downstream chemical entity", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the upstream chemical entity", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalDerivationAssociation", "type": "object"}, "ChemicalToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the disease or phenotype that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the chemical entity that is affecting the pathway", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToPathwayAssociation", "type": "object"}, "ChiSquaredAnalysisResult": {"additionalProperties": false, "description": "A result of a chi squared analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChiSquaredAnalysisResult", "type": "object"}, "ClinicalAttribute": {"additionalProperties": false, "description": "Attributes relating to a clinical manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalAttribute", "type": "object"}, "ClinicalCourse": {"additionalProperties": false, "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalCourse", "type": "object"}, "ClinicalEntity": {"additionalProperties": false, "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalEntity", "type": "object"}, "ClinicalFinding": {"additionalProperties": false, "description": "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalFinding", "type": "object"}, "ClinicalIntervention": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalIntervention", "type": "object"}, "ClinicalMeasurement": {"additionalProperties": false, "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalMeasurement", "type": "object"}, "ClinicalModifier": {"additionalProperties": false, "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalModifier", "type": "object"}, "ClinicalTrial": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalTrial", "type": "object"}, "CodingSequence": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CodingSequence", "type": "object"}, "Cohort": {"additionalProperties": false, "description": "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cohort", "type": "object"}, "CommonDataElement": {"additionalProperties": false, "description": "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CommonDataElement", "type": "object"}, "ComplexChemicalExposure": {"additionalProperties": false, "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ComplexChemicalExposure", "type": "object"}, "ComplexMolecularMixture": {"additionalProperties": false, "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ComplexMolecularMixture", "type": "object"}, "ConceptCountAnalysisResult": {"additionalProperties": false, "description": "A result of a concept count analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConceptCountAnalysisResult", "type": "object"}, "ConfidenceLevel": {"additionalProperties": false, "description": "Level of confidence in a statement", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConfidenceLevel", "type": "object"}, "ContributorAssociation": {"additionalProperties": false, "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "agent helping to realise the given entity (e.g. such as a publication)", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "information content entity which an agent has helped realise", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ContributorAssociation", "type": "object"}, "Dataset": {"additionalProperties": false, "description": "an item that refers to a collection of data from a data source.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Dataset", "type": "object"}, "DatasetDistribution": {"additionalProperties": false, "description": "an item that holds distribution level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "distribution_download_url": {"type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetDistribution", "type": "object"}, "DatasetSummary": {"additionalProperties": false, "description": "an item that holds summary level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "source_logo": {"type": "string"}, "source_web_page": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetSummary", "type": "object"}, "DatasetVersion": {"additionalProperties": false, "description": "an item that holds version level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_dataset": {"type": "string"}, "has_distribution": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "ingest_date": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetVersion", "type": "object"}, "Device": {"additionalProperties": false, "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Device", "type": "object"}, "DirectionQualifierEnum": {"description": "", "enum": ["increased", "upregulated", "decreased", "downregulated"], "title": "DirectionQualifierEnum", "type": "string"}, "Disease": {"additionalProperties": false, "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Disease", "type": "object"}, "DiseaseOrPhenotypicFeature": {"additionalProperties": false, "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DiseaseOrPhenotypicFeature", "type": "object"}, "DiseaseOrPhenotypicFeatureExposure": {"additionalProperties": false, "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DiseaseOrPhenotypicFeatureExposure", "type": "object"}, "DiseaseOrPhenotypicFeatureOutcome": {"additionalProperties": false, "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", "title": "DiseaseOrPhenotypicFeatureOutcome", "type": "object"}, "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "genetic inheritance associated with the specified disease or phenotypic feature.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "type": "object"}, "DiseaseOrPhenotypicFeatureToLocationAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "anatomical entity in which the disease or feature is found.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", "type": "object"}, "DiseaseToExposureEventAssociation": {"additionalProperties": false, "description": "An association between an exposure event and a disease.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToExposureEventAssociation", "type": "object"}, "DiseaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToPhenotypicFeatureAssociation", "type": "object"}, "Drug": {"additionalProperties": false, "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Drug", "type": "object"}, "DrugAvailabilityEnum": {"description": "", "enum": ["over_the_counter", "prescription"], "title": "DrugAvailabilityEnum", "type": "string"}, "DrugDeliveryEnum": {"description": "", "enum": ["inhalation", "oral", "absorption_through_the_skin", "intravenous_injection"], "title": "DrugDeliveryEnum", "type": "string"}, "DrugExposure": {"additionalProperties": false, "description": "A drug exposure is an intake of a particular drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugExposure", "type": "object"}, "DrugToGeneAssociation": {"additionalProperties": false, "description": "An interaction between a drug and a gene or gene product.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the drug"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DrugToGeneAssociation", "type": "object"}, "DrugToGeneInteractionExposure": {"additionalProperties": false, "description": "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugToGeneInteractionExposure", "type": "object"}, "DruggableGeneCategoryEnum": {"description": "", "enum": ["tclin", "tbio", "tchem", "tdark"], "title": "DruggableGeneCategoryEnum", "type": "string"}, "DruggableGeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"$ref": "#/$defs/DruggableGeneCategoryEnum"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DruggableGeneToDiseaseAssociation", "type": "object"}, "EntityToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToDiseaseAssociation", "type": "object"}, "EntityToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToPhenotypicFeatureAssociation", "type": "object"}, "EnvironmentalExposure": {"additionalProperties": false, "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "EnvironmentalExposure", "type": "object"}, "EnvironmentalFeature": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFeature", "type": "object"}, "EnvironmentalFoodContaminant": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFoodContaminant", "type": "object"}, "EnvironmentalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalProcess", "type": "object"}, "EpidemiologicalOutcome": {"additionalProperties": false, "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", "title": "EpidemiologicalOutcome", "type": "object"}, "Event": {"additionalProperties": false, "description": "Something that happens at a given place and time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Event", "type": "object"}, "EvidenceType": {"additionalProperties": false, "description": "Class of evidence that supports an association", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EvidenceType", "type": "object"}, "Exon": {"additionalProperties": false, "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Exon", "type": "object"}, "ExonToTranscriptRelationship": {"additionalProperties": false, "description": "A transcript is formed from multiple exons", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExonToTranscriptRelationship", "type": "object"}, "ExposureEventToOutcomeAssociation": {"additionalProperties": false, "description": "An association between an exposure event and an outcome.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/Outcome", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "population_context_qualifier": {"description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "temporal_context_qualifier": {"description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToOutcomeAssociation", "type": "object"}, "ExposureEventToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToPhenotypicFeatureAssociation", "type": "object"}, "FDAApprovalStatusEnum": {"description": "", "enum": ["discovery_and_development_phase", "preclinical_research_phase", "fda_clinical_research_phase", "fda_review_phase_4", "fda_post_market_safety_review", "fda_clinical_research_phase_1", "fda_clinical_research_phase_2", "fda_clinical_research_phase_3", "fda_clinical_research_phase_4", "fda_fast_track", "fda_breakthrough_therapy", "fda_accelerated_approval", "fda_priority_review", "regular_fda_approval", "post_approval_withdrawal"], "title": "FDAApprovalStatusEnum", "type": "string"}, "FDAIDAAdverseEventEnum": {"description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", "enum": ["life_threatening_adverse_event", "serious_adverse_event", "suspected_adverse_reaction", "unexpected_adverse_event"], "title": "FDAIDAAdverseEventEnum", "type": "string"}, "Food": {"additionalProperties": false, "description": "A substance consumed by a living organism as a source of nutrition", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Food", "type": "object"}, "FoodAdditive": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "FoodAdditive", "type": "object"}, "FunctionalAssociation": {"additionalProperties": false, "description": "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex that has the function associated with the GO term"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "FunctionalAssociation", "type": "object"}, "Gene": {"additionalProperties": false, "description": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "symbol": {"description": "Symbol for a particular thing", "type": "string"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Gene", "type": "object"}, "GeneAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneAsAModelOfDiseaseAssociation", "type": "object"}, "GeneFamily": {"additionalProperties": false, "description": "any grouping of multiple genes or gene products related by common descent", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneFamily", "type": "object"}, "GeneHasVariantThatContributesToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "subject_form_or_variant_qualifier": {"type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneHasVariantThatContributesToDiseaseAssociation", "type": "object"}, "GeneOrGeneProductOrChemicalEntityAspectEnum": {"description": "", "enum": ["activity_or_abundance", "abundance", "activity", "expression", "synthesis", "degradation", "cleavage", "hydrolysis", "metabolic_processing", "mutation_rate", "stability", "folding", "localization", "transport", "secretion", "uptake", "molecular_modification", "acetylation", "acylation", "alkylation", "amination", "carbamoylation", "ethylation", "glutathionylation", "glycation", "glycosylation", "glucuronidation", "n_linked_glycosylation", "o_linked_glycosylation", "hydroxylation", "lipidation", "farnesylation", "geranoylation", "myristoylation", "palmitoylation", "prenylation", "methylation", "nitrosation", "nucleotidylation", "phosphorylation", "ribosylation", "ADP-ribosylation", "sulfation", "sumoylation", "ubiquitination", "oxidation", "reduction", "carboxylation"], "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", "type": "string"}, "GeneOrGeneProductOrChemicalPartQualifierEnum": {"description": "", "enum": ["3_prime_utr", "5_prime_utr", "polya_tail", "promoter", "enhancer", "exon", "intron"], "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", "type": "string"}, "GeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToDiseaseAssociation", "type": "object"}, "GeneToExpressionSiteAssociation": {"additionalProperties": false, "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "location in which the gene is expressed", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "expression relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "can be used to indicate magnitude, or also ranking", "type": "string"}, "stage_qualifier": {"description": "stage at which the gene is expressed in the site", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToExpressionSiteAssociation", "type": "object"}, "GeneToGeneCoexpressionAssociation": {"additionalProperties": false, "description": "Indicates that two genes are co-expressed, generally under the same conditions.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneCoexpressionAssociation", "type": "object"}, "GeneToGeneFamilyAssociation": {"additionalProperties": false, "description": "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "membership of the gene in the given gene family.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneFamilyAssociation", "type": "object"}, "GeneToGeneHomologyAssociation": {"additionalProperties": false, "description": "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "homology relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneHomologyAssociation", "type": "object"}, "GeneToGeneProductRelationship": {"additionalProperties": false, "description": "A gene is transcribed and potentially translated to a gene product", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneProductMixin", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneProductRelationship", "type": "object"}, "GeneToGoTermAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "gene, product or macromolecular complex that has the function associated with the GO term", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGoTermAssociation", "type": "object"}, "GeneToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a gene or gene product and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that includes or is affected by the gene or gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product entity that participates or influences the pathway"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPathwayAssociation", "type": "object"}, "GeneToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPhenotypicFeatureAssociation", "type": "object"}, "GeneticInheritance": {"additionalProperties": false, "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneticInheritance", "type": "object"}, "Genome": {"additionalProperties": false, "description": "A genome is the sum of genetic material within a cell or virion.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genome", "type": "object"}, "GenomicBackgroundExposure": {"additionalProperties": false, "description": "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "has_attribute_type", "category"], "title": "GenomicBackgroundExposure", "type": "object"}, "GenomicSequenceLocalization": {"additionalProperties": false, "description": "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "end_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", "type": "integer"}, "genome_build": {"$ref": "#/$defs/StrandEnum", "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens."}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phase": {"$ref": "#/$defs/PhaseEnum", "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2."}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "start_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", "type": "integer"}, "strand": {"$ref": "#/$defs/StrandEnum", "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)."}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenomicSequenceLocalization", "type": "object"}, "Genotype": {"additionalProperties": false, "description": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_zygosity": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genotype", "type": "object"}, "GenotypeAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A genotype that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeAsAModelOfDiseaseAssociation", "type": "object"}, "GenotypeToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that genotype", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a genotype that is associated in some way with a disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToDiseaseAssociation", "type": "object"}, "GenotypeToGeneAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGeneAssociation", "type": "object"}, "GenotypeToGenotypePartAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "child genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGenotypePartAssociation", "type": "object"}, "GenotypeToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "genotype that is associated with the phenotypic feature", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToPhenotypicFeatureAssociation", "type": "object"}, "GenotypeToVariantAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a sequence variant.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToVariantAssociation", "type": "object"}, "GenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GenotypicSex", "type": "object"}, "GeographicExposure": {"additionalProperties": false, "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GeographicExposure", "type": "object"}, "GeographicLocation": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocation", "type": "object"}, "GeographicLocationAtTime": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates, for a particular time", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocationAtTime", "type": "object"}, "GrossAnatomicalStructure": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GrossAnatomicalStructure", "type": "object"}, "Haplotype": {"additionalProperties": false, "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Haplotype", "type": "object"}, "Hospitalization": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Hospitalization", "type": "object"}, "HospitalizationOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", "title": "HospitalizationOutcome", "type": "object"}, "IndividualOrganism": {"additionalProperties": false, "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "IndividualOrganism", "type": "object"}, "InformationContentEntityToNamedThingAssociation": {"additionalProperties": false, "description": "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "InformationContentEntityToNamedThingAssociation", "type": "object"}, "InformationResource": {"additionalProperties": false, "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "InformationResource", "type": "object"}, "LifeStage": {"additionalProperties": false, "description": "A stage of development or growth of an organism, including post-natal adult stages", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "LifeStage", "type": "object"}, "LogicalInterpretationEnum": {"description": "", "enum": ["some_some", "all_some", "inverse_all_some"], "title": "LogicalInterpretationEnum", "type": "string"}, "MacromolecularComplex": {"additionalProperties": false, "description": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MacromolecularComplex", "type": "object"}, "MacromolecularMachineToBiologicalProcessAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToBiologicalProcessAssociation", "type": "object"}, "MacromolecularMachineToCellularComponentAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToCellularComponentAssociation", "type": "object"}, "MacromolecularMachineToMolecularActivityAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToMolecularActivityAssociation", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MaterialSample", "type": "object"}, "MaterialSampleDerivationAssociation": {"additionalProperties": false, "description": "An association between a material sample and the material entity from which it is derived.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "derivation relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the material sample being described", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleDerivationAssociation", "type": "object"}, "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a material sample and a disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "MicroRNA": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MicroRNA", "type": "object"}, "MolecularActivity": {"additionalProperties": false, "description": "An execution of a molecular function carried out by a gene product or macromolecular complex.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "The gene product, gene, or complex that catalyzes the reaction", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "A chemical entity that is the input for the reaction", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "A chemical entity that is the output for the reaction", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularActivity", "type": "object"}, "MolecularActivityToChemicalEntityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToChemicalEntityAssociation", "type": "object"}, "MolecularActivityToMolecularActivityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToMolecularActivityAssociation", "type": "object"}, "MolecularActivityToPathwayAssociation": {"additionalProperties": false, "description": "Association that holds the relationship between a reaction and the pathway it participates in.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToPathwayAssociation", "type": "object"}, "MolecularEntity": {"additionalProperties": false, "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularEntity", "type": "object"}, "MolecularMixture": {"additionalProperties": false, "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularMixture", "type": "object"}, "MortalityOutcome": {"additionalProperties": false, "description": "An outcome of death from resulting from an exposure event.", "title": "MortalityOutcome", "type": "object"}, "NamedThing": {"additionalProperties": false, "description": "a databased entity or concept/class", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NamedThing", "type": "object"}, "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", "type": "object"}, "NoncodingRNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NoncodingRNAProduct", "type": "object"}, "NucleicAcidEntity": {"additionalProperties": false, "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidEntity", "type": "object"}, "NucleicAcidSequenceMotif": {"additionalProperties": false, "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidSequenceMotif", "type": "object"}, "NucleosomeModification": {"additionalProperties": false, "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleosomeModification", "type": "object"}, "ObservedExpectedFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a observed expected frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ObservedExpectedFrequencyAnalysisResult", "type": "object"}, "Onset": {"additionalProperties": false, "description": "The age group in which (disease) symptom manifestations appear", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Onset", "type": "object"}, "OrganismAttribute": {"additionalProperties": false, "description": "describes a characteristic of an organismal entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "OrganismAttribute", "type": "object"}, "OrganismTaxon": {"additionalProperties": false, "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "OrganismTaxon", "type": "object"}, "OrganismTaxonToOrganismTaxonInteraction": {"additionalProperties": false, "description": "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "associated_environmental_context": {"description": "the environment in which the two taxa interact", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the taxon that is the subject of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the taxon that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonInteraction", "type": "object"}, "OrganismTaxonToOrganismTaxonSpecialization": {"additionalProperties": false, "description": "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the more general taxon", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the more specific taxon", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonSpecialization", "type": "object"}, "OrganismToOrganismAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between two individual organisms.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismToOrganismAssociation", "type": "object"}, "OrganismalEntityAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismalEntityAsAModelOfDiseaseAssociation", "type": "object"}, "PairwiseGeneToGeneInteraction": {"additionalProperties": false, "description": "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseGeneToGeneInteraction", "type": "object"}, "PairwiseMolecularInteraction": {"additionalProperties": false, "description": "An interaction at the molecular level between two physical entities", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string"}, "interacting_molecules_category": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseMolecularInteraction", "type": "object"}, "PathologicalAnatomicalExposure": {"additionalProperties": false, "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalAnatomicalExposure", "type": "object"}, "PathologicalAnatomicalOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.", "title": "PathologicalAnatomicalOutcome", "type": "object"}, "PathologicalAnatomicalStructure": {"additionalProperties": false, "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalAnatomicalStructure", "type": "object"}, "PathologicalProcess": {"additionalProperties": false, "description": "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalProcess", "type": "object"}, "PathologicalProcessExposure": {"additionalProperties": false, "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalProcessExposure", "type": "object"}, "PathologicalProcessOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process.", "title": "PathologicalProcessOutcome", "type": "object"}, "Pathway": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Pathway", "type": "object"}, "PhaseEnum": {"description": "phase", "enum": ["0", "1", "2"], "title": "PhaseEnum", "type": "string"}, "Phenomenon": {"additionalProperties": false, "description": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Phenomenon", "type": "object"}, "PhenotypicFeature": {"additionalProperties": false, "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhenotypicFeature", "type": "object"}, "PhenotypicQuality": {"additionalProperties": false, "description": "A property of a phenotype", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicQuality", "type": "object"}, "PhenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicSex", "type": "object"}, "PhysicalEntity": {"additionalProperties": false, "description": "An entity that has material reality (a.k.a. physical essence).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysicalEntity", "type": "object"}, "PhysiologicalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysiologicalProcess", "type": "object"}, "PlanetaryEntity": {"additionalProperties": false, "description": "Any entity or process that exists at the level of the whole planet", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PlanetaryEntity", "type": "object"}, "Polypeptide": {"additionalProperties": false, "description": "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Polypeptide", "type": "object"}, "PopulationOfIndividualOrganisms": {"additionalProperties": false, "description": "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PopulationOfIndividualOrganisms", "type": "object"}, "PopulationToPopulationAssociation": {"additionalProperties": false, "description": "An association between a two populations", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that form the object of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the population that form the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PopulationToPopulationAssociation", "type": "object"}, "PosttranslationalModification": {"additionalProperties": false, "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PosttranslationalModification", "type": "object"}, "PredicateMapping": {"additionalProperties": false, "description": "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.", "properties": {"anatomical_context_qualifier": {"$ref": "#/$defs/AnatomicalContextQualifierEnum", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)."}, "broad_match": {"description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", "type": "string"}, "exact_match": {"description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", "items": {"type": "string"}, "type": "array"}, "mapped_predicate": {"description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", "type": "string"}, "narrow_match": {"description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "object_aspect_qualifier": {"type": "string"}, "object_context_qualifier": {"type": "string"}, "object_derivative_qualifier": {"type": "string"}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "object_form_or_variant_qualifier": {"type": "string"}, "object_part_qualifier": {"type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "species_context_qualifier": {"description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", "type": "string"}, "subject_aspect_qualifier": {"type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"type": "string"}, "subject_direction_qualifier": {"type": "string"}, "subject_form_or_variant_qualifier": {"type": "string"}, "subject_part_qualifier": {"type": "string"}}, "required": ["predicate"], "title": "PredicateMapping", "type": "object"}, "Procedure": {"additionalProperties": false, "description": "A series of actions conducted in a certain order or manner", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Procedure", "type": "object"}, "ProcessedMaterial": {"additionalProperties": false, "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProcessedMaterial", "type": "object"}, "Protein": {"additionalProperties": false, "description": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Protein", "type": "object"}, "ProteinDomain": {"additionalProperties": false, "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinDomain", "type": "object"}, "ProteinFamily": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinFamily", "type": "object"}, "ProteinIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinIsoform", "type": "object"}, "Publication": {"additionalProperties": false, "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", "type": "string"}, "pages": {"description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Publication", "type": "object"}, "QuantityValue": {"additionalProperties": false, "description": "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value", "properties": {"has_numeric_value": {"description": "connects a quantity value to a number", "type": "number"}, "has_unit": {"description": "connects a quantity value to a unit", "type": "string"}}, "title": "QuantityValue", "type": "object"}, "RNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProduct", "type": "object"}, "RNAProductIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference RNA", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProductIsoform", "type": "object"}, "ReactionDirectionEnum": {"description": "", "enum": ["left_to_right", "right_to_left", "bidirectional", "neutral"], "title": "ReactionDirectionEnum", "type": "string"}, "ReactionSideEnum": {"description": "", "enum": ["left", "right"], "title": "ReactionSideEnum", "type": "string"}, "ReactionToCatalystAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToCatalystAssociation", "type": "object"}, "ReactionToParticipantAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToParticipantAssociation", "type": "object"}, "ReagentTargetedGene": {"additionalProperties": false, "description": "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ReagentTargetedGene", "type": "object"}, "RelationshipType": {"additionalProperties": false, "description": "An OWL property used as an edge label", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "RelationshipType", "type": "object"}, "RelativeFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a relative frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RelativeFrequencyAnalysisResult", "type": "object"}, "SequenceAssociation": {"additionalProperties": false, "description": "An association between a sequence feature and a nucleic acid entity it is localized to.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceAssociation", "type": "object"}, "SequenceEnum": {"description": "type of sequence", "enum": ["na", "aa"], "title": "SequenceEnum", "type": "string"}, "SequenceFeatureRelationship": {"additionalProperties": false, "description": "For example, a particular exon is part of a particular transcript or gene", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceFeatureRelationship", "type": "object"}, "SequenceVariant": {"additionalProperties": false, "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "The state of the sequence w.r.t a reference sequence", "type": "string"}, "has_gene": {"description": "Each allele can be associated with any number of genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SequenceVariant", "type": "object"}, "Serial": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Serials (journals) should have industry-standard identifier such as from ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Serial", "type": "object"}, "SeverityValue": {"additionalProperties": false, "description": "describes the severity of a phenotypic feature or disease", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SeverityValue", "type": "object"}, "SiRNA": {"additionalProperties": false, "description": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SiRNA", "type": "object"}, "SmallMolecule": {"additionalProperties": false, "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SmallMolecule", "type": "object"}, "Snv": {"additionalProperties": false, "description": "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene": {"description": "connects an entity associated with one or more genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Snv", "type": "object"}, "SocioeconomicAttribute": {"additionalProperties": false, "description": "Attributes relating to a socioeconomic manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SocioeconomicAttribute", "type": "object"}, "SocioeconomicExposure": {"additionalProperties": false, "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category", "has_attribute"], "title": "SocioeconomicExposure", "type": "object"}, "SocioeconomicOutcome": {"additionalProperties": false, "description": "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event", "title": "SocioeconomicOutcome", "type": "object"}, "StrandEnum": {"description": "strand", "enum": ["+", "-", ".", "?"], "title": "StrandEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "a detailed investigation and/or analysis", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Study", "type": "object"}, "StudyPopulation": {"additionalProperties": false, "description": "A group of people banded together or treated as a group as participants in a research study.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyPopulation", "type": "object"}, "StudyVariable": {"additionalProperties": false, "description": "a variable that is used as a measure in the investigation of a study", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyVariable", "type": "object"}, "TaxonToTaxonAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between individuals of different taxa.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "TaxonToTaxonAssociation", "type": "object"}, "TaxonomicRank": {"additionalProperties": false, "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "TaxonomicRank", "type": "object"}, "TextMiningResult": {"additionalProperties": false, "description": "A result of text mining.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TextMiningResult", "type": "object"}, "Transcript": {"additionalProperties": false, "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Transcript", "type": "object"}, "TranscriptToGeneRelationship": {"additionalProperties": false, "description": "A gene is a collection of transcripts", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "TranscriptToGeneRelationship", "type": "object"}, "Treatment": {"additionalProperties": false, "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_device": {"description": "connects an entity to one or more (medical) devices", "items": {"type": "string"}, "type": "array"}, "has_drug": {"description": "connects an entity to one or more drugs", "items": {"type": "string"}, "type": "array"}, "has_procedure": {"description": "connects an entity to one or more (medical) procedures", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Treatment", "type": "object"}, "VariantAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A variant that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantAsAModelOfDiseaseAssociation", "type": "object"}, "VariantToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that variant", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToDiseaseAssociation", "type": "object"}, "VariantToGeneAssociation": {"additionalProperties": false, "description": "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneAssociation", "type": "object"}, "VariantToGeneExpressionAssociation": {"additionalProperties": false, "description": "An association between a variant and expression of a gene (i.e. e-QTL)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneExpressionAssociation", "type": "object"}, "VariantToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the phenotype state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPhenotypicFeatureAssociation", "type": "object"}, "VariantToPopulationAssociation": {"additionalProperties": false, "description": "An association between a variant and a population, where the variant has particular frequency in the population", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number in object population that carry a particular allele, aka allele count", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", "type": "number"}, "has_total": {"description": "number all populations that carry a particular allele, aka allele number", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that is observed to have the frequency", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "an allele that has a certain frequency in a given population", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPopulationAssociation", "type": "object"}, "Virus": {"additionalProperties": false, "description": "A virus is a microorganism that replicates itself as a microRNA and infects the host cell.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Virus", "type": "object"}, "Zygosity": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Zygosity", "type": "object"}}, "$id": "https://w3id.org/biolink/biolink-model", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, "metamodel_version": "1.7.0", "title": "Biolink-Model", "type": "object", "version": "3.1.1"} +{"$defs": {"Activity": {"additionalProperties": false, "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "person, group, organization or project that provides a piece of information (i.e. a knowledge association)", "properties": {"address": {"description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", "type": "string"}, "affiliation": {"description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Agent", "type": "object"}, "AnatomicalContextQualifierEnum": {"description": "", "enum": [], "title": "AnatomicalContextQualifierEnum", "type": "string"}, "AnatomicalEntity": {"additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "AnatomicalEntity", "type": "object"}, "AnatomicalEntityToAnatomicalEntityOntogenicAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the structure at an earlier time", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the structure at a later time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityOntogenicAssociation", "type": "object"}, "AnatomicalEntityToAnatomicalEntityPartOfAssociation": {"additionalProperties": false, "description": "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the whole", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the part", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "AnatomicalEntityToAnatomicalEntityPartOfAssociation", "type": "object"}, "Article": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category", "type"], "title": "Article", "type": "object"}, "Association": {"additionalProperties": false, "description": "A typed association between two entities, supported by evidence", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "Association", "type": "object"}, "Attribute": {"additionalProperties": false, "description": "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Attribute", "type": "object"}, "Behavior": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Behavior", "type": "object"}, "BehaviorToBehavioralFeatureAssociation": {"additionalProperties": false, "description": "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "behavioral feature that is the object of the association", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "behavior that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "BehaviorToBehavioralFeatureAssociation", "type": "object"}, "BehavioralExposure": {"additionalProperties": false, "description": "A behavioral exposure is a factor relating to behavior impacting an individual.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BehavioralExposure", "type": "object"}, "BehavioralFeature": {"additionalProperties": false, "description": "A phenotypic feature which is behavioral in nature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BehavioralFeature", "type": "object"}, "BehavioralOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of human behavior.", "title": "BehavioralOutcome", "type": "object"}, "BiologicalProcess": {"additionalProperties": false, "description": "One or more causally connected executions of molecular functions", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcess", "type": "object"}, "BiologicalProcessOrActivity": {"additionalProperties": false, "description": "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "BiologicalProcessOrActivity", "type": "object"}, "BiologicalSex": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BiologicalSex", "type": "object"}, "BioticExposure": {"additionalProperties": false, "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "BioticExposure", "type": "object"}, "Book": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Books should have industry-standard identifier such as from ISBN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'book'.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Book", "type": "object"}, "BookChapter": {"additionalProperties": false, "description": "", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "chapter": {"description": "chapter of a book", "type": "string"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "published_in": {"description": "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.", "type": "string"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["published_in", "id", "category", "type"], "title": "BookChapter", "type": "object"}, "Case": {"additionalProperties": false, "description": "An individual (human) organism that has a patient role in some clinical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Case", "type": "object"}, "CaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CaseToPhenotypicFeatureAssociation", "type": "object"}, "CausalMechanismQualifierEnum": {"description": "", "enum": ["binding", "inhibition", "antibody_inhibition", "antagonism", "molecular_channel_blockage", "inverse_agonism", "negative_allosteric_modulation", "agonism", "molecular_channel_opening", "positive_allosteric_modulation", "potentiation", "activation", "inducer", "transcriptional_regulation", "signaling_mediated_control", "stabilization", "stimulation", "releasing_activity"], "title": "CausalMechanismQualifierEnum", "type": "string"}, "Cell": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cell", "type": "object"}, "CellLine": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellLine", "type": "object"}, "CellLineAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineAsAModelOfDiseaseAssociation", "type": "object"}, "CellLineToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "CellularComponent": {"additionalProperties": false, "description": "A location in or around a cell", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularComponent", "type": "object"}, "CellularOrganism": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CellularOrganism", "type": "object"}, "ChemicalAffectsGeneAssociation": {"additionalProperties": false, "description": "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"$ref": "#/$defs/CausalMechanismQualifierEnum", "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_aspect_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalAffectsGeneAssociation", "type": "object"}, "ChemicalEntity": {"additionalProperties": false, "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalEntity", "type": "object"}, "ChemicalEntityAssessesNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityAssessesNamedThingAssociation", "type": "object"}, "ChemicalEntityDerivativeEnum": {"description": "", "enum": ["metabolite"], "title": "ChemicalEntityDerivativeEnum", "type": "string"}, "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": {"additionalProperties": false, "description": "A regulatory relationship between two genes", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the direction is always from regulator to regulated", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", "type": "object"}, "ChemicalExposure": {"additionalProperties": false, "description": "A chemical exposure is an intake of a particular chemical entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalExposure", "type": "object"}, "ChemicalGeneInteractionAssociation": {"additionalProperties": false, "description": "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "anatomical_context_qualifier": {"description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "object_context_qualifier": {"type": "string"}, "object_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "object_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"$ref": "#/$defs/ChemicalEntityDerivativeEnum"}, "subject_form_or_variant_qualifier": {"$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum"}, "subject_part_qualifier": {"$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalGeneInteractionAssociation", "type": "object"}, "ChemicalMixture": {"additionalProperties": false, "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChemicalMixture", "type": "object"}, "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", "properties": {"FDA_adverse_event_level": {"$ref": "#/$defs/FDAIDAAdverseEventEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalOrGeneOrGeneProductFormOrVariantEnum": {"description": "", "enum": ["genetic_variant_form", "modified_form", "loss_of_function_variant_form", "gain_of_function_variant_form", "polymorphic_form", "snp_form", "analog_form"], "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", "type": "string"}, "ChemicalRole": {"additionalProperties": false, "description": "A role played by the molecular entity or part thereof within a chemical context.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ChemicalRole", "type": "object"}, "ChemicalToChemicalAssociation": {"additionalProperties": false, "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the chemical element that is the target of the statement", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalAssociation", "type": "object"}, "ChemicalToChemicalDerivationAssociation": {"additionalProperties": false, "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "catalyst_qualifier": {"description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the downstream chemical entity", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the upstream chemical entity", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToChemicalDerivationAssociation", "type": "object"}, "ChemicalToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the disease or phenotype that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "ChemicalToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a chemical entity and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that is affected by the chemical", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the chemical entity that is affecting the pathway", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ChemicalToPathwayAssociation", "type": "object"}, "ChiSquaredAnalysisResult": {"additionalProperties": false, "description": "A result of a chi squared analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ChiSquaredAnalysisResult", "type": "object"}, "ClinicalAttribute": {"additionalProperties": false, "description": "Attributes relating to a clinical manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalAttribute", "type": "object"}, "ClinicalCourse": {"additionalProperties": false, "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalCourse", "type": "object"}, "ClinicalEntity": {"additionalProperties": false, "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalEntity", "type": "object"}, "ClinicalFinding": {"additionalProperties": false, "description": "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalFinding", "type": "object"}, "ClinicalIntervention": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalIntervention", "type": "object"}, "ClinicalMeasurement": {"additionalProperties": false, "description": "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalMeasurement", "type": "object"}, "ClinicalModifier": {"additionalProperties": false, "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ClinicalModifier", "type": "object"}, "ClinicalTrial": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ClinicalTrial", "type": "object"}, "CodingSequence": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CodingSequence", "type": "object"}, "Cohort": {"additionalProperties": false, "description": "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Cohort", "type": "object"}, "CommonDataElement": {"additionalProperties": false, "description": "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "CommonDataElement", "type": "object"}, "ComplexChemicalExposure": {"additionalProperties": false, "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "ComplexChemicalExposure", "type": "object"}, "ComplexMolecularMixture": {"additionalProperties": false, "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ComplexMolecularMixture", "type": "object"}, "ConceptCountAnalysisResult": {"additionalProperties": false, "description": "A result of a concept count analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConceptCountAnalysisResult", "type": "object"}, "ConfidenceLevel": {"additionalProperties": false, "description": "Level of confidence in a statement", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ConfidenceLevel", "type": "object"}, "ContributorAssociation": {"additionalProperties": false, "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "agent helping to realise the given entity (e.g. such as a publication)", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "information content entity which an agent has helped realise", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ContributorAssociation", "type": "object"}, "Dataset": {"additionalProperties": false, "description": "an item that refers to a collection of data from a data source.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Dataset", "type": "object"}, "DatasetDistribution": {"additionalProperties": false, "description": "an item that holds distribution level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "distribution_download_url": {"type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetDistribution", "type": "object"}, "DatasetSummary": {"additionalProperties": false, "description": "an item that holds summary level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "source_logo": {"type": "string"}, "source_web_page": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetSummary", "type": "object"}, "DatasetVersion": {"additionalProperties": false, "description": "an item that holds version level information about a dataset.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_dataset": {"type": "string"}, "has_distribution": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "ingest_date": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DatasetVersion", "type": "object"}, "Device": {"additionalProperties": false, "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Device", "type": "object"}, "DirectionQualifierEnum": {"description": "", "enum": ["increased", "upregulated", "decreased", "downregulated"], "title": "DirectionQualifierEnum", "type": "string"}, "Disease": {"additionalProperties": false, "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Disease", "type": "object"}, "DiseaseOrPhenotypicFeature": {"additionalProperties": false, "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "DiseaseOrPhenotypicFeature", "type": "object"}, "DiseaseOrPhenotypicFeatureExposure": {"additionalProperties": false, "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DiseaseOrPhenotypicFeatureExposure", "type": "object"}, "DiseaseOrPhenotypicFeatureOutcome": {"additionalProperties": false, "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", "title": "DiseaseOrPhenotypicFeatureOutcome", "type": "object"}, "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "genetic inheritance associated with the specified disease or phenotypic feature.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "type": "object"}, "DiseaseOrPhenotypicFeatureToLocationAssociation": {"additionalProperties": false, "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "anatomical entity in which the disease or feature is found.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", "type": "object"}, "DiseaseToExposureEventAssociation": {"additionalProperties": false, "description": "An association between an exposure event and a disease.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToExposureEventAssociation", "type": "object"}, "DiseaseToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DiseaseToPhenotypicFeatureAssociation", "type": "object"}, "Drug": {"additionalProperties": false, "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Drug", "type": "object"}, "DrugAvailabilityEnum": {"description": "", "enum": ["over_the_counter", "prescription"], "title": "DrugAvailabilityEnum", "type": "string"}, "DrugDeliveryEnum": {"description": "", "enum": ["inhalation", "oral", "absorption_through_the_skin", "intravenous_injection"], "title": "DrugDeliveryEnum", "type": "string"}, "DrugExposure": {"additionalProperties": false, "description": "A drug exposure is an intake of a particular drug.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugExposure", "type": "object"}, "DrugToGeneAssociation": {"additionalProperties": false, "description": "An interaction between a drug and a gene or gene product.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product that is affected by the drug"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DrugToGeneAssociation", "type": "object"}, "DrugToGeneInteractionExposure": {"additionalProperties": false, "description": "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "DrugToGeneInteractionExposure", "type": "object"}, "DruggableGeneCategoryEnum": {"description": "", "enum": ["tclin", "tbio", "tchem", "tdark"], "title": "DruggableGeneCategoryEnum", "type": "string"}, "DruggableGeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"$ref": "#/$defs/DruggableGeneCategoryEnum"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "DruggableGeneToDiseaseAssociation", "type": "object"}, "EntityToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToDiseaseAssociation", "type": "object"}, "EntityToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"FDA_approval_status": {"$ref": "#/$defs/FDAApprovalStatusEnum"}, "aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "EntityToPhenotypicFeatureAssociation", "type": "object"}, "EnvironmentalExposure": {"additionalProperties": false, "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "EnvironmentalExposure", "type": "object"}, "EnvironmentalFeature": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFeature", "type": "object"}, "EnvironmentalFoodContaminant": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalFoodContaminant", "type": "object"}, "EnvironmentalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EnvironmentalProcess", "type": "object"}, "EpidemiologicalOutcome": {"additionalProperties": false, "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", "title": "EpidemiologicalOutcome", "type": "object"}, "Event": {"additionalProperties": false, "description": "Something that happens at a given place and time.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Event", "type": "object"}, "EvidenceType": {"additionalProperties": false, "description": "Class of evidence that supports an association", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "EvidenceType", "type": "object"}, "Exon": {"additionalProperties": false, "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Exon", "type": "object"}, "ExonToTranscriptRelationship": {"additionalProperties": false, "description": "A transcript is formed from multiple exons", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExonToTranscriptRelationship", "type": "object"}, "ExposureEventToOutcomeAssociation": {"additionalProperties": false, "description": "An association between an exposure event and an outcome.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/Outcome", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "population_context_qualifier": {"description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "temporal_context_qualifier": {"description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToOutcomeAssociation", "type": "object"}, "ExposureEventToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ExposureEventToPhenotypicFeatureAssociation", "type": "object"}, "FDAApprovalStatusEnum": {"description": "", "enum": ["discovery_and_development_phase", "preclinical_research_phase", "fda_clinical_research_phase", "fda_review_phase_4", "fda_post_market_safety_review", "fda_clinical_research_phase_1", "fda_clinical_research_phase_2", "fda_clinical_research_phase_3", "fda_clinical_research_phase_4", "fda_fast_track", "fda_breakthrough_therapy", "fda_accelerated_approval", "fda_priority_review", "regular_fda_approval", "post_approval_withdrawal"], "title": "FDAApprovalStatusEnum", "type": "string"}, "FDAIDAAdverseEventEnum": {"description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", "enum": ["life_threatening_adverse_event", "serious_adverse_event", "suspected_adverse_reaction", "unexpected_adverse_event"], "title": "FDAIDAAdverseEventEnum", "type": "string"}, "Food": {"additionalProperties": false, "description": "A substance consumed by a living organism as a source of nutrition", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Food", "type": "object"}, "FoodAdditive": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "FoodAdditive", "type": "object"}, "FunctionalAssociation": {"additionalProperties": false, "description": "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "gene, product or macromolecular complex that has the function associated with the GO term"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "FunctionalAssociation", "type": "object"}, "Gene": {"additionalProperties": false, "description": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "symbol": {"description": "Symbol for a particular thing", "type": "string"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Gene", "type": "object"}, "GeneAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneAsAModelOfDiseaseAssociation", "type": "object"}, "GeneFamily": {"additionalProperties": false, "description": "any grouping of multiple genes or gene products related by common descent", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneFamily", "type": "object"}, "GeneHasVariantThatContributesToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease."}, "subject_form_or_variant_qualifier": {"type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneHasVariantThatContributesToDiseaseAssociation", "type": "object"}, "GeneOrGeneProductOrChemicalEntityAspectEnum": {"description": "", "enum": ["activity_or_abundance", "abundance", "activity", "expression", "synthesis", "degradation", "cleavage", "hydrolysis", "metabolic_processing", "mutation_rate", "stability", "folding", "localization", "transport", "secretion", "uptake", "molecular_modification", "acetylation", "acylation", "alkylation", "amination", "carbamoylation", "ethylation", "glutathionylation", "glycation", "glycosylation", "glucuronidation", "n_linked_glycosylation", "o_linked_glycosylation", "hydroxylation", "lipidation", "farnesylation", "geranoylation", "myristoylation", "palmitoylation", "prenylation", "methylation", "nitrosation", "nucleotidylation", "phosphorylation", "ribosylation", "ADP-ribosylation", "sulfation", "sumoylation", "ubiquitination", "oxidation", "reduction", "carboxylation"], "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", "type": "string"}, "GeneOrGeneProductOrChemicalPartQualifierEnum": {"description": "", "enum": ["3_prime_utr", "5_prime_utr", "polya_tail", "promoter", "enhancer", "exon", "intron"], "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", "type": "string"}, "GeneToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToDiseaseAssociation", "type": "object"}, "GeneToExpressionSiteAssociation": {"additionalProperties": false, "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "location in which the gene is expressed", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "expression relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "can be used to indicate magnitude, or also ranking", "type": "string"}, "stage_qualifier": {"description": "stage at which the gene is expressed in the site", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToExpressionSiteAssociation", "type": "object"}, "GeneToGeneCoexpressionAssociation": {"additionalProperties": false, "description": "Indicates that two genes are co-expressed, generally under the same conditions.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneCoexpressionAssociation", "type": "object"}, "GeneToGeneFamilyAssociation": {"additionalProperties": false, "description": "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "membership of the gene in the given gene family.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneFamilyAssociation", "type": "object"}, "GeneToGeneHomologyAssociation": {"additionalProperties": false, "description": "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "homology relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneHomologyAssociation", "type": "object"}, "GeneToGeneProductRelationship": {"additionalProperties": false, "description": "A gene is transcribed and potentially translated to a gene product", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneProductMixin", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGeneProductRelationship", "type": "object"}, "GeneToGoTermAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "class describing the activity, process or localization of the gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "gene, product or macromolecular complex that has the function associated with the GO term", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToGoTermAssociation", "type": "object"}, "GeneToPathwayAssociation": {"additionalProperties": false, "description": "An interaction between a gene or gene product and a biological process or pathway.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the pathway that includes or is affected by the gene or gene product", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "the gene or gene product entity that participates or influences the pathway"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPathwayAssociation", "type": "object"}, "GeneToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the phenotypic feature"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GeneToPhenotypicFeatureAssociation", "type": "object"}, "GeneticInheritance": {"additionalProperties": false, "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeneticInheritance", "type": "object"}, "Genome": {"additionalProperties": false, "description": "A genome is the sum of genetic material within a cell or virion.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genome", "type": "object"}, "GenomicBackgroundExposure": {"additionalProperties": false, "description": "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "has_attribute_type", "category"], "title": "GenomicBackgroundExposure", "type": "object"}, "GenomicSequenceLocalization": {"additionalProperties": false, "description": "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "end_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", "type": "integer"}, "genome_build": {"$ref": "#/$defs/StrandEnum", "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens."}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phase": {"$ref": "#/$defs/PhaseEnum", "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2."}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "start_interbase_coordinate": {"description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", "type": "integer"}, "strand": {"$ref": "#/$defs/StrandEnum", "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)."}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenomicSequenceLocalization", "type": "object"}, "Genotype": {"additionalProperties": false, "description": "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_zygosity": {"type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Genotype", "type": "object"}, "GenotypeAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A genotype that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeAsAModelOfDiseaseAssociation", "type": "object"}, "GenotypeToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that genotype", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a genotype that is associated in some way with a disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToDiseaseAssociation", "type": "object"}, "GenotypeToGeneAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGeneAssociation", "type": "object"}, "GenotypeToGenotypePartAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "child genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToGenotypePartAssociation", "type": "object"}, "GenotypeToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "genotype that is associated with the phenotypic feature", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToPhenotypicFeatureAssociation", "type": "object"}, "GenotypeToVariantAssociation": {"additionalProperties": false, "description": "Any association between a genotype and a sequence variant.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "gene implicated in genotype", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "the relationship type used to connect genotype to gene", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "parent genotype", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "GenotypeToVariantAssociation", "type": "object"}, "GenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GenotypicSex", "type": "object"}, "GeographicExposure": {"additionalProperties": false, "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "GeographicExposure", "type": "object"}, "GeographicLocation": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocation", "type": "object"}, "GeographicLocationAtTime": {"additionalProperties": false, "description": "a location that can be described in lat/long coordinates, for a particular time", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GeographicLocationAtTime", "type": "object"}, "GrossAnatomicalStructure": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "GrossAnatomicalStructure", "type": "object"}, "Haplotype": {"additionalProperties": false, "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Haplotype", "type": "object"}, "Hospitalization": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Hospitalization", "type": "object"}, "HospitalizationOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", "title": "HospitalizationOutcome", "type": "object"}, "IndividualOrganism": {"additionalProperties": false, "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "IndividualOrganism", "type": "object"}, "InformationContentEntityToNamedThingAssociation": {"additionalProperties": false, "description": "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "InformationContentEntityToNamedThingAssociation", "type": "object"}, "InformationResource": {"additionalProperties": false, "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "InformationResource", "type": "object"}, "LifeStage": {"additionalProperties": false, "description": "A stage of development or growth of an organism, including post-natal adult stages", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "LifeStage", "type": "object"}, "LogicalInterpretationEnum": {"description": "", "enum": ["some_some", "all_some", "inverse_all_some"], "title": "LogicalInterpretationEnum", "type": "string"}, "MacromolecularComplex": {"additionalProperties": false, "description": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MacromolecularComplex", "type": "object"}, "MacromolecularMachineToBiologicalProcessAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToBiologicalProcessAssociation", "type": "object"}, "MacromolecularMachineToCellularComponentAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToCellularComponentAssociation", "type": "object"}, "MacromolecularMachineToMolecularActivityAssociation": {"additionalProperties": false, "description": "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/MacromolecularMachineMixin", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MacromolecularMachineToMolecularActivityAssociation", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MaterialSample", "type": "object"}, "MaterialSampleDerivationAssociation": {"additionalProperties": false, "description": "An association between a material sample and the material entity from which it is derived.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "derivation relationship", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the material sample being described", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleDerivationAssociation", "type": "object"}, "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "An association between a material sample and a disease or phenotype.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation", "type": "object"}, "MicroRNA": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MicroRNA", "type": "object"}, "MolecularActivity": {"additionalProperties": false, "description": "An execution of a molecular function carried out by a gene product or macromolecular complex.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "The gene product, gene, or complex that catalyzes the reaction", "items": {"$ref": "#/$defs/MacromolecularMachineMixin"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "A chemical entity that is the input for the reaction", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "A chemical entity that is the output for the reaction", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularActivity", "type": "object"}, "MolecularActivityToChemicalEntityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToChemicalEntityAssociation", "type": "object"}, "MolecularActivityToMolecularActivityAssociation": {"additionalProperties": false, "description": "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToMolecularActivityAssociation", "type": "object"}, "MolecularActivityToPathwayAssociation": {"additionalProperties": false, "description": "Association that holds the relationship between a reaction and the pathway it participates in.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "MolecularActivityToPathwayAssociation", "type": "object"}, "MolecularEntity": {"additionalProperties": false, "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularEntity", "type": "object"}, "MolecularMixture": {"additionalProperties": false, "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "MolecularMixture", "type": "object"}, "MortalityOutcome": {"additionalProperties": false, "description": "An outcome of death from resulting from an exposure event.", "title": "MortalityOutcome", "type": "object"}, "NamedThing": {"additionalProperties": false, "description": "a databased entity or concept/class", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NamedThing", "type": "object"}, "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", "type": "object"}, "NoncodingRNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NoncodingRNAProduct", "type": "object"}, "NucleicAcidEntity": {"additionalProperties": false, "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidEntity", "type": "object"}, "NucleicAcidSequenceMotif": {"additionalProperties": false, "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleicAcidSequenceMotif", "type": "object"}, "NucleosomeModification": {"additionalProperties": false, "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "NucleosomeModification", "type": "object"}, "ObservedExpectedFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a observed expected frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ObservedExpectedFrequencyAnalysisResult", "type": "object"}, "Onset": {"additionalProperties": false, "description": "The age group in which (disease) symptom manifestations appear", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Onset", "type": "object"}, "OrganismAttribute": {"additionalProperties": false, "description": "describes a characteristic of an organismal entity.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "OrganismAttribute", "type": "object"}, "OrganismTaxon": {"additionalProperties": false, "description": "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "OrganismTaxon", "type": "object"}, "OrganismTaxonToOrganismTaxonInteraction": {"additionalProperties": false, "description": "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "associated_environmental_context": {"description": "the environment in which the two taxa interact", "type": "string"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the taxon that is the subject of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the taxon that is the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonInteraction", "type": "object"}, "OrganismTaxonToOrganismTaxonSpecialization": {"additionalProperties": false, "description": "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the more general taxon", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the more specific taxon", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismTaxonToOrganismTaxonSpecialization", "type": "object"}, "OrganismToOrganismAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between two individual organisms.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismToOrganismAssociation", "type": "object"}, "OrganismalEntityAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "OrganismalEntityAsAModelOfDiseaseAssociation", "type": "object"}, "PairwiseGeneToGeneInteraction": {"additionalProperties": false, "description": "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseGeneToGeneInteraction", "type": "object"}, "PairwiseMolecularInteraction": {"additionalProperties": false, "description": "An interaction at the molecular level between two physical entities", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string"}, "interacting_molecules_category": {"type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "interaction relationship type", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PairwiseMolecularInteraction", "type": "object"}, "PathologicalAnatomicalExposure": {"additionalProperties": false, "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalAnatomicalExposure", "type": "object"}, "PathologicalAnatomicalOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.", "title": "PathologicalAnatomicalOutcome", "type": "object"}, "PathologicalAnatomicalStructure": {"additionalProperties": false, "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalAnatomicalStructure", "type": "object"}, "PathologicalProcess": {"additionalProperties": false, "description": "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PathologicalProcess", "type": "object"}, "PathologicalProcessExposure": {"additionalProperties": false, "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PathologicalProcessExposure", "type": "object"}, "PathologicalProcessOutcome": {"additionalProperties": false, "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process.", "title": "PathologicalProcessOutcome", "type": "object"}, "Pathway": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Pathway", "type": "object"}, "PhaseEnum": {"description": "phase", "enum": ["0", "1", "2"], "title": "PhaseEnum", "type": "string"}, "Phenomenon": {"additionalProperties": false, "description": "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Phenomenon", "type": "object"}, "PhenotypicFeature": {"additionalProperties": false, "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhenotypicFeature", "type": "object"}, "PhenotypicQuality": {"additionalProperties": false, "description": "A property of a phenotype", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicQuality", "type": "object"}, "PhenotypicSex": {"additionalProperties": false, "description": "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "PhenotypicSex", "type": "object"}, "PhysicalEntity": {"additionalProperties": false, "description": "An entity that has material reality (a.k.a. physical essence).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysicalEntity", "type": "object"}, "PhysiologicalProcess": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "enabled_by": {"description": "holds between a process and a physical entity, where the physical entity executes the process", "items": {"type": "string"}, "type": "array"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_input": {"description": "holds between a process and a continuant, where the continuant is an input into the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "has_output": {"description": "holds between a process and a continuant, where the continuant is an output of the process", "items": {"$ref": "#/$defs/Occurrent"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PhysiologicalProcess", "type": "object"}, "PlanetaryEntity": {"additionalProperties": false, "description": "Any entity or process that exists at the level of the whole planet", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PlanetaryEntity", "type": "object"}, "Polypeptide": {"additionalProperties": false, "description": "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Polypeptide", "type": "object"}, "PopulationOfIndividualOrganisms": {"additionalProperties": false, "description": "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PopulationOfIndividualOrganisms", "type": "object"}, "PopulationToPopulationAssociation": {"additionalProperties": false, "description": "An association between a two populations", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that form the object of the association", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "the population that form the subject of the association", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "PopulationToPopulationAssociation", "type": "object"}, "PosttranslationalModification": {"additionalProperties": false, "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "PosttranslationalModification", "type": "object"}, "PredicateMapping": {"additionalProperties": false, "description": "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.", "properties": {"anatomical_context_qualifier": {"$ref": "#/$defs/AnatomicalContextQualifierEnum", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)."}, "broad_match": {"description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "causal_mechanism_qualifier": {"description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", "type": "string"}, "exact_match": {"description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", "items": {"type": "string"}, "type": "array"}, "mapped_predicate": {"description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", "type": "string"}, "narrow_match": {"description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": {"type": "string"}, "type": "array"}, "object_aspect_qualifier": {"type": "string"}, "object_context_qualifier": {"type": "string"}, "object_derivative_qualifier": {"type": "string"}, "object_direction_qualifier": {"$ref": "#/$defs/DirectionQualifierEnum"}, "object_form_or_variant_qualifier": {"type": "string"}, "object_part_qualifier": {"type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "qualified_predicate": {"description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", "type": "string"}, "species_context_qualifier": {"description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", "type": "string"}, "subject_aspect_qualifier": {"type": "string"}, "subject_context_qualifier": {"type": "string"}, "subject_derivative_qualifier": {"type": "string"}, "subject_direction_qualifier": {"type": "string"}, "subject_form_or_variant_qualifier": {"type": "string"}, "subject_part_qualifier": {"type": "string"}}, "required": ["predicate"], "title": "PredicateMapping", "type": "object"}, "Procedure": {"additionalProperties": false, "description": "A series of actions conducted in a certain order or manner", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Procedure", "type": "object"}, "ProcessedMaterial": {"additionalProperties": false, "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "drug_regulatory_status_world_wide": {"description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "highest_FDA_approval_status": {"description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_supplement": {"type": "string"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "routes_of_delivery": {"description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": {"$ref": "#/$defs/DrugDeliveryEnum"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProcessedMaterial", "type": "object"}, "Protein": {"additionalProperties": false, "description": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Protein", "type": "object"}, "ProteinDomain": {"additionalProperties": false, "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinDomain", "type": "object"}, "ProteinFamily": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_gene_or_gene_product": {"description": "connects an entity with one or more gene or gene products", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinFamily", "type": "object"}, "ProteinIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ProteinIsoform", "type": "object"}, "Publication": {"additionalProperties": false, "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", "type": "string"}, "pages": {"description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Publication", "type": "object"}, "QuantityValue": {"additionalProperties": false, "description": "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value", "properties": {"has_numeric_value": {"description": "connects a quantity value to a number", "type": "number"}, "has_unit": {"description": "connects a quantity value to a unit", "type": "string"}}, "title": "QuantityValue", "type": "object"}, "RNAProduct": {"additionalProperties": false, "description": "", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProduct", "type": "object"}, "RNAProductIsoform": {"additionalProperties": false, "description": "Represents a protein that is a specific isoform of the canonical or reference RNA", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RNAProductIsoform", "type": "object"}, "ReactionDirectionEnum": {"description": "", "enum": ["left_to_right", "right_to_left", "bidirectional", "neutral"], "title": "ReactionDirectionEnum", "type": "string"}, "ReactionSideEnum": {"description": "", "enum": ["left", "right"], "title": "ReactionSideEnum", "type": "string"}, "ReactionToCatalystAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object."}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToCatalystAssociation", "type": "object"}, "ReactionToParticipantAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "reaction_direction": {"$ref": "#/$defs/ReactionDirectionEnum", "description": "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)"}, "reaction_side": {"$ref": "#/$defs/ReactionSideEnum", "description": "the side of a reaction being modeled (ie: left or right)"}, "stoichiometry": {"description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", "type": "integer"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "ReactionToParticipantAssociation", "type": "object"}, "ReagentTargetedGene": {"additionalProperties": false, "description": "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "ReagentTargetedGene", "type": "object"}, "RelationshipType": {"additionalProperties": false, "description": "An OWL property used as an edge label", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "RelationshipType", "type": "object"}, "RelativeFrequencyAnalysisResult": {"additionalProperties": false, "description": "A result of a relative frequency analysis.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "RelativeFrequencyAnalysisResult", "type": "object"}, "SequenceAssociation": {"additionalProperties": false, "description": "An association between a sequence feature and a nucleic acid entity it is localized to.", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceAssociation", "type": "object"}, "SequenceEnum": {"description": "type of sequence", "enum": ["na", "aa"], "title": "SequenceEnum", "type": "string"}, "SequenceFeatureRelationship": {"additionalProperties": false, "description": "For example, a particular exon is part of a particular transcript or gene", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "SequenceFeatureRelationship", "type": "object"}, "SequenceVariant": {"additionalProperties": false, "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "The state of the sequence w.r.t a reference sequence", "type": "string"}, "has_gene": {"description": "Each allele can be associated with any number of genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SequenceVariant", "type": "object"}, "Serial": {"additionalProperties": false, "description": "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.", "properties": {"authors": {"description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "Serials (journals) should have industry-standard identifier such as from ISSN.", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "iso_abbreviation": {"description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", "type": "string"}, "issue": {"description": "issue of a newspaper, a scientific journal or magazine for reference purpose", "type": "string"}, "keywords": {"description": "keywords tagging a publication", "items": {"type": "string"}, "type": "array"}, "license": {"type": "string"}, "mesh_terms": {"description": "mesh terms tagging a publication", "items": {"type": "string"}, "type": "array"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "pages": {"description": "page number of source referenced for statement or publication", "items": {"type": "string"}, "type": "array"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "summary": {"description": "executive summary of a publication", "type": "string"}, "type": {"description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "type": "string"}, "volume": {"description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", "type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category", "type"], "title": "Serial", "type": "object"}, "SeverityValue": {"additionalProperties": false, "description": "describes the severity of a phenotypic feature or disease", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SeverityValue", "type": "object"}, "SiRNA": {"additionalProperties": false, "description": "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "synonym": {"description": "Alternate human-readable names for a thing", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SiRNA", "type": "object"}, "SmallMolecule": {"additionalProperties": false, "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "SmallMolecule", "type": "object"}, "Snv": {"additionalProperties": false, "description": "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_gene": {"description": "connects an entity associated with one or more genes", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Snv", "type": "object"}, "SocioeconomicAttribute": {"additionalProperties": false, "description": "Attributes relating to a socioeconomic manifestation", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "SocioeconomicAttribute", "type": "object"}, "SocioeconomicExposure": {"additionalProperties": false, "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category", "has_attribute"], "title": "SocioeconomicExposure", "type": "object"}, "SocioeconomicOutcome": {"additionalProperties": false, "description": "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event", "title": "SocioeconomicOutcome", "type": "object"}, "StrandEnum": {"description": "strand", "enum": ["+", "-", ".", "?"], "title": "StrandEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "a detailed investigation and/or analysis", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Study", "type": "object"}, "StudyPopulation": {"additionalProperties": false, "description": "A group of people banded together or treated as a group as participants in a research study.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyPopulation", "type": "object"}, "StudyVariable": {"additionalProperties": false, "description": "a variable that is used as a measure in the investigation of a study", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "StudyVariable", "type": "object"}, "TaxonToTaxonAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "An association between individuals of different taxa.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "TaxonToTaxonAssociation", "type": "object"}, "TaxonomicRank": {"additionalProperties": false, "description": "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)", "properties": {"id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}}, "required": ["id"], "title": "TaxonomicRank", "type": "object"}, "TextMiningResult": {"additionalProperties": false, "description": "A result of text mining.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "creation_date": {"description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", "type": "string"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "format": {"type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "license": {"type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "rights": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "TextMiningResult", "type": "object"}, "Transcript": {"additionalProperties": false, "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "properties": {"available_from": {"items": {"$ref": "#/$defs/DrugAvailabilityEnum"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_biological_sequence": {"description": "connects a genomic feature to its sequence", "type": "string"}, "has_chemical_role": {"description": "A role is particular behaviour which a chemical entity may exhibit.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "is_metabolite": {"description": "indicates whether a molecular entity is a metabolite", "type": "boolean"}, "is_toxic": {"type": "boolean"}, "max_tolerated_dose": {"description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "trade_name": {"type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Transcript", "type": "object"}, "TranscriptToGeneRelationship": {"additionalProperties": false, "description": "A gene is a collection of transcripts", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "TranscriptToGeneRelationship", "type": "object"}, "Treatment": {"additionalProperties": false, "description": "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_device": {"description": "connects an entity to one or more (medical) devices", "items": {"type": "string"}, "type": "array"}, "has_drug": {"description": "connects an entity to one or more drugs", "items": {"type": "string"}, "type": "array"}, "has_procedure": {"description": "connects an entity to one or more (medical) procedures", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Treatment", "type": "object"}, "VariantAsAModelOfDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "A variant that has a role in modeling the disease.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantAsAModelOfDiseaseAssociation", "type": "object"}, "VariantToDiseaseAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "a disease that is associated with that variant", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "E.g. is pathogenic for", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the disease state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToDiseaseAssociation", "type": "object"}, "VariantToGeneAssociation": {"additionalProperties": false, "description": "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneAssociation", "type": "object"}, "VariantToGeneExpressionAssociation": {"additionalProperties": false, "description": "An association between a variant and expression of a gene (i.e. e-QTL)", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "expression_site": {"description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "phenotypic_state": {"description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "quantifier_qualifier": {"description": "A measurable quantity for the object of the association", "type": "string"}, "stage_qualifier": {"description": "stage during which gene or protein expression of takes place.", "type": "string"}, "subject": {"description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToGeneExpressionAssociation", "type": "object"}, "VariantToPhenotypicFeatureAssociation": {"additionalProperties": false, "description": "", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number of things with a particular property", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"type": "number"}, "has_total": {"description": "total number of things in a particular reference set", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string"}, "onset_qualifier": {"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "severity_qualifier": {"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string"}, "sex_qualifier": {"description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string"}, "subject": {"description": "a sequence variant in which the allele state is associated in some way with the phenotype state", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPhenotypicFeatureAssociation", "type": "object"}, "VariantToPopulationAssociation": {"additionalProperties": false, "description": "An association between a variant and a population, where the variant has particular frequency in the population", "properties": {"aggregator_knowledge_source": {"description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": {"type": "string"}, "type": "array"}, "category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "frequency_qualifier": {"description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_count": {"description": "number in object population that carry a particular allele, aka allele count", "type": "integer"}, "has_evidence": {"description": "connects an association to an instance of supporting evidence", "items": {"type": "string"}, "type": "array"}, "has_percentage": {"description": "equivalent to has quotient multiplied by 100", "type": "number"}, "has_quotient": {"description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", "type": "number"}, "has_total": {"description": "number all populations that carry a particular allele, aka allele number", "type": "integer"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "knowledge_source": {"description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "negated": {"description": "if set to true, then the association is negated i.e. is not true", "type": "boolean"}, "object": {"description": "the population that is observed to have the frequency", "type": "string"}, "original_object": {"description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_predicate": {"description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "original_subject": {"description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string"}, "predicate": {"description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string"}, "primary_knowledge_source": {"description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to caputre non-primary sources.", "type": "string"}, "publications": {"description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": {"type": "string"}, "type": "array"}, "qualifiers": {"description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": {"type": "string"}, "type": "array"}, "subject": {"description": "an allele that has a certain frequency in a given population", "type": "string"}, "timepoint": {"description": "a point in time", "format": "time", "type": "string"}, "type": {"type": "string"}}, "required": ["subject", "predicate", "object", "id"], "title": "VariantToPopulationAssociation", "type": "object"}, "Virus": {"additionalProperties": false, "description": "A virus is a microorganism that replicates itself as a microRNA and infects the host cell.", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "in_taxon": {"description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": {"type": "string"}, "type": "array"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["id", "category"], "title": "Virus", "type": "object"}, "Zygosity": {"additionalProperties": false, "description": "", "properties": {"category": {"description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": {"type": "string"}, "pattern": "^biolink:\\d+$", "type": "array"}, "description": {"description": "a human-readable description of an entity", "type": "string"}, "has_attribute": {"description": "connects any entity to an attribute", "items": {"type": "string"}, "type": "array"}, "has_attribute_type": {"description": "connects an attribute to a class that describes it", "type": "string"}, "has_qualitative_value": {"description": "connects an attribute to a value", "type": "string"}, "has_quantitative_value": {"description": "connects an attribute to a value", "items": {"$ref": "#/$defs/QuantityValue"}, "type": "array"}, "id": {"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "iri": {"description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string"}, "name": {"description": "A human-readable name for an attribute or entity.", "type": "string"}, "provided_by": {"description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": {"type": "string"}, "type": "array"}, "type": {"type": "string"}, "xref": {"description": "Alternate CURIEs for a thing", "items": {"type": "string"}, "type": "array"}}, "required": ["has_attribute_type", "id", "category"], "title": "Zygosity", "type": "object"}}, "$id": "https://w3id.org/biolink/biolink-model", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, "metamodel_version": "1.7.0", "title": "Biolink-Model", "type": "object", "version": "3.1.2"}