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add guthub url and spec output of tsvs from yaml
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rsc3 committed Mar 13, 2024
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2 changes: 1 addition & 1 deletion content/linkml/AnVILBioCoreMinimal.yaml
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name: AnVILBioCoreMinimal
description: AnVIL minimal BioCore schema
id: https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
id: https://github.com/DataBiosphere/biocore-data-model/tree/main/content
prefixes:
linkml: https://w3id.org/linkml/
anvil: https://anvilproject.org/
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30 changes: 30 additions & 0 deletions content/linkml/specs/concise.tsv
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slot class alias aliases comments description domain domain_of from_schema identifier is_a multivalued owner range slot_uri
>slot class alias aliases comments description domain domain_of from_schema identifier is_a multivalued owner range slot_uri
> "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|"""
donor_id_fk hasDonor This property references the Donor organism from which the BioSample was acquired. AnvilBioSample AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false AnvilDonor https://datamodel.terra.bio/TerraCore#hasDonor
id https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true uriorcurie
biosample_id AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id
donor_id AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id
diagnosis_id https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id
file_id AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id
anatomical_site hasAnatomicalSite A reference to the site within the organism from which the BioSample was taken. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
apriori_cell_type hasAprioriCellType A priori cell type(s) for the sample, a human assignment of cell type. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true
biosample_type The type of biosample represented by the record. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
disease hasDisease A property that identifies a disease or condition has been reported in this entity. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
donor_age_at_collection_unit The units (e.g. years or days) of the Age of the Donor at the point in time that the BioSample was obtained or other representative entity (test, diagnosis, treatment...) was created. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
donor_age_at_collection_lower_bound Lower bound for age of donor at time sample was taken. If any age at collection data is present, must specify a unit as well. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 float
donor_age_at_collection_upper_bound Upper bound for age of donor at time sample was taken. If any age at collection data is present, must specify a unit as well. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 float
organism_type hasOrganismType For example: Homo sapiens from NCBITaxon or http://purl.obolibrary.org/obo/NCBITaxon_9606 A reference to the organism type. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
phenotypic_sex hasPhenotypicSex "A reference to the BiologicalSex of the Donor organism. \""An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. [PATO_0001894]\" AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
reported_ethnicity hasReportedEthnicity Recommend using HANCESTRO ancestry categories. http://purl.obolibrary.org/obo/HANCESTRO_0004. A property that relects a Human Donor's reported ethnic origins. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true
genetic_ancestry hasGeneticAncestry Recommend using HANCESTRO ancestry categories. http://purl.obolibrary.org/obo/HANCESTRO_0004 A property that relects a HumanDonor's reported major contributing ancestral origins based on genetic/genomic data. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true
data_modality hasDataModality Data modality describes the biological nature of the information gathered as the result of an Activity, independent of the technology or methods used to produce the information. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true
file_name The name of the file. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
file_ref The fully qualified path to the file. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
file_format hasFileFormat The definition of this field follows the convention used by the Human Cell Atlas. An indication of the format of an electronic file; include the full file extension including compression extensions. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
file_size hasFileSize Property that describes the approximate size of a file in megabytes. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false integer
file_md5sum md5 checksum for the file AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false
reference_assembly usesReferenceAssembly A reference to the collection of sequences taken as the standard for a given organism. May be defined by https://www.ncbi.nlm.nih.gov/grc. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true
AnvilBioSample Contains information about the sample(s) included in the study. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
AnvilDonor Demographic and phenotypic information about the donor. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
AnvilFile Information for files associated with the study. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180
31 changes: 31 additions & 0 deletions content/linkml/specs/exhaustive.tsv
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slot class examples values structured_pattern unit symbol abstract alias aliases apply_to asymmetric broad mappings categories children_are_mutually_disjoint class_uri close mappings comments conforms_to contributors created_by created_on defining_slots definition_uri deprecated deprecated element has exact replacement deprecated element has possible replacement description designates_type disjoint_with domain domain_of equals_expression equals_number equals_string equals_string_in exact mappings exact_cardinality from_schema id_prefixes id_prefixes_are_closed identifier ifabsent implements implicit_prefix imported_from in_language in_subset inherited inlined inlined_as_list instantiates inverse irreflexive is_a is_class_field is_grouping_slot is_usage_slot key keywords last_updated_on list_elements_ordered list_elements_unique locally_reflexive mappings maximum_cardinality minimum_cardinality mixin mixins modified_by multivalued name narrow mappings notes owner pattern range rank readonly recommended reflexive reflexive_transitive_form_of related mappings relational_role represents_relationship required role see_also shared singular_name slot_conditions slot_group slot_names_unique slot_uri source status string_serialization subclass_of subproperty_of symmetric title todos transitive transitive_form_of tree_root union_of usage_slot_name value_presence values_from
>slot class examples structured_pattern unit abstract alias aliases apply_to asymmetric broad_mappings categories children_are_mutually_disjoint class_uri close_mappings comments conforms_to contributors created_by created_on defining_slots definition_uri deprecated deprecated_element_has_exact_replacement deprecated_element_has_possible_replacement description designates_type disjoint_with domain domain_of equals_expression equals_number equals_string equals_string_in exact_mappings exact_cardinality from_schema id_prefixes id_prefixes_are_closed identifier ifabsent implements implicit_prefix imported_from in_language in_subset inherited inlined inlined_as_list instantiates inverse irreflexive is_a is_class_field is_grouping_slot is_usage_slot key keywords last_updated_on list_elements_ordered list_elements_unique locally_reflexive mappings maximum_cardinality minimum_cardinality mixin mixins modified_by multivalued name narrow_mappings notes owner pattern range rank readonly recommended reflexive reflexive_transitive_form_of related_mappings relational_role represents_relationship required role see_also shared singular_name slot_conditions slot_group slot_names_unique slot_uri source status string_serialization subclass_of subproperty_of symmetric title todos transitive transitive_form_of tree_root union_of usage_slot_name value_presence values_from
> "inner_key: ""value""" "inner_key: ""syntax""" "inner_key: ""symbol"""
> "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|""" "internal_separator: ""|"""
donor_id_fk hasDonor This property references the Donor organism from which the BioSample was acquired. AnvilBioSample AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false donor_id_fk AnvilDonor https://datamodel.terra.bio/TerraCore#hasDonor
id https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true id uriorcurie
biosample_id AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id biosample_id
donor_id AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id donor_id
diagnosis_id https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id diagnosis_id
file_id AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 id file_id
anatomical_site hasAnatomicalSite A reference to the site within the organism from which the BioSample was taken. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false anatomical_site
apriori_cell_type hasAprioriCellType A priori cell type(s) for the sample, a human assignment of cell type. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true apriori_cell_type
biosample_type The type of biosample represented by the record. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false biosample_type
disease hasDisease A property that identifies a disease or condition has been reported in this entity. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false disease
donor_age_at_collection_unit The units (e.g. years or days) of the Age of the Donor at the point in time that the BioSample was obtained or other representative entity (test, diagnosis, treatment...) was created. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 donor_age_at_collection_unit
donor_age_at_collection_lower_bound Lower bound for age of donor at time sample was taken. If any age at collection data is present, must specify a unit as well. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 donor_age_at_collection_lower_bound float
donor_age_at_collection_upper_bound Upper bound for age of donor at time sample was taken. If any age at collection data is present, must specify a unit as well. AnvilBioSample https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 donor_age_at_collection_upper_bound float
organism_type hasOrganismType For example: Homo sapiens from NCBITaxon or http://purl.obolibrary.org/obo/NCBITaxon_9606 A reference to the organism type. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false organism_type
phenotypic_sex hasPhenotypicSex "A reference to the BiologicalSex of the Donor organism. \""An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. [PATO_0001894]\" AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false phenotypic_sex
reported_ethnicity hasReportedEthnicity Recommend using HANCESTRO ancestry categories. http://purl.obolibrary.org/obo/HANCESTRO_0004. A property that relects a Human Donor's reported ethnic origins. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true reported_ethnicity
genetic_ancestry hasGeneticAncestry Recommend using HANCESTRO ancestry categories. http://purl.obolibrary.org/obo/HANCESTRO_0004 A property that relects a HumanDonor's reported major contributing ancestral origins based on genetic/genomic data. AnvilDonor https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true genetic_ancestry
data_modality hasDataModality Data modality describes the biological nature of the information gathered as the result of an Activity, independent of the technology or methods used to produce the information. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true data_modality
file_name The name of the file. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 file_name
file_ref The fully qualified path to the file. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 file_ref
file_format hasFileFormat The definition of this field follows the convention used by the Human Cell Atlas. An indication of the format of an electronic file; include the full file extension including compression extensions. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false file_format
file_size hasFileSize Property that describes the approximate size of a file in megabytes. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false file_size integer
file_md5sum md5 checksum for the file AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 false file_md5sum
reference_assembly usesReferenceAssembly A reference to the collection of sequences taken as the standard for a given organism. May be defined by https://www.ncbi.nlm.nih.gov/grc. AnvilFile https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 true reference_assembly
AnvilBioSample Contains information about the sample(s) included in the study. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 AnvilBioSample
AnvilDonor Demographic and phenotypic information about the donor. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 AnvilDonor
AnvilFile Information for files associated with the study. https://docs.google.com/spreadsheets/d/1kOWpQV7pIUXcFx5jGgx75qnNI5-g_c2D/edit#gid=1482408180 AnvilFile

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