From fb461993789bb11e4daa23d1cd874f4d04ad73d7 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 29 Aug 2022 18:20:54 -0700 Subject: [PATCH] remake pydantic --- biolink/pydanticmodel.py | 750 ++++++++++++++++++++++++++++++++------- 1 file changed, 625 insertions(+), 125 deletions(-) diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py index 8941ae38f9..b665f4dfb6 100644 --- a/biolink/pydanticmodel.py +++ b/biolink/pydanticmodel.py @@ -5,7 +5,7 @@ from pydantic import BaseModel as BaseModel, Field metamodel_version = "None" -version = "2.4.5" +version = "3.0.1" class WeakRefShimBaseModel(BaseModel): __slots__ = '__weakref__' @@ -19,6 +19,120 @@ class ConfiguredBaseModel(WeakRefShimBaseModel, pass +class AnatomicalContextQualifierEnum(str, Enum): + + + dummy = "dummy" + + +class DirectionQualifierEnum(str, Enum): + + increased = "increased" + upregulated = "upregulated" + decreased = "decreased" + downregulated = "downregulated" + + + +class ChemicalEntityDerivativeEnum(str, Enum): + + metabolite = "metabolite" + + + +class ChemicalOrGeneOrGeneProductFormEnum(str, Enum): + + modified_form = "modified form" + mutant_form = "mutant form" + polymorphism = "polymorphism" + SNP = "SNP" + analog = "analog" + + + +class GeneOrGeneProductOrChemicalPartQualifierEnum(str, Enum): + + number_3APOSTROPHE_UTR = "3' UTR" + number_5APOSTROPHE_UTR = "5' UTR" + polyA_tail = "polyA tail" + promoter = "promoter" + enhancer = "enhancer" + exon = "exon" + intron = "intron" + + + +class GeneOrGeneProductOrChemicalEntityAspectEnum(str, Enum): + + expression = "expression" + mutation_rate = "mutation rate" + abundance = "abundance" + synthesis = "synthesis" + degradation = "degradation" + cleavage = "cleavage" + hydrolysis = "hydrolysis" + activity = "activity" + metabolic_processing = "metabolic processing" + stability = "stability" + localization = "localization" + transport = "transport" + secretion = "secretion" + uptake = "uptake" + molecular_modification = "molecular modification" + acetylation = "acetylation" + acylation = "acylation" + alkylation = "alkylation" + amination = "amination" + carbamoylation = "carbamoylation" + ethylation = "ethylation" + glutathionylation = "glutathionylation" + glycation = "glycation" + glycosylation = "glycosylation" + glucuronidation = "glucuronidation" + N_linked_glycosylation = "N-linked glycosylation" + O_linked_glycosylation = "O-linked glycosylation" + hydroxylation = "hydroxylation" + lipidation = "lipidation" + farnesylation = "farnesylation" + geranoylation = "geranoylation" + myristoylation = "myristoylation" + palmitoylation = "palmitoylation" + prenylation = "prenylation" + methylation = "methylation" + nitrosation = "nitrosation" + nucleotidylation = "nucleotidylation" + phosphorylation = "phosphorylation" + ribosylation = "ribosylation" + ADP_ribosylation = "ADP-ribosylation" + sulfation = "sulfation" + sumoylation = "sumoylation" + ubiquitination = "ubiquitination" + oxidation = "oxidation" + reduction = "reduction" + carboxylation = "carboxylation" + + + +class CausalMechanismQualifierEnum(str, Enum): + + binding = "binding" + inhibition = "inhibition" + antibody_inhibition = "antibody inhibition" + antagonism = "antagonism" + molecular_channel_blockage = "molecular channel blockage" + inverse_agonism = "inverse agonism" + negative_allosteric_modulation = "negative allosteric modulation" + agonism = "agonism" + molecular_channel_opening = "molecular channel opening" + positive_allosteric_modulation = "positive allosteric modulation" + potentiation = "potentiation" + activation = "activation" + inducer = "inducer" + transcriptional_regulation = "transcriptional regulation" + signaling_mediated_control = "signaling-mediated control" + + + class LogicalInterpretationEnum(str, Enum): SomeSome = "SomeSome" @@ -67,17 +181,6 @@ class SequenceEnum(str, Enum): -class PredicateQualifierEnum(str, Enum): - - predicted = "predicted" - possibly = "possibly" - hypothesized = "hypothesized" - validated = "validated" - supported_by_real_world_evidence = "supported by real-world evidence" - supported_by_clinical_evidence = "supported by clinical evidence" - - - class DruggableGeneCategoryEnum(str, Enum): Tclin = "Tclin" @@ -506,6 +609,156 @@ class InformationContentEntity(NamedThing): +class StudyResult(InformationContentEntity): + """ + A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ConceptCountAnalysisResult(StudyResult): + """ + A result of a concept count analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ObservedExpectedFrequencyAnalysisResult(StudyResult): + """ + A result of a observed expected frequency analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RelativeFrequencyAnalysisResult(StudyResult): + """ + A result of a relative frequency analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class TextMiningResult(StudyResult): + """ + A result of text mining. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChiSquaredAnalysisResult(StudyResult): + """ + A result of a chi squared analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class Dataset(InformationContentEntity): """ an item that refers to a collection of data from a data source. @@ -1149,12 +1402,6 @@ class GenomicEntity(ConfiguredBaseModel): -class ChemicalSubstance(ConfiguredBaseModel): - - None - - - class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): """ Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. @@ -1349,7 +1596,7 @@ class PhenotypicQuality(OrganismAttribute): class Inheritance(OrganismAttribute): """ - 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. + The name of this attribute and its inheritance from organism attribute, indeed, its designation as an attribute is problematic. First, the isolated word 'inheritance' is too ambiguous (especially when embedded inside an ontology with inheritance!). 'Genetic inheritance' would be more precise. Second, in terms of the scientific usage here, genetic inheritance would not be a direct property at the topmost organism level, but rather (as hinted in the definition) is more a commentary on the nature of phenotype (including genetic disease as a characteristic set of associated phenotypes) against the (hidden) context of (meiotic/somatic/mitochondrial) DNA segregation and expression. Third, placing the term in the attribute, rather than named thing category concept hierarchy, is perhaps less flexible in terms of its usage as a first class concept for semantic queries. Thus, we deprecate this term, moving it to the 'new' category of 'genetic inheritance', as a child of 'biological entity' (to emphasize its biological conceptual nature). """ name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") has_attribute_type: str = Field(None, description="""connects an attribute to a class that describes it""") @@ -1371,6 +1618,28 @@ class Inheritance(OrganismAttribute): +class GeneticInheritance(BiologicalEntity): + """ + 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. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class OrganismalEntity(BiologicalEntity): """ A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities @@ -1393,6 +1662,48 @@ class OrganismalEntity(BiologicalEntity): +class Virus(OrganismalEntity): + """ + A virus is a microorganism that replicates itself as a microRNA and infects the host cell. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class CellularOrganism(OrganismalEntity): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[str] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class LifeStage(OrganismalEntity): """ A stage of development or growth of an organism, including post-natal adult stages @@ -1483,7 +1794,7 @@ class StudyPopulation(PopulationOfIndividualOrganisms): class DiseaseOrPhenotypicFeature(BiologicalEntity): """ - 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. + 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. 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. """ in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -1504,7 +1815,9 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): class Disease(DiseaseOrPhenotypicFeature): - + """ + 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. + """ in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") @@ -1525,7 +1838,7 @@ class Disease(DiseaseOrPhenotypicFeature): class PhenotypicFeature(DiseaseOrPhenotypicFeature): """ - A combination of entity and quality that makes up a phenotyping statement. + 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. A combination of entity and quality that makes up a phenotyping statement. """ in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -1695,7 +2008,7 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1722,7 +2035,7 @@ class MolecularEntity(ChemicalEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1749,7 +2062,7 @@ class SmallMolecule(MolecularEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1779,7 +2092,7 @@ class ChemicalMixture(ChemicalEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1809,7 +2122,7 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -1838,7 +2151,7 @@ class MolecularMixture(ChemicalMixture): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1868,7 +2181,7 @@ class ComplexMolecularMixture(ChemicalMixture): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1898,7 +2211,7 @@ class ProcessedMaterial(ChemicalMixture): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1929,7 +2242,7 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -1952,7 +2265,7 @@ class EnvironmentalFoodContaminant(ChemicalEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -1976,7 +2289,7 @@ class FoodAdditive(ChemicalEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2000,7 +2313,7 @@ class Nutrient(ChemicalEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2024,7 +2337,7 @@ class Macronutrient(Nutrient): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2048,7 +2361,7 @@ class Micronutrient(Nutrient): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2072,7 +2385,7 @@ class Vitamin(Micronutrient): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2102,7 +2415,7 @@ class Food(ChemicalMixture): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2224,7 +2537,7 @@ class Exon(NucleicAcidEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -2253,7 +2566,7 @@ class Transcript(NucleicAcidEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -2280,7 +2593,7 @@ class CodingSequence(NucleicAcidEntity): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""Alternate CURIEs for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") @@ -2399,7 +2712,7 @@ class RNAProduct(Transcript, GeneProductMixin): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[str] = Field(["biolink:RNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2429,7 +2742,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[str] = Field(["biolink:RNAProductIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2457,7 +2770,7 @@ class NoncodingRNAProduct(RNAProduct): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[str] = Field(["biolink:NoncodingRNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2485,7 +2798,7 @@ class MicroRNA(NoncodingRNAProduct): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[str] = Field(["biolink:MicroRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2515,7 +2828,7 @@ class SiRNA(NoncodingRNAProduct): available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) max_tolerated_dose: Optional[str] = Field(None, 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.""") is_toxic: Optional[bool] = Field(None) - has_chemical_role: Optional[List[str]] = Field(None, description=""" A role is particular behaviour which a material entity may exhibit.""") + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a material entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[str] = Field(["biolink:SiRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3548,7 +3861,7 @@ class Association(Entity): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3577,7 +3890,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3608,7 +3921,7 @@ class ContributorAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3639,7 +3952,7 @@ class GenotypeToGenotypePartAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3670,7 +3983,7 @@ class GenotypeToGeneAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3701,7 +4014,7 @@ class GenotypeToVariantAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3732,7 +4045,7 @@ class GeneToGeneAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3763,7 +4076,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3809,7 +4122,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3840,7 +4153,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3872,7 +4185,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3943,7 +4256,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -3975,7 +4288,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4007,7 +4320,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4046,7 +4359,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4077,7 +4390,7 @@ class MolecularActivityToPathwayAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4108,7 +4421,7 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4127,6 +4440,35 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association +class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): + + subject: str = Field(None, 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.""") + predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(None, 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.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, 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.""") + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: Optional[List[str]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class ChemicalToGeneAssociation(ChemicalToEntityAssociationMixin, Association): """ An interaction between a chemical entity and a gene or gene product. @@ -4139,7 +4481,7 @@ class ChemicalToGeneAssociation(ChemicalToEntityAssociationMixin, Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4158,6 +4500,89 @@ class ChemicalToGeneAssociation(ChemicalToEntityAssociationMixin, Association): +class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Association): + """ + 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) + """ + subject_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormEnum] = Field(None) + subject_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_derivative_qualifier: Optional[ChemicalEntityDerivativeEnum] = Field(None) + subject_context_qualifier: Optional[str] = Field(None) + object_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormEnum] = Field(None) + object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_context_qualifier: Optional[str] = Field(None) + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or subcellular location).""") + subject: str = Field(None, 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.""") + predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(None, 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.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, 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.""") + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: Optional[List[str]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalAffectsGeneAssociation(Association): + """ + 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.) + """ + subject_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormEnum] = Field(None) + subject_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_derivative_qualifier: Optional[ChemicalEntityDerivativeEnum] = Field(None) + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + subject_context_qualifier: Optional[str] = Field(None) + subject_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + object_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormEnum] = Field(None) + object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_context_qualifier: Optional[str] = Field(None) + causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, 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')""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or subcellular location).""") + qualified_predicate: Optional[str] = Field(None, 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""") + subject: str = Field(None, 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.""") + predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(None, 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.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, 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.""") + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: Optional[List[str]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): """ An interaction between a drug and a gene or gene product. @@ -4170,7 +4595,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4209,7 +4634,7 @@ class MaterialSampleDerivationAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4254,7 +4679,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4301,7 +4726,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Exposur publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4359,7 +4784,7 @@ class InformationContentEntityToNamedThingAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4406,7 +4831,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4425,6 +4850,37 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature +class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenotypicFeatureToEntityAssociationMixin, Association): + """ + An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. + """ + subject: str = Field(None, 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.""") + predicate: str = Field(None, description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(None, description="""genetic inheritance associated with the specified disease or phenotypic feature.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, 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.""") + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: Optional[List[str]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(ConfiguredBaseModel): None @@ -4443,7 +4899,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4474,7 +4930,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4505,7 +4961,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4543,7 +4999,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4578,7 +5034,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4613,7 +5069,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4648,7 +5104,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4683,7 +5139,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4723,7 +5179,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4759,7 +5215,7 @@ class GeneToPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, EntityToP publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4791,7 +5247,7 @@ class GeneToDiseaseAssociation(GeneToEntityAssociationMixin, EntityToDiseaseAsso publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4823,7 +5279,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[DruggableGeneCategoryEnum]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4857,7 +5313,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4892,7 +5348,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4928,7 +5384,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4959,7 +5415,7 @@ class PopulationToPopulationAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -4989,7 +5445,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5021,7 +5477,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5053,7 +5509,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5093,7 +5549,7 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5125,7 +5581,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5157,7 +5613,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5189,7 +5645,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5221,7 +5677,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5253,7 +5709,7 @@ class OrganismToOrganismAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5282,7 +5738,7 @@ class TaxonToTaxonAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5312,7 +5768,7 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5348,7 +5804,7 @@ class GeneToExpressionSiteAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5379,7 +5835,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5410,7 +5866,7 @@ class FunctionalAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5449,7 +5905,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5480,7 +5936,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5511,7 +5967,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5542,7 +5998,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5573,7 +6029,7 @@ class MolecularActivityToMolecularActivityAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5602,7 +6058,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5632,7 +6088,7 @@ class EntityToDiseaseAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5662,7 +6118,7 @@ class EntityToPhenotypicFeatureAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5693,7 +6149,7 @@ class SequenceAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5729,7 +6185,7 @@ class GenomicSequenceLocalization(SequenceAssociation): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5760,7 +6216,7 @@ class SequenceFeatureRelationship(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5791,7 +6247,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5822,7 +6278,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5853,7 +6309,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5884,7 +6340,7 @@ class GeneRegulatoryRelationship(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5903,6 +6359,38 @@ class GeneRegulatoryRelationship(Association): +class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): + """ + A regulatory relationship between two genes + """ + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + subject: str = Field(None, 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.""") + predicate: str = Field(None, description="""the direction is always from regulator to regulated""") + object: str = Field(None, 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.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, 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.""") + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(None, description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: Optional[List[str]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[str] = Field(None) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + source: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + class AnatomicalEntityToAnatomicalEntityAssociation(Association): subject: str = Field(None, 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.""") @@ -5913,7 +6401,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5944,7 +6432,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -5975,7 +6463,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -6014,7 +6502,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -6045,7 +6533,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -6077,7 +6565,7 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -6099,15 +6587,14 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, Association): subject: str = Field(None, description="""the taxon that is the subject of the association""") - predicate: str = Field(None, description="""predicate describing the relationship between the taxon and the environment - """) + predicate: str = Field(None, description="""predicate describing the relationship between the taxon and the environment""") object: str = Field(None, description="""the environment in which the organism occurs""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") publications: Optional[List[str]] = Field(default_factory=list, description="""connects an association to publications supporting the association""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, 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.""") - original_knowledge_source: Optional[str] = Field(None) + original_knowledge_source: Optional[str] = Field(None, description="""The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).""") aggregator_knowledge_source: Optional[List[str]] = Field(None, 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.""") timepoint: Optional[str] = Field(None, description="""a point in time""") @@ -6155,6 +6642,12 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As AdministrativeEntity.update_forward_refs() Agent.update_forward_refs() InformationContentEntity.update_forward_refs() +StudyResult.update_forward_refs() +ConceptCountAnalysisResult.update_forward_refs() +ObservedExpectedFrequencyAnalysisResult.update_forward_refs() +RelativeFrequencyAnalysisResult.update_forward_refs() +TextMiningResult.update_forward_refs() +ChiSquaredAnalysisResult.update_forward_refs() Dataset.update_forward_refs() DatasetDistribution.update_forward_refs() DatasetVersion.update_forward_refs() @@ -6186,7 +6679,6 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As ThingWithTaxon.update_forward_refs() BiologicalEntity.update_forward_refs() GenomicEntity.update_forward_refs() -ChemicalSubstance.update_forward_refs() BiologicalProcessOrActivity.update_forward_refs() MolecularActivity.update_forward_refs() BiologicalProcess.update_forward_refs() @@ -6196,7 +6688,10 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As OrganismAttribute.update_forward_refs() PhenotypicQuality.update_forward_refs() Inheritance.update_forward_refs() +GeneticInheritance.update_forward_refs() OrganismalEntity.update_forward_refs() +Virus.update_forward_refs() +CellularOrganism.update_forward_refs() LifeStage.update_forward_refs() IndividualOrganism.update_forward_refs() PopulationOfIndividualOrganisms.update_forward_refs() @@ -6320,7 +6815,10 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As ChemicalToChemicalDerivationAssociation.update_forward_refs() MolecularActivityToPathwayAssociation.update_forward_refs() ChemicalToPathwayAssociation.update_forward_refs() +NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.update_forward_refs() ChemicalToGeneAssociation.update_forward_refs() +ChemicalGeneInteractionAssociation.update_forward_refs() +ChemicalAffectsGeneAssociation.update_forward_refs() DrugToGeneAssociation.update_forward_refs() MaterialSampleToEntityAssociationMixin.update_forward_refs() MaterialSampleDerivationAssociation.update_forward_refs() @@ -6337,6 +6835,7 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As EntityToDiseaseAssociationMixin.update_forward_refs() DiseaseOrPhenotypicFeatureToEntityAssociationMixin.update_forward_refs() DiseaseOrPhenotypicFeatureToLocationAssociation.update_forward_refs() +DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.update_forward_refs() EntityToDiseaseOrPhenotypicFeatureAssociationMixin.update_forward_refs() CellLineToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() ChemicalToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() @@ -6388,6 +6887,7 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As GeneToGeneProductRelationship.update_forward_refs() ExonToTranscriptRelationship.update_forward_refs() GeneRegulatoryRelationship.update_forward_refs() +ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.update_forward_refs() AnatomicalEntityToAnatomicalEntityAssociation.update_forward_refs() AnatomicalEntityToAnatomicalEntityPartOfAssociation.update_forward_refs() AnatomicalEntityToAnatomicalEntityOntogenicAssociation.update_forward_refs()