diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json index 7529016ef..7c0fc4bea 100644 --- a/generated/jsonschema/allianceModel.schema.json +++ b/generated/jsonschema/allianceModel.schema.json @@ -106,10 +106,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the disease annotation. When available, this is used for determination of distinctness instead of the Unique ID field.", "type": "string" @@ -122,6 +118,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-AGRKB) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Disease annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -181,11 +181,11 @@ "type": "string" }, "asserted_allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele to which something is manually asserted to be associated", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele to which something is manually asserted to be associated", "type": "string" }, "asserted_gene_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", "items": { "type": "string" }, @@ -226,7 +226,7 @@ "type": "string" }, "disease_genetic_modifier_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of BiologcalEntity that modifies the disease model", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model", "items": { "type": "string" }, @@ -263,21 +263,17 @@ "type": "string" }, "inferred_allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline", "type": "string" }, "inferred_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", "type": "string" }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -296,6 +292,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" @@ -309,7 +309,7 @@ "type": "string" }, "with_gene_identifiers": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", "items": { "type": "string" }, @@ -395,10 +395,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -422,6 +418,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Phenotype annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -466,11 +466,11 @@ "type": "string" }, "asserted_allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele to which something is manually asserted to be associated", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele to which something is manually asserted to be associated", "type": "string" }, "asserted_gene_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", "items": { "type": "string" }, @@ -514,21 +514,17 @@ "type": "string" }, "inferred_allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline", "type": "string" }, "inferred_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", "type": "string" }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -554,6 +550,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" @@ -879,10 +879,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -898,6 +894,10 @@ "parental_populations": { "type": "string" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -992,7 +992,7 @@ "description": "", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -1097,10 +1097,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -1113,6 +1109,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curies": { "description": "External reference curies used for ingest", "items": { @@ -1121,7 +1121,7 @@ "type": "array" }, "sequence_targeting_reagent_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the STRs", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the STRs", "items": { "type": "string" }, @@ -1143,7 +1143,7 @@ "required": [ "subtype_name", "taxon_curie", - "mod_entity_id", + "primary_external_id", "data_provider_dto", "internal" ], @@ -1444,10 +1444,6 @@ "$ref": "#/$defs/Laboratory", "description": "The laboratory of origin for the entity." }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -1456,6 +1452,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -1571,7 +1571,7 @@ "description": "Association between an allele and another allele", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -1617,7 +1617,7 @@ "$ref": "#/$defs/NoteDTO" }, "object_allele_identifier": { - "description": "The identifier (curie/mod_entity_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation", + "description": "The identifier (curie/primary_external_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation", "type": "string" }, "obsolete": { @@ -1713,11 +1713,11 @@ "description": "The relationship between an allele and a cell line. Includes mutant/ embryonic stem cell lines known to carry the allele, and parental cell line of alleles made in embryonic stem cells.", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "cell_line_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the cell line", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the cell line", "type": "string" }, "created_by_curie": { @@ -1856,7 +1856,7 @@ "description": "The relationship between an allele and constructs contained in that allele.", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "construct_identifier": { @@ -2040,10 +2040,6 @@ "description": "The curie of the laboratory of origin for the entity.", "type": "string" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -2058,6 +2054,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curies": { "description": "External reference curies used for ingest", "items": { @@ -2081,7 +2081,7 @@ "required": [ "allele_symbol_dto", "taxon_curie", - "mod_entity_id", + "primary_external_id", "data_provider_dto", "internal" ], @@ -2308,10 +2308,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the disease annotation. When available, this is used for determination of distinctness instead of the Unique ID field.", "type": "string" @@ -2324,6 +2320,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-AGRKB) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Disease annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -2376,7 +2376,7 @@ "description": "Ingest class for an association between an allele and a disease", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "annotation_type_name": { @@ -2384,7 +2384,7 @@ "type": "string" }, "asserted_gene_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", "items": { "type": "string" }, @@ -2425,7 +2425,7 @@ "type": "string" }, "disease_genetic_modifier_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of BiologcalEntity that modifies the disease model", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model", "items": { "type": "string" }, @@ -2462,17 +2462,13 @@ "type": "string" }, "inferred_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", "type": "string" }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -2491,6 +2487,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" @@ -2504,7 +2504,7 @@ "type": "string" }, "with_gene_identifiers": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", "items": { "type": "string" }, @@ -2826,7 +2826,7 @@ "description": "Association between an allele and a gene", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -2865,7 +2865,7 @@ "type": "array" }, "gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the gene", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the gene", "type": "string" }, "internal": { @@ -2978,7 +2978,7 @@ "description": "", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -3020,7 +3020,7 @@ "type": "boolean" }, "mutation_target_strain_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the particular strain that is targeted by the generation method for a particular allele (MGI only)", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the particular strain that is targeted by the generation method for a particular allele (MGI only)", "type": "string" }, "obsolete": { @@ -3247,7 +3247,7 @@ "description": "The relationship between an allele and an image.", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -3776,7 +3776,7 @@ "type": "string" }, "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -3896,10 +3896,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -3923,6 +3919,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Phenotype annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -3964,11 +3964,11 @@ "description": "Ingest class for an association between an allele and a phenotype", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "asserted_gene_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated", "items": { "type": "string" }, @@ -4012,17 +4012,13 @@ "type": "string" }, "inferred_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline", "type": "string" }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -4048,6 +4044,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" @@ -4145,7 +4145,7 @@ "description": "Association between an allele and a protein", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -4518,7 +4518,7 @@ "description": "Association between an allele and a transcript", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -4667,7 +4667,7 @@ "description": "The relationship between an allele and a variant is many to many. An Allele may have many variants and a variant can be present in many alleles.", "properties": { "allele_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the allele", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", "type": "string" }, "created_by_curie": { @@ -4725,7 +4725,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" } }, @@ -4815,6 +4815,7 @@ "description": "The set of terms that define a specific anatomical site within a specimen.", "properties": { "anatomical_structure": { + "description": "The primary anatomical structure referred to within the context of an AnatomicalSite object.", "type": "string" }, "anatomical_structure_qualifiers": { @@ -4831,6 +4832,7 @@ "type": "array" }, "anatomical_substructure": { + "description": "Primary anatomical substructure referenced within the context of an AnatomicalSite.", "type": "string" }, "anatomical_substructure_qualifiers": { @@ -4847,6 +4849,7 @@ "type": "array" }, "cellular_component": { + "description": "The primary cellular component referred to within the context of an AnatomicalSite object.", "type": "string" }, "cellular_component_qualifiers": { @@ -4898,6 +4901,97 @@ "title": "AnatomicalSite", "type": "object" }, + "AnatomicalSiteDTO": { + "additionalProperties": false, + "description": "The set of terms that define a specific anatomical site within a specimen.", + "properties": { + "anatomical_structure_curie": { + "description": "The primary anatomical structure referred to within the context of an AnatomicalSite object. The range is any string representing an AnatomicalTerm ontology term", + "type": "string" + }, + "anatomical_structure_qualifier_names": { + "items": { + "type": "string" + }, + "type": "array" + }, + "anatomical_structure_uberon_term_curies": { + "description": "UBERON slim terms that apply to the anatomical structure.", + "items": { + "type": "string" + }, + "type": "array" + }, + "anatomical_substructure_curie": { + "description": "Primary anatomical substructure referenced within the context of an AnatomicalSiteDTO. The range is any string representing an AnatomicalTerm ontology term.", + "type": "string" + }, + "anatomical_substructure_qualifier_names": { + "items": { + "type": "string" + }, + "type": "array" + }, + "anatomical_substructure_uberon_term_curies": { + "description": "String representations of UBERON slim terms that apply to the anatomical substructure.", + "items": { + "type": "string" + }, + "type": "array" + }, + "cellular_component_curie": { + "description": "The primary cellular component referred to within the context of an AnatomicalSite object. The range is any string representing a GOTerm ontology term", + "type": "string" + }, + "cellular_component_qualifier_names": { + "items": { + "type": "string" + }, + "type": "array" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "AnatomicalSiteDTO", + "type": "object" + }, "Annotation": { "additionalProperties": false, "description": "An annotation describing the link between a \"first class citizen\" of the database (e.g. Gene / Allele / AGM) and an ontology term or description, supported by a single reference and an optional list of condition relations.", @@ -4944,10 +5038,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -4956,6 +5046,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Holds between an object and a list of related Note objects.", "items": { @@ -5073,10 +5167,6 @@ }, "type": "array" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -5096,6 +5186,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -5143,7 +5237,7 @@ "description": "Ingest class for immunoglobulin proteins that bind specific molecule(s). Can be used experimentally for the purposes of detection or purification.", "properties": { "antibody_target_gene_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of the genes whose gene products are recognized by the antibody.", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of the genes whose gene products are recognized by the antibody.", "items": { "type": "string" }, @@ -5211,10 +5305,6 @@ "description": "Identifier for Reagent manufactured_by field. ", "type": "string" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -5237,6 +5327,10 @@ "description": "The reference providing the original description of the antibody's generation.", "type": "string" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curies": { "description": "External reference curies used for ingest", "items": { @@ -5323,10 +5417,6 @@ "$ref": "#/$defs/Chromosome", "description": "The chromosome(s) to which a chromosome assembly or unlocalized scaffold or contig maps." }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -5339,6 +5429,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -5404,10 +5498,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -5420,6 +5510,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -5809,29 +5903,26 @@ "title": "BackendBulkLoadTypeEnum", "type": "string" }, - "BulkFMSLoad": { + "BioSampleAge": { "additionalProperties": false, - "description": "This bulk load automatically pulls files from the BulkFMSLoad", + "description": "An object that holds the temporal aspect of a sample.", "properties": { - "backend_bulk_load_type": { - "$ref": "#/$defs/BackendBulkLoadTypeEnum" - }, - "bulkload_group": { - "$ref": "#/$defs/BulkLoadGroup", - "description": "Bulk load group designed to group together bulk loads" - }, - "bulkload_status": { - "$ref": "#/$defs/BulkLoadStatusEnum", - "description": "Status used to capture the progress of the load" + "age": { + "description": "free text for the age of the sample", + "type": "string" }, "created_by": { "description": "The individual that created the entity.", "type": "string" }, - "cron_schedule": { - "description": "A string describing the cron syntax for the schedule", + "curie": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, + "data_provider": { + "$ref": "#/$defs/DataProvider", + "description": "Object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, "date_created": { "description": "The date on which an entity was created. This can be applied to nodes or edges.", "format": "date-time", @@ -5852,77 +5943,58 @@ "format": "date-time", "type": "string" }, - "error_message": { - "description": "Error message string if an error occurs", - "type": "string" - }, - "fms_data_sub_type": { - "description": "The dataSubType paramater in the FMS", - "type": "string" - }, - "fms_data_type": { - "description": "The dataType paramater in the FMS", - "type": "string" - }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "load_files": { - "items": { - "$ref": "#/$defs/BulkLoadFile" - }, - "type": "array" - }, - "name": { - "description": "a human-readable name for an entity", + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", "type": "string" }, "obsolete": { "description": "Entity is no longer current.", "type": "boolean" }, - "ontology_type": { - "$ref": "#/$defs/OntologyBulkLoadTypeEnum" - }, - "schedule_active": { - "description": "This determines if the the schedule is active or not", - "type": "boolean" - }, - "scheduling_error_message": { - "description": "Any errors in syntax on the cron_schedule", + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", "type": "string" }, + "stage": { + "$ref": "#/$defs/TemporalContext", + "description": "The life stage of an organism or biosample as expressed by a TemporalContext entity" + }, "updated_by": { "description": "The individual that last modified the entity.", "type": "string" + }, + "when_expressed_stage_name": { + "description": "A human-readable stage name. To be used when an ontology term for the relevant stage is not available.", + "type": "string" } }, "required": [ + "data_provider", "internal" ], - "title": "BulkFMSLoad", + "title": "BioSampleAge", "type": "object" }, - "BulkLoad": { + "BioSampleAgeDTO": { "additionalProperties": false, - "description": "Base class for all loads", + "description": "An object that holds the temporal aspect of a sample.", "properties": { - "backend_bulk_load_type": { - "$ref": "#/$defs/BackendBulkLoadTypeEnum" - }, - "bulkload_group": { - "$ref": "#/$defs/BulkLoadGroup", - "description": "Bulk load group designed to group together bulk loads" - }, - "bulkload_status": { - "$ref": "#/$defs/BulkLoadStatusEnum", - "description": "Status used to capture the progress of the load" + "age": { + "description": "free text for the age of the sample", + "type": "string" }, - "created_by": { - "description": "The individual that created the entity.", + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", "type": "string" }, + "data_provider_dto": { + "$ref": "#/$defs/DataProviderDTO", + "description": "Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, "date_created": { "description": "The date on which an entity was created. This can be applied to nodes or edges.", "format": "date-time", @@ -5943,40 +6015,261 @@ "format": "date-time", "type": "string" }, - "error_message": { - "description": "Error message string if an error occurs", - "type": "string" - }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "load_files": { - "items": { - "$ref": "#/$defs/BulkLoadFile" - }, - "type": "array" - }, - "name": { - "description": "a human-readable name for an entity", + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", "type": "string" }, "obsolete": { "description": "Entity is no longer current.", "type": "boolean" }, - "ontology_type": { - "$ref": "#/$defs/OntologyBulkLoadTypeEnum" + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" }, - "updated_by": { - "description": "The individual that last modified the entity.", + "stage_dto": { + "$ref": "#/$defs/TemporalContextDTO", + "description": "The life stage of an organism or biosample as expressed by a TemporalContext entity" + }, + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + }, + "when_expressed_stage_name": { + "description": "A human-readable stage name. To be used when an ontology term for the relevant stage is not available.", "type": "string" } }, "required": [ + "data_provider_dto", "internal" ], - "title": "BulkLoad", + "title": "BioSampleAgeDTO", + "type": "object" + }, + "BioSampleGenomicInformation": { + "additionalProperties": false, + "description": "A basic entry for defining a biosample's genomic information", + "properties": { + "biosample_agm": { + "$ref": "#/$defs/AffectedGenomicModel", + "description": "An affected genomic model (AGM) from which a biosample has been derived" + }, + "biosample_agm_type": { + "description": "Indicates the type of AGM biosample; enum: fish, genotype, strain", + "type": "string" + }, + "biosample_allele": { + "$ref": "#/$defs/Allele", + "description": "An allele of focus for a particular biosample" + }, + "biosample_text": { + "description": "The free text of the biosample genomic information if no biosample is available", + "type": "string" + } + }, + "title": "BioSampleGenomicInformation", + "type": "object" + }, + "BioSampleGenomicInformationDTO": { + "additionalProperties": false, + "description": "A basic (DTO) entry for defining a biosample's genomic information", + "properties": { + "agm_identifier": { + "type": "string" + }, + "allele_identifier": { + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the allele", + "type": "string" + }, + "biosample_agm_type_name": { + "description": "Indicates the type of AGM biosample; enum: fish, genotype, strain", + "type": "string" + }, + "biosample_text": { + "description": "The free text of the biosample genomic information if no biosample is available", + "type": "string" + } + }, + "required": [ + "allele_identifier", + "agm_identifier" + ], + "title": "BioSampleGenomicInformationDTO", + "type": "object" + }, + "BulkFMSLoad": { + "additionalProperties": false, + "description": "This bulk load automatically pulls files from the BulkFMSLoad", + "properties": { + "backend_bulk_load_type": { + "$ref": "#/$defs/BackendBulkLoadTypeEnum" + }, + "bulkload_group": { + "$ref": "#/$defs/BulkLoadGroup", + "description": "Bulk load group designed to group together bulk loads" + }, + "bulkload_status": { + "$ref": "#/$defs/BulkLoadStatusEnum", + "description": "Status used to capture the progress of the load" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "cron_schedule": { + "description": "A string describing the cron syntax for the schedule", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "error_message": { + "description": "Error message string if an error occurs", + "type": "string" + }, + "fms_data_sub_type": { + "description": "The dataSubType paramater in the FMS", + "type": "string" + }, + "fms_data_type": { + "description": "The dataType paramater in the FMS", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "load_files": { + "items": { + "$ref": "#/$defs/BulkLoadFile" + }, + "type": "array" + }, + "name": { + "description": "a human-readable name for an entity", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "ontology_type": { + "$ref": "#/$defs/OntologyBulkLoadTypeEnum" + }, + "schedule_active": { + "description": "This determines if the the schedule is active or not", + "type": "boolean" + }, + "scheduling_error_message": { + "description": "Any errors in syntax on the cron_schedule", + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "BulkFMSLoad", + "type": "object" + }, + "BulkLoad": { + "additionalProperties": false, + "description": "Base class for all loads", + "properties": { + "backend_bulk_load_type": { + "$ref": "#/$defs/BackendBulkLoadTypeEnum" + }, + "bulkload_group": { + "$ref": "#/$defs/BulkLoadGroup", + "description": "Bulk load group designed to group together bulk loads" + }, + "bulkload_status": { + "$ref": "#/$defs/BulkLoadStatusEnum", + "description": "Status used to capture the progress of the load" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "error_message": { + "description": "Error message string if an error occurs", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "load_files": { + "items": { + "$ref": "#/$defs/BulkLoadFile" + }, + "type": "array" + }, + "name": { + "description": "a human-readable name for an entity", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "ontology_type": { + "$ref": "#/$defs/OntologyBulkLoadTypeEnum" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "BulkLoad", "type": "object" }, "BulkLoadFile": { @@ -6917,10 +7210,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -6929,6 +7218,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -6988,10 +7281,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -7000,6 +7289,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -7011,7 +7304,7 @@ }, "required": [ "taxon_curie", - "mod_entity_id", + "primary_external_id", "data_provider_dto", "internal" ], @@ -7199,10 +7492,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -7215,6 +7504,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -7283,10 +7576,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -7299,6 +7588,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -7677,10 +7970,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -7689,6 +7978,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -7938,10 +8231,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -7950,6 +8239,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curies": { "description": "External reference curies used for ingest", "items": { @@ -8745,7 +9038,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -8897,7 +9190,7 @@ "description": "", "properties": { "associated_transcript_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned.", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned.", "items": { "type": "string" }, @@ -8991,7 +9284,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -9219,7 +9512,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -9654,10 +9947,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -9666,6 +9955,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "secondary_identifiers": { "items": { "type": "string" @@ -10472,10 +10765,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -10488,6 +10777,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -10556,10 +10849,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -10572,6 +10861,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -10964,14 +11257,25 @@ "title": "ExpressionPattern", "type": "object" }, - "ExternalDatabaseLink": { + "ExternalDataBaseEntity": { "additionalProperties": false, - "description": "Base relation that holds the identifier prefix, base url and url suffix to help in generating URLs in crossReferences.", + "description": "A local database entry representing an external database entry; used currently for datasets or dataset samples; htpId.json in agr_schemas json", "properties": { "created_by": { "description": "The individual that created the entity.", "type": "string" }, + "cross_references": { + "description": "Optional cross references to the MOD sample or dataset page.", + "items": { + "$ref": "#/$defs/CrossReference" + }, + "type": "array" + }, + "curie": { + "description": "The ID from the data provider for the dataset. When available, this is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID. When these both are unavailable, it will be the MOD ID.", + "type": "string" + }, "date_created": { "description": "The date on which an entity was created. This can be applied to nodes or edges.", "format": "date-time", @@ -10992,10 +11296,6 @@ "format": "date-time", "type": "string" }, - "dbkey": { - "description": "Typically the primary key on the table. Should be a global sequence in the database to insure uniqueness over the entire suite of tables. Alternatively, could be a serial8 identifier. Tables with a dbkey should have an alternate key to establish uniqueness based on the data in the table.", - "type": "string" - }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -11004,11 +11304,142 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "prefix": { - "description": "Denormalization to help with classifying types of crossReferences, distinguishing DOIs from PMC ids, etc.", - "type": "string" + "preferred_cross_reference": { + "$ref": "#/$defs/CrossReference", + "description": "The cross reference to the preferred page to link to in search" }, - "prefix_order": { + "secondary_identifiers": { + "description": "list of optional cross reference ids to the primary dataset id.", + "items": { + "type": "string" + }, + "type": "array" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "ExternalDataBaseEntity", + "type": "object" + }, + "ExternalDataBaseEntityDTO": { + "additionalProperties": false, + "description": "DTO entity for a local database entry representing an external database entry; used currently for datasets or dataset samples; htpId.json in agr_schemas json", + "properties": { + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", + "type": "string" + }, + "cross_reference_dtos": { + "description": "Optional cross references to the MOD sample or dataset page.", + "items": { + "$ref": "#/$defs/CrossReferenceDTO" + }, + "type": "array" + }, + "curie": { + "description": "The ID from the data provider for the dataset. When available, this is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID. When these both are unavailable, it will be the MOD ID.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "preferred_cross_reference_dto": { + "$ref": "#/$defs/CrossReferenceDTO", + "description": "The cross reference to the preferred page to link to in search" + }, + "secondary_identifiers": { + "description": "list of optional cross reference ids to the primary dataset id.", + "items": { + "type": "string" + }, + "type": "array" + }, + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "ExternalDataBaseEntityDTO", + "type": "object" + }, + "ExternalDatabaseLink": { + "additionalProperties": false, + "description": "Base relation that holds the identifier prefix, base url and url suffix to help in generating URLs in crossReferences.", + "properties": { + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "dbkey": { + "description": "Typically the primary key on the table. Should be a global sequence in the database to insure uniqueness over the entire suite of tables. Alternatively, could be a serial8 identifier. Tables with a dbkey should have an alternate key to establish uniqueness based on the data in the table.", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "prefix": { + "description": "Denormalization to help with classifying types of crossReferences, distinguishing DOIs from PMC ids, etc.", + "type": "string" + }, + "prefix_order": { "description": "The relative order of the resource when listed with other crossReferences.", "type": "string" }, @@ -11527,10 +11958,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -11539,6 +11966,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "single_reference": { "$ref": "#/$defs/Reference", "description": "holds between an object and a single reference" @@ -11943,10 +12374,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -11955,6 +12382,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "product_binds_matrix": { "description": "WB specific. ID of position matrix object", "items": { @@ -12000,7 +12431,7 @@ "gene_symbol", "gene_type", "taxon", - "mod_entity_id", + "primary_external_id", "data_provider", "internal" ], @@ -12252,10 +12683,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -12264,6 +12691,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_note": { "$ref": "#/$defs/Note", "description": "Holds between an object and a Note object." @@ -12338,10 +12769,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -12350,6 +12777,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_note": { "$ref": "#/$defs/Note", "description": "Holds between an object and a Note object." @@ -12441,10 +12872,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -12459,6 +12886,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -12472,7 +12903,7 @@ "gene_symbol_dto", "gene_type_curie", "taxon_curie", - "mod_entity_id", + "primary_external_id", "data_provider_dto", "internal" ], @@ -12566,10 +12997,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the disease annotation. When available, this is used for determination of distinctness instead of the Unique ID field.", "type": "string" @@ -12582,6 +13009,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-AGRKB) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. \"WBDOannot00000907\"", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Disease annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -12675,7 +13106,7 @@ "type": "string" }, "disease_genetic_modifier_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of BiologcalEntity that modifies the disease model", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model", "items": { "type": "string" }, @@ -12708,7 +13139,7 @@ "type": "array" }, "gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the gene", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the gene", "type": "string" }, "genetic_sex_name": { @@ -12719,10 +13150,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -12741,6 +13168,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" @@ -12750,7 +13181,7 @@ "description": "Ingest object representing organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source, and a CrossReference to that organisation's site" }, "sgd_strain_background_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of SGD strain background AGM", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of SGD strain background AGM", "type": "string" }, "updated_by_curie": { @@ -12758,7 +13189,7 @@ "type": "string" }, "with_gene_identifiers": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8", "items": { "type": "string" }, @@ -12837,10 +13268,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database identifier/curie for the ExpressionAnnotation.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database internal identifier for the ExpressionAnnotation.", "type": "string" @@ -12853,6 +13280,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-AGRKB) database identifier/curie for the ExpressionAnnotation.", + "type": "string" + }, "related_figures": { "description": "The figure(s) that support(s) the expression annotation.", "items": { @@ -12977,10 +13408,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The MOD internal identifier for an expression experiment, if no curie is available. Can be constructed at the MOD just for submission.", "type": "string" @@ -12989,6 +13416,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Holds between an object and a list of related Note objects.", "items": { @@ -13155,7 +13586,7 @@ "type": "boolean" }, "object_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the object gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association", "type": "string" }, "obsolete": { @@ -13163,7 +13594,7 @@ "type": "boolean" }, "subject_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the subject gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association", "type": "string" }, "updated_by_curie": { @@ -13400,7 +13831,7 @@ "type": "boolean" }, "object_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the object gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association", "type": "string" }, "obsolete": { @@ -13414,7 +13845,7 @@ "type": "array" }, "subject_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the subject gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association", "type": "string" }, "updated_by_curie": { @@ -13819,7 +14250,7 @@ "type": "boolean" }, "object_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the object gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association", "type": "string" }, "obsolete": { @@ -13827,7 +14258,7 @@ "type": "boolean" }, "subject_gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the subject gene in a gene-to-gene association", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association", "type": "string" }, "updated_by_curie": { @@ -14045,10 +14476,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -14072,6 +14499,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Phenotype annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -14153,17 +14584,13 @@ "type": "string" }, "gene_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the gene", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the gene", "type": "string" }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -14189,12 +14616,16 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curie": { "description": "External reference curie used for ingest", "type": "string" }, "sgd_strain_background_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of SGD strain background AGM", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of SGD strain background AGM", "type": "string" }, "updated_by_curie": { @@ -15028,10 +15459,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -15040,6 +15467,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "specimen_genomic_model": { "$ref": "#/$defs/AffectedGenomicModel", "description": "The strain or genotype of origin for the genome sequence." @@ -15103,10 +15534,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -15115,6 +15542,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "specimen_genomic_model_identifier": { "description": "The identifier of the AffectedGenomicModel of the specimen. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.", "type": "string" @@ -15183,10 +15614,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -15195,6 +15622,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -15254,10 +15685,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -15266,6 +15693,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -15384,26 +15815,517 @@ }, "type": "array" }, - "synonyms": { - "description": "A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class", - "items": { - "type": "string" - }, - "type": "array" + "synonyms": { + "description": "A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "curie", + "internal" + ], + "title": "HPTerm", + "type": "object" + }, + "HighThroughputExpressionAssayValues": { + "description": "", + "enum": [ + "MMO:0000659", + "MMO:0000648", + "MMO:0000650", + "MMO:0000649", + "MMO:0000664", + "MMO:0000666", + "MMO:0000000", + "MMO:0000862" + ], + "title": "HighThroughputExpressionAssayValues", + "type": "string" + }, + "HighThroughputExpressionDatasetAnnotation": { + "additionalProperties": false, + "description": "An entry for a published high-throughput expression dataset annotation.", + "properties": { + "category_tags": { + "description": "A list of controlled vocabulary terms to describe the experiment", + "items": { + "type": "string" + }, + "type": "array" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "htp_expression_dataset": { + "$ref": "#/$defs/ExternalDataBaseEntity", + "description": "A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "name": { + "description": "The free text title of the dataset", + "type": "string" + }, + "number_of_channels": { + "description": "For microarrays, the number of channels used; This can be one of two values: 1 or 2", + "type": "integer" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "references": { + "description": "The list of publications associated with this dataset", + "items": { + "$ref": "#/$defs/Reference" + }, + "type": "array" + }, + "related_note": { + "$ref": "#/$defs/Note", + "description": "When using the \"summary\" note type, this is the free text summary or description of the dataset" + }, + "sub_series": { + "description": "If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset", + "items": { + "type": "string" + }, + "type": "array" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "htp_expression_dataset", + "name", + "category_tags", + "date_created", + "internal" + ], + "title": "HighThroughputExpressionDatasetAnnotation", + "type": "object" + }, + "HighThroughputExpressionDatasetAnnotationDTO": { + "additionalProperties": false, + "description": "A DTO entry for a published high-throughput expression dataset annotation.", + "properties": { + "category_tag_names": { + "description": "A list of controlled vocabulary terms to describe the experiment", + "items": { + "type": "string" + }, + "type": "array" + }, + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", + "type": "string" + }, + "data_provider_dto": { + "$ref": "#/$defs/DataProviderDTO", + "description": "Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "htp_expression_dataset_dto": { + "$ref": "#/$defs/ExternalDataBaseEntityDTO", + "description": "An id associated with a dataset object; these will external or MOD IDs." + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", + "type": "string" + }, + "name": { + "description": "The free text title of the dataset", + "type": "string" + }, + "note_dto": { + "$ref": "#/$defs/NoteDTO" + }, + "number_of_channels": { + "description": "For microarrays, the number of channels used; This can be one of two values: 1 or 2", + "type": "integer" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, + "reference_curies": { + "description": "External reference curies used for ingest", + "items": { + "type": "string" + }, + "type": "array" + }, + "sub_series": { + "description": "If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset", + "items": { + "type": "string" + }, + "type": "array" + }, + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + } + }, + "required": [ + "htp_expression_dataset_dto", + "name", + "category_tag_names", + "data_provider_dto", + "date_created", + "internal" + ], + "title": "HighThroughputExpressionDatasetAnnotationDTO", + "type": "object" + }, + "HighThroughputExpressionDatasetSampleAnnotation": { + "additionalProperties": false, + "description": "An entry with dataset sample object associations.", + "properties": { + "abundance": { + "description": "The free text describing the amount of sample used", + "type": "string" + }, + "assembly_versions": { + "description": "single or paired end sequencing; might be better in experiment info", + "items": { + "type": "string" + }, + "type": "array" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "curie": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "data_provider": { + "$ref": "#/$defs/DataProvider", + "description": "Object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, + "dataset_ids": { + "description": "list of primary dataset ids that a sample is associated with", + "items": { + "type": "string" + }, + "type": "array" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "expression_assay_used": { + "$ref": "#/$defs/HighThroughputExpressionAssayValues", + "description": "ID of the type of assay used for this sample; sample or experiment property? See enumeration below." + }, + "genetic_sex": { + "description": "The sex of the organism the sample came from", + "type": "string" + }, + "genomic_information": { + "$ref": "#/$defs/BioSampleGenomicInformation", + "description": "A collection of information that represents the strain or genomic background of the sample, either an id or free text" + }, + "htp_expression_sample": { + "$ref": "#/$defs/ExternalDataBaseEntity", + "description": "The dataset for this sample object" + }, + "htp_expression_sample_age": { + "$ref": "#/$defs/BioSampleAge", + "description": "a collection of terms that when used together represent the age and stage of the sample" + }, + "htp_expression_sample_locations": { + "description": "A collection of terms that when used together represents the location within an organism from which the sample was taken", + "items": { + "$ref": "#/$defs/AnatomicalSite" + }, + "type": "array" + }, + "htp_expression_sample_title": { + "description": "The free text title of the sample", + "type": "string" + }, + "htp_expression_sample_type": { + "description": "Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below.", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "microarray_sample_details": { + "$ref": "#/$defs/MicroarraySampleDetails", + "description": "collection of information that is specific for microarray samples" + }, + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, + "related_notes": { + "description": "Holds between an object and a list of related Note objects.", + "items": { + "$ref": "#/$defs/Note" + }, + "type": "array" + }, + "sequencing_format": { + "description": "single or paired end sequencing; might be better in experiment info", + "type": "string" + }, + "taxon": { + "description": "The taxon from which the biological entity derives.", + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + }, + "when_expressed_stage_name": { + "description": "A human-readable stage name. To be used when an ontology term for the relevant stage is not available.", + "type": "string" + }, + "where_expressed_statement": { + "description": "A human-readable free-text description of the anatomical location of the expression pattern.", + "type": "string" + } + }, + "required": [ + "htp_expression_sample_type", + "where_expressed_statement", + "expression_assay_used", + "dataset_ids", + "data_provider", + "internal" + ], + "title": "HighThroughputExpressionDatasetSampleAnnotation", + "type": "object" + }, + "HighThroughputExpressionDatasetSampleAnnotationDTO": { + "additionalProperties": false, + "description": "An entry with dataset sample object associations.", + "properties": { + "abundance": { + "description": "The free text describing the amount of sample used", + "type": "string" + }, + "assembly_versions": { + "description": "single or paired end sequencing; might be better in experiment info", + "items": { + "type": "string" + }, + "type": "array" + }, + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", + "type": "string" + }, + "data_provider_dto": { + "$ref": "#/$defs/DataProviderDTO", + "description": "Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, + "dataset_ids": { + "description": "list of primary dataset ids that a sample is associated with", + "items": { + "type": "string" + }, + "type": "array" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "expression_assay_curie": { + "description": "The assay used to experimentally determine gene expression.", + "type": "string" + }, + "genetic_sex": { + "description": "The sex of the organism the sample came from", + "type": "string" + }, + "genomic_information_dto": { + "$ref": "#/$defs/BioSampleGenomicInformationDTO", + "description": "A collection of information that represents the strain or genomic background of the sample, either an id or free text" + }, + "htp_expression_sample_age_dto": { + "$ref": "#/$defs/BioSampleAgeDTO", + "description": "a collection of terms that when used together represent the age and stage of the sample" + }, + "htp_expression_sample_dto": { + "$ref": "#/$defs/ExternalDataBaseEntityDTO", + "description": "The ID for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId" + }, + "htp_expression_sample_location_dtos": { + "description": "A collection of terms that when used together represents the location within an organism from which the sample was taken", + "items": { + "$ref": "#/$defs/AnatomicalSiteDTO" + }, + "type": "array" + }, + "htp_expression_sample_title": { + "description": "The free text title of the sample", + "type": "string" + }, + "htp_expression_sample_type_curie": { + "description": "Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below.", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "microarray_sample_details_dto": { + "$ref": "#/$defs/MicroarraySampleDetails", + "description": "collection of information that is specific for microarray samples" + }, + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", + "type": "string" + }, + "note_dtos": { + "items": { + "$ref": "#/$defs/NoteDTO" + }, + "type": "array" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, + "sequencing_format": { + "description": "single or paired end sequencing; might be better in experiment info", + "type": "string" }, - "type": { + "taxon": { + "description": "The taxon from which the biological entity derives.", "type": "string" }, - "updated_by": { - "description": "The individual that last modified the entity.", + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + }, + "where_expressed_statement": { + "description": "A human-readable free-text description of the anatomical location of the expression pattern.", "type": "string" } }, "required": [ - "curie", + "htp_expression_sample_title", + "htp_expression_sample_type_curie", + "where_expressed_statement", + "expression_assay_curie", + "dataset_ids", + "data_provider_dto", "internal" ], - "title": "HPTerm", + "title": "HighThroughputExpressionDatasetSampleAnnotationDTO", "type": "object" }, "Identifier": { @@ -15823,6 +16745,18 @@ }, "type": "array" }, + "high_throughput_expression_dataset_annotation_ingest_set": { + "items": { + "$ref": "#/$defs/HighThroughputExpressionDatasetAnnotationDTO" + }, + "type": "array" + }, + "high_throughput_expression_dataset_sample_annotation_ingest_set": { + "items": { + "$ref": "#/$defs/HighThroughputExpressionDatasetSampleAnnotationDTO" + }, + "type": "array" + }, "linkml_version": { "description": "Version of LinkML schema used for submitted file in the format n.n.n (e.g. 1.2.4 or 2.0.0)", "type": "string" @@ -16051,10 +16985,6 @@ "description": "middle names of a person", "type": "string" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "obsolete": { "description": "Entity is no longer current.", "type": "boolean" @@ -16078,6 +17008,10 @@ "description": "Open Researcher and Contributor ID", "type": "string" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "unique_id": { "description": "A non-curie unique identifier for a thing.", "type": "string" @@ -17027,6 +17961,78 @@ "title": "MeshDetail", "type": "object" }, + "MicroarraySampleDetails": { + "additionalProperties": false, + "description": "An entry with microarray-specific metadata", + "properties": { + "channel_id": { + "description": "for microarray experiments, channel ID", + "type": "string" + }, + "channel_number": { + "description": "for micorarray data, which channel this sample is in, 1 or 2", + "type": "integer" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "curie": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "data_provider": { + "$ref": "#/$defs/DataProvider", + "description": "Object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "mod_internal_id": { + "description": "The model organism database (MOD) internal identifier for the object", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "data_provider", + "internal" + ], + "title": "MicroarraySampleDetails", + "type": "object" + }, "ModCorpusAssociation": { "additionalProperties": false, "description": "For a given reference and Mod, whether it is inside corpus, outside corpus, or needs review, as well as where this sorting came from.", @@ -17983,10 +18989,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -17995,6 +18997,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_note": { "$ref": "#/$defs/Note", "description": "Holds between an object and a Note object." @@ -18489,10 +19495,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -18501,6 +19503,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -18573,10 +19579,6 @@ "description": "middle names of a person", "type": "string" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "obsolete": { "description": "Entity is no longer current.", "type": "boolean" @@ -18592,6 +19594,10 @@ "description": "Open Researcher and Contributor ID", "type": "string" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "unique_id": { "description": "A non-curie unique identifier for a thing.", "type": "string" @@ -18708,10 +19714,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -18735,6 +19737,10 @@ }, "type": "array" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "related_notes": { "description": "Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the \"Phenotype annotation note types\" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.", "items": { @@ -18951,10 +19957,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -18967,6 +19969,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -19024,10 +20030,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -19036,6 +20038,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "proteins": { "items": { "$ref": "#/$defs/Protein" @@ -19101,10 +20107,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -19117,6 +20119,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -19270,10 +20276,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -19282,6 +20284,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "secondary_identifiers": { "items": { "type": "string" @@ -19590,10 +20596,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -19602,6 +20604,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "secondary_identifiers": { "items": { "type": "string" @@ -19660,10 +20666,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -19672,6 +20674,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "secondary_identifiers": { "items": { "type": "string" @@ -20233,6 +21239,21 @@ "title": "SOTerm", "type": "object" }, + "SampleTypeValues": { + "description": "", + "enum": [ + "OBI:0000895", + "OBI:0000869", + "OBI:0000880", + "OBI:0000862", + "OBI:0000423", + "OBI:0000876", + "OBI:0002573", + "OBI:0002627" + ], + "title": "SampleTypeValues", + "type": "string" + }, "SecondaryIdSlotAnnotation": { "additionalProperties": false, "description": "", @@ -20396,10 +21417,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -20412,6 +21429,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -20498,10 +21519,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -20514,6 +21531,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "reference_curies": { "description": "External reference curies used for ingest", "items": { @@ -20545,7 +21566,7 @@ }, "required": [ "taxon_curie", - "mod_entity_id", + "primary_external_id", "data_provider_dto", "internal" ], @@ -20686,6 +21707,15 @@ "title": "SequenceTargetingReagentGeneAssociationDTO", "type": "object" }, + "SequencingFormatValues": { + "description": "", + "enum": [ + "single", + "paired" + ], + "title": "SequencingFormatValues", + "type": "string" + }, "SiftPredictionLevels": { "description": "", "enum": [ @@ -21114,7 +22144,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -21267,7 +22297,7 @@ "description": "", "properties": { "associated_transcript_identifiers": { - "description": "Identifiers (curie/mod_entity_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned.", + "description": "Identifiers (curie/primary_external_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned.", "items": { "type": "string" }, @@ -21365,7 +22395,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -21598,7 +22628,7 @@ "type": "string" }, "variant_identifier": { - "description": "Identifier (curie/mod_entity_id/mod_internal_id) of the variant", + "description": "Identifier (curie/primary_external_id/mod_internal_id) of the variant", "type": "string" }, "variant_sequence": { @@ -21762,10 +22792,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -21774,6 +22800,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "updated_by": { "description": "The individual that last modified the entity.", "type": "string" @@ -21822,10 +22852,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -21834,6 +22860,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "updated_by_curie": { "description": "Curie of the Person object representing the individual that updated the entity", "type": "string" @@ -22096,6 +23126,79 @@ "title": "TemporalContext", "type": "object" }, + "TemporalContextDTO": { + "additionalProperties": false, + "description": "The developmental stage and/or age of the specimen in an annotation. The developmental_stage_stop slot is optional.", + "properties": { + "age": { + "description": "The age at which an annotated event was observed.", + "type": "string" + }, + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "developmental_stage_start_curie": { + "description": "The beginning developmental stage at which an annotated event was observed.", + "type": "string" + }, + "developmental_stage_stop_curie": { + "description": "The end developmental stage at which an annotated event was observed. This is not required if the annotation applies to a single stage.", + "type": "string" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "stage_uberon_slim_term_curies": { + "description": "The high-level UBERON slim terms that apply to the developmental range of the TemporalContext component of an ExpressionPattern. The following UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON term is also allowed: post embryonic, pre-adult.", + "items": { + "type": "string" + }, + "type": "array" + }, + "temporal_qualifier_names": { + "description": "Qualifiers of the stage or age in an annotation. The range is a string representing vocabulary term", + "items": { + "type": "string" + }, + "type": "array" + }, + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + } + }, + "required": [ + "internal" + ], + "title": "TemporalContextDTO", + "type": "object" + }, "Transcript": { "additionalProperties": false, "description": "A contiguous RNA molecule representing a sequence of a genome, often the result of a DNA-dependent RNA polymerase gene transcription event", @@ -22143,10 +23246,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -22159,6 +23258,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -22312,10 +23415,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -22328,6 +23427,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -22747,10 +23850,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -22759,6 +23858,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -22967,10 +24070,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -22979,6 +24078,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "references": { "description": "holds between an object and a list of references", "items": { @@ -23088,10 +24191,6 @@ "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, - "mod_entity_id": { - "description": "The model organism database (MOD) identifier/curie for the object. Note that this may be an external identifier for an object, like a UniProt ID for a protein, but acts as the MOD's primary key for the entity.", - "type": "string" - }, "mod_internal_id": { "description": "The model organism database (MOD) internal identifier for the object", "type": "string" @@ -23106,6 +24205,10 @@ "description": "Entity is no longer current.", "type": "boolean" }, + "primary_external_id": { + "description": "The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.", + "type": "string" + }, "source_general_consequence_dtos": { "items": { "$ref": "#/$defs/VariantSourceGeneralConsequenceSlotAnnotationDTO" @@ -25344,6 +26447,18 @@ }, "type": "array" }, + "high_throughput_expression_dataset_annotation_ingest_set": { + "items": { + "$ref": "#/$defs/HighThroughputExpressionDatasetAnnotationDTO" + }, + "type": "array" + }, + "high_throughput_expression_dataset_sample_annotation_ingest_set": { + "items": { + "$ref": "#/$defs/HighThroughputExpressionDatasetSampleAnnotationDTO" + }, + "type": "array" + }, "linkml_version": { "description": "Version of LinkML schema used for submitted file in the format n.n.n (e.g. 1.2.4 or 2.0.0)", "type": "string" @@ -25446,18 +26561,18 @@ "anyOf": [ { "properties": { - "anatomical_structure": {} + "anatomical_structure_curie": {} }, "required": [ - "anatomical_structure" + "anatomical_structure_curie" ] }, { "properties": { - "cellular_component": {} + "cellular_component_curie": {} }, "required": [ - "cellular_component" + "cellular_component_curie" ] } ] diff --git a/model/schema/affectedGenomicModel.yaml b/model/schema/affectedGenomicModel.yaml index f6ba7e549..fe91b7df2 100644 --- a/model/schema/affectedGenomicModel.yaml +++ b/model/schema/affectedGenomicModel.yaml @@ -64,7 +64,7 @@ classes: - sequence_targeting_reagent_identifiers - component_dtos slot_usage: - mod_entity_id: + primary_external_id: required: true AgmSecondaryIdSlotAnnotation: @@ -177,7 +177,7 @@ slots: range: string multivalued: true description: >- - Identifiers (curie/mod_entity_id/mod_internal_id) of the STRs + Identifiers (curie/primary_external_id/mod_internal_id) of the STRs parental_populations: singular_name: parental_population diff --git a/model/schema/agent.yaml b/model/schema/agent.yaml index a63e5014d..eb51ea5bf 100644 --- a/model/schema/agent.yaml +++ b/model/schema/agent.yaml @@ -79,7 +79,7 @@ classes: - orcid - emails - old_emails - - mod_entity_id + - primary_external_id - unique_id - affiliated_alliance_member exact_mappings: diff --git a/model/schema/allele.yaml b/model/schema/allele.yaml index e06ec143a..676507daf 100644 --- a/model/schema/allele.yaml +++ b/model/schema/allele.yaml @@ -123,7 +123,7 @@ classes: slot_usage: note_dtos: notes: note_type CV 'Allele Note Type' - mod_entity_id: + primary_external_id: required: true # Some classes roughly grouped with the Allele class because they have relationships to Allele and were @@ -139,7 +139,7 @@ classes: description: >- Dummy cell line DTO class slot_usage: - mod_entity_id: + primary_external_id: required: true GenerationMethod: @@ -182,7 +182,7 @@ classes: - synonyms - secondary_identifiers slot_usage: - mod_entity_id: + primary_external_id: required: true SequenceTargetingReagentAssociation: @@ -708,7 +708,7 @@ slots: allele_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the allele + Identifier (curie/primary_external_id/mod_internal_id) of the allele range: string required: true @@ -892,7 +892,7 @@ slots: cell_line_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the cell line + Identifier (curie/primary_external_id/mod_internal_id) of the cell line range: string required: true @@ -1081,8 +1081,8 @@ slots: mutation_target_strain_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the particular strain that is targeted by the generation method - for a particular allele (MGI only) + Identifier (curie/primary_external_id/mod_internal_id) of the particular strain + that is targeted by the generation method for a particular allele (MGI only) domain: AlleleGenerationMethodAssociationDTO range: string @@ -1117,7 +1117,7 @@ slots: object_allele_identifier: description: >- - The identifier (curie/mod_entity_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation + The identifier (curie/primary_external_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation domain: AlleleAlleleAssociationDTO range: string @@ -1149,7 +1149,7 @@ slots: multivalued: false domain: SequenceTargetingReagentAssociationDTO description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the STR + Identifier (curie/primary_external_id/mod_internal_id) of the STR sequence_targeting_reagent_gene_associations: domain: SequenceTargetingReagent diff --git a/model/schema/allianceModel.yaml b/model/schema/allianceModel.yaml index 1ebb14bc1..142617bef 100644 --- a/model/schema/allianceModel.yaml +++ b/model/schema/allianceModel.yaml @@ -40,12 +40,13 @@ imports: - expression - gene - geneInteraction + - highThroughputExpression + - homology - image - ingest - - modCorpusAssociation - linkml:types + - modCorpusAssociation - ontologyTerm - - homology - phenotypeAndDiseaseAnnotation - reagent - reference diff --git a/model/schema/core.yaml b/model/schema/core.yaml index 896402727..b434f14e9 100644 --- a/model/schema/core.yaml +++ b/model/schema/core.yaml @@ -96,14 +96,14 @@ classes: Parent class for LinkML classes of submitted entities that may have a public or internal MOD ID/curie slots: - - mod_entity_id + - primary_external_id - mod_internal_id - data_provider SubmittedObjectDTO: is_a: AuditedObjectDTO slots: - - mod_entity_id + - primary_external_id - mod_internal_id - data_provider_dto @@ -1243,11 +1243,11 @@ slots: multivalued: false range: string - mod_entity_id: + primary_external_id: description: >- - The model organism database (MOD) identifier/curie for the object. Note - that this may be an external identifier for an object, like a UniProt ID - for a protein, but acts as the MOD's primary key for the entity. + The primary external (non-Alliance) database identifier/curie for the object. Note + that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID + for a protein, and may act as the MOD's/Alliance member's primary key for the entity. range: string mod_internal_id: diff --git a/model/schema/expression.yaml b/model/schema/expression.yaml index 5939c8d12..8c084cda4 100644 --- a/model/schema/expression.yaml +++ b/model/schema/expression.yaml @@ -1,4 +1,7 @@ id: https://github.com/alliance-genome/agr_persistent_schema/src/schema/expression.yaml +name: Alliance-Expression-Model +title: Alliance Expression Model +description: Alliance expression experiment and annotations imports: - affectedGenomicModel @@ -143,9 +146,9 @@ classes: AGR if not submitted by the model organism database. notes: >- Slot is inherited from Annotation class. - mod_entity_id: + primary_external_id: description: >- - The model organism database identifier/curie for the + The primary external (non-AGRKB) database identifier/curie for the ExpressionAnnotation. notes: >- Slot is inherited from Annotation class. @@ -186,6 +189,8 @@ classes: description: >- Images for the ExpressionAnnotation. required: false + when_expressed_stage_name: + required: true GeneExpressionAnnotation: is_a: ExpressionAnnotation @@ -217,7 +222,7 @@ classes: postconditions requirements in the AnatomicalSite object, though these postconditions are still not as specific as the FMS model. New required slots: relation. - New non-required slots: curie, unique_id, mod_entity_id, mod_internal_id, + New non-required slots: curie, unique_id, primary_external_id, mod_internal_id, related_notes, expression_qualifiers, negated, uncertain, related_figures, expression_annotation_image_associations, condition_relations. @@ -255,6 +260,18 @@ classes: - temporal_qualifiers - stage_uberon_slim_terms + TemporalContextDTO: + is_a: AuditedObjectDTO + description: >- + The developmental stage and/or age of the specimen in an annotation. The + developmental_stage_stop slot is optional. + slots: + - developmental_stage_start_curie + - developmental_stage_stop_curie + - age + - temporal_qualifier_names + - stage_uberon_slim_term_curies + AnatomicalSite: is_a: AuditedObject description: >- @@ -279,6 +296,30 @@ classes: required: true description: At least one of anatomical_structure or cellular_component should be populated. + AnatomicalSiteDTO: + is_a: AuditedObject + description: >- + The set of terms that define a specific anatomical site within a specimen. + slots: + - anatomical_structure_curie + - anatomical_structure_qualifier_names + - anatomical_structure_uberon_term_curies + - anatomical_substructure_curie + - anatomical_substructure_qualifier_names + - anatomical_substructure_uberon_term_curies + - cellular_component_curie + - cellular_component_qualifier_names + rules: + - postconditions: + any_of: + - slot_conditions: + anatomical_structure_curie: + required: true + - slot_conditions: + cellular_component_curie: + required: true + description: At least one of anatomical_structure_curie or cellular_component_curie should be populated. + ExpressionAnnotationAssociation: is_a: EvidenceAssociation abstract: true @@ -303,15 +344,25 @@ slots: age: description: >- The age at which an annotated event was observed. - domain: TemporalContext range: string multivalued: false anatomical_substructure: + description: >- + Primary anatomical substructure referenced within the context of an AnatomicalSite. domain: AnatomicalSite range: AnatomicalTerm multivalued: false + anatomical_substructure_curie: + description: >- + Primary anatomical substructure referenced within the context of an AnatomicalSiteDTO. The range + is any string representing an AnatomicalTerm ontology term. + domain: AnatomicalSiteDTO + range: string + multivalued: false + + # ACTION ITEM: Load needed qualifiers as Vocabulary/OntologyTerms. # ACTION ITEM: Add FlyBase qualifiers to BSPO; SCRUM-1291 (Sian). # ACTION ITEM: Submit FB qualifiers with FBcv curies as OntologyTerms, @@ -323,6 +374,13 @@ slots: range: VocabularyTerm multivalued: true + anatomical_substructure_qualifier_names: + notes: >- + See the spatial_qualifier_set enum at the bottom of this file for terms. + domain: AnatomicalSiteDTO + range: string + multivalued: true + # DQM NOTE: Leave empty instead of submitting Other if no terms apply. anatomical_substructure_uberon_terms: description: >- @@ -340,14 +398,43 @@ slots: Use of a placeholder term, Other, is no longer required or allowed. domain: AnatomicalSite range: UBERONTerm - required: False + required: false + multivalued: true + + anatomical_substructure_uberon_term_curies: + description: >- + String representations of UBERON slim terms that apply to the anatomical substructure. + notes: >- + Allowable terms: UBERON:0001009, UBERON:0005409, UBERON:0000949, + UBERON:0001008, UBERON:0002330, UBERON:0002193, + UBERON:0002416, UBERON:0002423, UBERON:0002204, + UBERON:0001016, UBERON:0000990, UBERON:0001004, + UBERON:0001032, UBERON:0005726, UBERON:0007037, + UBERON:0002105, UBERON:0002104, UBERON:0000924, + UBERON:0000925, UBERON:0000926, UBERON:0003104, + UBERON:0001013, UBERON:0000026, UBERON:0016887, + UBERON:6005023, UBERON:0002539 + Use of a placeholder term, Other, is no longer required or allowed. + domain: AnatomicalSiteDTO + range: string + required: false multivalued: true anatomical_structure: + description: >- + The primary anatomical structure referred to within the context of an AnatomicalSite object. domain: AnatomicalSite range: AnatomicalTerm multivalued: false + anatomical_structure_curie: + description: >- + The primary anatomical structure referred to within the context of an AnatomicalSite object. The range + is any string representing an AnatomicalTerm ontology term + domain: AnatomicalSiteDTO + range: string + multivalued: false + # ACTION ITEM: Load needed qualifiers as Vocabulary/OntologyTerms. anatomical_structure_qualifiers: notes: >- @@ -356,6 +443,13 @@ slots: range: VocabularyTerm multivalued: true + anatomical_structure_qualifier_names: + notes: >- + See the spatial_qualifier_set enum at the bottom of this file for terms. + domain: AnatomicalSiteDTO + range: string + multivalued: true + # DQM NOTE: Leave empty instead of submitting Other if no terms apply. anatomical_structure_uberon_terms: description: >- @@ -376,18 +470,57 @@ slots: required: False multivalued: true + anatomical_structure_uberon_term_curies: + description: >- + UBERON slim terms that apply to the anatomical structure. + notes: >- + Allowable terms: UBERON:0001009, UBERON:0005409, UBERON:0000949, + UBERON:0001008, UBERON:0002330, UBERON:0002193, + UBERON:0002416, UBERON:0002423, UBERON:0002204, + UBERON:0001016, UBERON:0000990, UBERON:0001004, + UBERON:0001032, UBERON:0005726, UBERON:0007037, + UBERON:0002105, UBERON:0002104, UBERON:0000924, + UBERON:0000925, UBERON:0000926, UBERON:0003104, + UBERON:0001013, UBERON:0000026, UBERON:0016887, + UBERON:6005023, UBERON:0002539 + Use of a placeholder term, Other, is no longer required or allowed. + domain: AnatomicalSiteDTO + range: string + required: False + multivalued: true + expression_assay_used: description: >- The assay used to experimentally determine gene expression. range: MMOTerm required: true + expression_assay_curie: + description: >- + The assay used to experimentally determine gene expression. + range: string + required: true + cellular_component: + description: >- + The primary cellular component referred to within the context of an AnatomicalSite object. notes: >- I would like to restrict the range to GOTerm in cellular_component branch, but I'm not sure how to do this. domain: AnatomicalSite range: GOTerm + multivalued: false + + cellular_component_curie: + description: >- + The primary cellular component referred to within the context of an AnatomicalSite object. The range + is any string representing a GOTerm ontology term + notes: >- + I would like to restrict the range to GOTerm in cellular_component + branch, but I'm not sure how to do this. + domain: AnatomicalSiteDTO + range: string + multivalued: false # ACTION ITEM: Load needed qualifiers as Vocabulary/OntologyTerms. cellular_component_qualifiers: @@ -395,6 +528,11 @@ slots: range: VocabularyTerm multivalued: true + cellular_component_qualifier_names: + domain: AnatomicalSiteDTO + range: string + multivalued: true + developmental_stage_start: description: >- The beginning developmental stage at which an annotated event was observed. @@ -406,6 +544,17 @@ slots: multivalued: false required: false + developmental_stage_start_curie: + description: >- + The beginning developmental stage at which an annotated event was observed. + notes: >- + Currently, we limit this to a single stage, but we could consider allowing + for stage ranges for a single annotation. + domain: TemporalContextDTO + range: string + multivalued: false + required: false + developmental_stage_stop: description: >- The end developmental stage at which an annotated event was observed. @@ -418,6 +567,18 @@ slots: multivalued: false required: false + developmental_stage_stop_curie: + description: >- + The end developmental stage at which an annotated event was observed. + This is not required if the annotation applies to a single stage. + notes: >- + Currently, we limit this to a single stage, but we could consider allowing + for stage ranges for a single annotation. + domain: TemporalContextDTO + range: string + multivalued: false + required: false + entity_assayed: description: >- The subject of the ExpressionExperiment. This will usually be a Gene, but @@ -495,6 +656,15 @@ slots: range: VocabularyTerm multivalued: true + temporal_qualifier_names: + description: >- + Qualifiers of the stage or age in an annotation. The range is a string representing vocabulary term + notes: >- + See the temporal_qualifier_set enum at the bottom of this file for terms. + domain: TemporalContextDTO + range: string + multivalued: true + # ACTION ITEM: Create one Vocabulary term for: post embryonic, pre-adult. # ACTION ITEM: Make VocabularyTerms that map to the UBERONTerms for now. # ACTION ITEM: Ask UBERON to make the missing term (and wait). @@ -513,6 +683,21 @@ slots: range: VocabularyTerm multivalued: true + stage_uberon_slim_term_curies: + description: >- + The high-level UBERON slim terms that apply to the developmental range + of the TemporalContext component of an ExpressionPattern. The following + UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON + term is also allowed: post embryonic, pre-adult. + notes: >- + FMS submission allowed for a string due to absence of appropriate UBERON + term. This term must, for example, cover Drosophila larval and pupal + stages (there are UBERON terms for each, but not a single term spanning + both developmental phases). + domain: TemporalContextDTO + range: string + multivalued: true + when_expressed: description: >- When some entity is observed to be present in a specimen. If no temporal @@ -529,10 +714,8 @@ slots: relevant stage is not available. notes: >- Corresponds to whenExpressed.stageName in frozen JSON schema. - domain: ExpressionAnnotation range: string multivalued: false - required: true where_expressed: description: >- diff --git a/model/schema/gene.yaml b/model/schema/gene.yaml index ad07a3f71..9b8adccbd 100644 --- a/model/schema/gene.yaml +++ b/model/schema/gene.yaml @@ -85,7 +85,7 @@ classes: - WB - ZFIN slot_usage: - mod_entity_id: + primary_external_id: required: true related_notes: description: >- @@ -106,7 +106,7 @@ classes: - gene_type_curie - note_dtos slot_usage: - mod_entity_id: + primary_external_id: required: true GeneSymbolSlotAnnotation: @@ -394,7 +394,7 @@ slots: gene_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the gene + Identifier (curie/primary_external_id/mod_internal_id) of the gene range: string required: true diff --git a/model/schema/geneInteraction.yaml b/model/schema/geneInteraction.yaml index d457bb0e4..c79882b6e 100644 --- a/model/schema/geneInteraction.yaml +++ b/model/schema/geneInteraction.yaml @@ -376,7 +376,7 @@ slots: range: string object_gene_identifier: - description: Identifier (curie/mod_entity_id/mod_internal_id) of the object gene in a gene-to-gene association + description: Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association domain: GeneGeneAssociationDTO range: string required: true @@ -388,7 +388,7 @@ slots: range: string # should eventually be updated to the Phenotype class subject_gene_identifier: - description: Identifier (curie/mod_entity_id/mod_internal_id) of the subject gene in a gene-to-gene association + description: Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association domain: GeneGeneAssociationDTO range: string required: true diff --git a/model/schema/highThroughputExpression.yaml b/model/schema/highThroughputExpression.yaml new file mode 100644 index 000000000..20c685774 --- /dev/null +++ b/model/schema/highThroughputExpression.yaml @@ -0,0 +1,603 @@ +id: https://github.com/alliance-genome/agr_persistent_schema/src/schema/highThroughputExpression.yaml +name: High-Throughput-Expression-Dataset-Annotation +title: High Throughput Expression Dataset Annotation +description: Annotations for high-throughput gene expression experiments and datasets + +imports: + - core + - expression + - allele + - affectedGenomicModel + - linkml:types + +prefixes: + alliance: 'http://alliancegenome.org/' + linkml: 'https://w3id.org/linkml/' + gff: 'https://w3id.org/gff' + faldo: 'http://biohackathon.org/resource/faldo#' + biolink: 'https://w3id.org/biolink/vocab/' + NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=' + schema: 'http://schema.org/' + dct: 'http://purl.org/dc/terms/' + WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:' + obograph: 'https://github.com/biodatamodels/obograph' + +default_prefix: alliance +default_range: string + +default_curi_maps: + - obo_context + - idot_context + - semweb_context + - monarch_context + +emit_prefixes: + - rdf + - rdfs + - xsd + - owl + + +classes: + + HighThroughputExpressionDatasetAnnotation: + is_a: AuditedObject + description: >- + An entry for a published high-throughput expression dataset annotation. + slots: + - htp_expression_dataset # datasetId in agr_schemas datasetAnnotation.json + - name # title in agr_schemas datasetAnnotation.json + - references # publications in agr_schemas datasetAnnotation.json + - related_note # use 'summary' note type; summary in agr_schemas datasetAnnotation.json + - number_of_channels # numChannels in agr_schemas datasetAnnotation.json + - sub_series # subSeries in agr_schemas datasetAnnotation.json + - category_tags # categoryTags in agr_schemas datasetAnnotation.json + slot_usage: + htp_expression_dataset: + required: true + name: + description: >- + The free text title of the dataset + required: true + date_created: + required: true + related_note: + description: >- + When using the "summary" note type, this is the free text summary or description of the dataset + references: + description: >- + The list of publications associated with this dataset + + HighThroughputExpressionDatasetAnnotationDTO: + is_a: SubmittedObjectDTO + description: >- + A DTO entry for a published high-throughput expression dataset annotation. + slots: + - htp_expression_dataset_dto # datasetId in agr_schemas datasetAnnotation.json + - name # title in agr_schemas datasetAnnotation.json + - reference_curies # publications in agr_schemas datasetAnnotation.json + - note_dto # use 'summary' note type; summary in agr_schemas datasetAnnotation.json + - number_of_channels # numChannels in agr_schemas datasetAnnotation.json + - sub_series # subSeries in agr_schemas datasetAnnotation.json + - category_tag_names # categoryTags in agr_schemas datasetAnnotation.json + slot_usage: + htp_expression_dataset_dto: + description: >- + An id associated with a dataset object; these will external or MOD IDs. + required: true + name: + description: >- + The free text title of the dataset + required: true + date_created: + required: true + related_note: + description: >- + When using the "summary" note type, this is the free text summary or description of the dataset + references: + description: >- + The list of publications associated with this dataset + + HighThroughputExpressionDatasetSampleAnnotation: + is_a: SubmittedObject + description: >- + An entry with dataset sample object associations. + slots: + - htp_expression_sample # sampleId in agr_schemas json + - htp_expression_sample_title # sampleTitle in agr_schemas json + - htp_expression_sample_type # sampleType in agr_schemas json + - htp_expression_sample_age # sampleAge in agr_schemas json + - htp_expression_sample_locations # sampleLocations in agr_schemas json + - where_expressed_statement # whereExpressedStatement in whereExpressed.json + - abundance # abundance in agr_schemas json + - genomic_information # genomicInformation in agr_schemas json + - taxon # taxonId in agr_schemas json + - genetic_sex # sex in agr_schemas json + - expression_assay_used # assayType in agr_schemas json + - sequencing_format # sequencingFormat in agr_schemas json + - assembly_versions # assemblyVersions in agr_schemas json + - related_notes # notes in agr_schemas json + - dataset_ids # datasetIds in agr_schemas json + - microarray_sample_details # microarraySampleDetails in agr_schemas json + - when_expressed_stage_name # biosampleAge.json > stage > when_expressed.json > stageName in agr_schemas json + slot_usage: + htp_expression_sample: + description: >- + The dataset for this sample object + genetic_sex: + description: >- + The sex of the organism the sample came from + expression_assay_used: + description: >- + ID of the type of assay used for this sample; sample or experiment property? See enumeration below. + range: high_throughput_expression_assay_values + required: true + dataset_ids: + required: true + htp_expression_sample_type: + required: true + rules: + - postconditions: + any_of: + - slot_conditions: + htp_expression_sample: + required: true + - slot_conditions: + htp_expression_sample_title: + required: true + description: >- + At least htp_expression_sample_id, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated OR + at least htp_expression_sample_title, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated + + HighThroughputExpressionDatasetSampleAnnotationDTO: + is_a: SubmittedObjectDTO + description: >- + An entry with dataset sample object associations. + slots: + - htp_expression_sample_dto # sampleId in agr_schemas json + - htp_expression_sample_title # sampleTitle in agr_schemas json + - htp_expression_sample_type_curie # sampleType in agr_schemas json + - htp_expression_sample_age_dto # sampleAge in agr_schemas json + - htp_expression_sample_location_dtos # sampleLocations in agr_schemas json + - where_expressed_statement # whereExpressedStatement in whereExpressed.json + - abundance # abundance in agr_schemas json + - genomic_information_dto # genomicInformation in agr_schemas json + - taxon # taxonId in agr_schemas json + - genetic_sex # sex in agr_schemas json + - expression_assay_curie # assayType in agr_schemas json + - sequencing_format # sequencingFormat in agr_schemas json + - assembly_versions # assemblyVersions in agr_schemas json + - note_dtos # notes in agr_schemas json + - dataset_ids # datasetIds in agr_schemas json + - microarray_sample_details_dto # microarraySampleDetails in agr_schemas json + slot_usage: + htp_expression_sample_dto: + description: >- + The ID for this sample object, MOD or external database ID (ex: GEO); + primaryId and secondaryId + genetic_sex: + description: >- + The sex of the organism the sample came from + expression_assay_used: + description: >- + ID of the type of assay used for this sample; sample or experiment property? See enumeration below. + range: high_throughput_expression_assay_values + required: true + htp_expression_sample_title: + required: true + dataset_ids: + required: true + htp_expression_sample_type_curie: + required: true + rules: + - postconditions: + any_of: + - slot_conditions: + htp_expression_sample_dto: + required: true + - slot_conditions: + htp_expression_sample_title: + required: true + description: >- + At least htp_expression_sample_id, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated OR + at least htp_expression_sample_title, dataset_ids, expression_assay_used, and htp_expression_sample_type should be populated + + ExternalDataBaseEntity: # htpId.json in agr_schemas + is_a: CurieObject + description: >- + A local database entry representing an external database entry; + used currently for datasets or dataset samples; htpId.json in agr_schemas json + slots: + - secondary_identifiers # alternateIds in agr_schemas htpId.json + - preferred_cross_reference # preferredCrossReference in agr_schemas htpId.json + - cross_references # crossReferences in agr_schemas htpId.json + slot_usage: + curie: # primaryId in agr_schemas htpId.json + description: >- + The ID from the data provider for the dataset. When available, this is the GEO ID. + When no GEO ID is available, it will be the ArrayExpress ID. When these both are + unavailable, it will be the MOD ID. + secondary_identifiers: + description: >- + list of optional cross reference ids to the primary dataset id. + preferred_cross_reference: + description: >- + The cross reference to the preferred page to link to in search + cross_references: + description: >- + Optional cross references to the MOD sample or dataset page. + + ExternalDataBaseEntityDTO: # htpId.json in agr_schemas + is_a: AuditedObjectDTO + description: >- + DTO entity for a local database entry representing an external database entry; + used currently for datasets or dataset samples; htpId.json in agr_schemas json + slots: + - curie # primaryId in agr_schemas htpId.json + - secondary_identifiers # alternateIds in agr_schemas htpId.json + - preferred_cross_reference_dto # preferredCrossReference in agr_schemas htpId.json + - cross_reference_dtos # crossReferences in agr_schemas htpId.json + slot_usage: + curie: + description: >- + The ID from the data provider for the dataset. When available, this is the GEO ID. + When no GEO ID is available, it will be the ArrayExpress ID. When these both are + unavailable, it will be the MOD ID. + secondary_identifiers: + description: >- + list of optional cross reference ids to the primary dataset id. + preferred_cross_reference_dto: + description: >- + The cross reference to the preferred page to link to in search + cross_reference_dtos: + description: >- + Optional cross references to the MOD sample or dataset page. + + MicroarraySampleDetails: + is_a: SubmittedObject + description: >- + An entry with microarray-specific metadata + slots: + - channel_id # channelId in agr_schemas json + - channel_number # channelNum in agr_schemas json + + BioSampleAge: + is_a: SubmittedObject + description: >- + An object that holds the temporal aspect of a sample. + slots: + - stage + - age + - when_expressed_stage_name + slot_usage: + age: + description: free text for the age of the sample + + BioSampleAgeDTO: + is_a: SubmittedObjectDTO + description: >- + An object that holds the temporal aspect of a sample. + slots: + - stage_dto + - age + - when_expressed_stage_name + slot_usage: + age: + description: free text for the age of the sample + + BioSampleGenomicInformation: + description: >- + A basic entry for defining a biosample's genomic information + slots: + - biosample_allele + - biosample_agm + - biosample_agm_type + - biosample_text + rules: + - postconditions: + any_of: + - slot_conditions: + biosample_text: + required: true + - slot_conditions: + biosample_allele: + required: true + - slot_conditions: + biosample_agm: + required: true + description: >- + Either biosample_text, biosample_allele or biosample_agm are required + + BioSampleGenomicInformationDTO: + description: >- + A basic (DTO) entry for defining a biosample's genomic information + slots: + - allele_identifier + - agm_identifier + - biosample_agm_type_name + - biosample_text + rules: + - postconditions: + any_of: + - slot_conditions: + biosample_text: + required: true + - slot_conditions: + allele_identifier: + required: true + - slot_conditions: + agm_identifier: + required: true + description: >- + Either biosample_text, allele_identifier or agm_identifier are required + +slots: + + abundance: # abundance in agr_schemas json + description: >- + The free text describing the amount of sample used + domain: HighThroughputExpressionDatasetSampleAnnotation + range: string + + assembly_versions: # assemblyVersions in agr_schemas json + description: >- + single or paired end sequencing; might be better in experiment info + domain: HighThroughputExpressionDatasetSampleAnnotation + range: string + multivalued: true + + biosample_agm: + description: >- + An affected genomic model (AGM) from which a biosample has been derived + range: AffectedGenomicModel + + biosample_agm_type: + description: >- + Indicates the type of AGM biosample; enum: fish, genotype, strain + domain: BioSampleGenomicInformation + range: VocabularyTerm + + biosample_agm_type_name: + description: >- + Indicates the type of AGM biosample; enum: fish, genotype, strain + domain: BioSampleGenomicInformationDTO + range: string + + biosample_allele: + description: >- + An allele of focus for a particular biosample + range: Allele + + biosample_text: + description: >- + The free text of the biosample genomic information if no biosample is available + domain: BioSampleGenomicInformation + range: string + + category_tags: + description: >- + A list of controlled vocabulary terms to describe the experiment + domain: HighThroughputExpressionDatasetAnnotation + range: VocabularyTerm + multivalued: true + required: true + + category_tag_names: + description: >- + A list of controlled vocabulary terms to describe the experiment + domain: HighThroughputExpressionDatasetAnnotationDTO + range: string + multivalued: true + required: true + + channel_id: # channelId in agr_schemas json + description: >- + for microarray experiments, channel ID + domain: MicroarraySampleDetails + range: string + multivalued: false + + channel_number: # channelNum in agr_schemas json + description: >- + for micorarray data, which channel this sample is in, 1 or 2 + domain: MicroarraySampleDetails + range: integer # enum [1,2] + multivalued: false + + dataset_ids: # datasetIds in agr_schemas datasetSampleAnnotation.json + description: >- + list of primary dataset ids that a sample is associated with + domain: HighThroughputExpressionDatasetSampleAnnotation + range: uriorcurie + multivalued: true + + genomic_information: # genomicInformation in agr_schemas datasetSampleAnnotation.json + description: >- + A collection of information that represents the strain or genomic background of the sample, either an id or free text + domain: HighThroughputExpressionDatasetSampleAnnotation + range: BioSampleGenomicInformation + + genomic_information_dto: # genomicInformation in agr_schemas datasetSampleAnnotation.json + description: >- + A collection of information that represents the strain or genomic background of the sample, either an id or free text + inlined: true + domain: HighThroughputExpressionDatasetSampleAnnotation + range: BioSampleGenomicInformationDTO + + htp_expression_dataset: # datasetId in agr_schemas datasetAnnotation.json + description: >- + A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json + range: ExternalDataBaseEntity + multivalued: false + + htp_expression_dataset_dto: # datasetId in agr_schemas datasetAnnotation.json + description: >- + A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json + inlined: true + range: ExternalDataBaseEntityDTO + multivalued: false + + htp_expression_sample_age: # sampleAge in agr_schemas json + description: >- + a collection of terms that when used together represent the age and stage of the sample + domain: HighThroughputExpressionDatasetSampleAnnotation + range: BioSampleAge + + htp_expression_sample_age_dto: # sampleAge in agr_schemas json + description: >- + a collection of terms that when used together represent the age and stage of the sample + inlined: true + domain: HighThroughputExpressionDatasetSampleAnnotationDTO + range: BioSampleAgeDTO + + htp_expression_sample: + description: >- + The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId + domain: HighThroughputExpressionDatasetSampleAnnotation + range: ExternalDataBaseEntity + multivalued: false + required: false + + htp_expression_sample_dto: + description: >- + The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId + inlined: true + domain: HighThroughputExpressionDatasetSampleAnnotationDTO + range: ExternalDataBaseEntityDTO + multivalued: false + required: false + + htp_expression_sample_locations: # sampleLocations in agr_schemas json + description: >- + A collection of terms that when used together represents the location within an organism from which the sample was taken + domain: HighThroughputExpressionDatasetSampleAnnotation + range: AnatomicalSite + multivalued: true + + htp_expression_sample_location_dtos: # sampleLocations in agr_schemas json + description: >- + A collection of terms that when used together represents the location within an organism from which the sample was taken + inlined: true + inlined_as_list: true + domain: HighThroughputExpressionDatasetSampleAnnotationDTO + range: AnatomicalSiteDTO + multivalued: true + + htp_expression_sample_title: # sampleTitle in agr_schemas json + description: >- + The free text title of the sample + domain: HighThroughputExpressionDatasetSampleAnnotation + range: string + + htp_expression_sample_type: # sampleType in agr_schemas json + description: >- + Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below. + domain: HighThroughputExpressionDatasetSampleAnnotation + range: OBITerm + required: true + + htp_expression_sample_type_curie: # sampleType in agr_schemas json + description: >- + Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below. + domain: HighThroughputExpressionDatasetSampleAnnotationDTO + range: string + required: true + + microarray_sample_details: # microarraySampleDetails in agr_schemas datasetSampleAnnotation.json + description: >- + collection of information that is specific for microarray samples + domain: HighThroughputExpressionDatasetSampleAnnotation + range: MicroarraySampleDetails + + microarray_sample_details_dto: # microarraySampleDetails in agr_schemas datasetSampleAnnotation.json + description: >- + collection of information that is specific for microarray samples + inlined: true + domain: HighThroughputExpressionDatasetSampleAnnotation + range: MicroarraySampleDetails + + number_of_channels: + description: >- + For microarrays, the number of channels used; This can be one of two values: 1 or 2 + domain: HighThroughputExpressionDatasetAnnotation + range: integer + multivalued: false + required: false + # TO DO from agr_schemas: need to make required for microarray assays + + preferred_cross_reference: + description: >- + cross reference to the preferred page to link to in search + domain: ExternalDataBaseEntity + range: CrossReference + multivalued: false + required: false + + preferred_cross_reference_dto: + description: >- + cross reference to the preferred page to link to in search + inlined: true + domain: ExternalDataBaseEntityDTO + range: CrossReferenceDTO + multivalued: false + required: false + + sequencing_format: # sequencingFormat in agr_schemas json + description: >- + single or paired end sequencing; might be better in experiment info + domain: HighThroughputExpressionDatasetSampleAnnotation + range: VocabularyTerm # accepted values: 'single' OR 'paired' + + stage: + description: >- + The life stage of an organism or biosample as expressed by a TemporalContext entity + domain: BioSampleAge + range: TemporalContext + + stage_dto: + description: >- + The life stage of an organism or biosample as expressed by a TemporalContext entity + inlined: true + domain: BioSampleAgeDTO + range: TemporalContextDTO + + sub_series: + description: >- + If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset + domain: HighThroughputExpressionDatasetAnnotation + range: uriorcurie + multivalued: true + required: false + + +enums: + +# For enumerations below, I don't know if we need to establish an ontology subset vocabulary as we do for +# disease annotation evidence codes (CG 2024-06-26) + + sample_type_values: + permissible_values: + OBI:0000895: + OBI:0000869: + OBI:0000880: + OBI:0000862: + OBI:0000423: + OBI:0000876: + OBI:0002573: + OBI:0002627: + + sequencing_format_values: + permissible_values: + single: + paired: + + high_throughput_expression_assay_values: + permissible_values: + MMO:0000659: + MMO:0000648: + MMO:0000650: + MMO:0000649: + MMO:0000664: + MMO:0000666: + MMO:0000000: + MMO:0000862: diff --git a/model/schema/ingest.yaml b/model/schema/ingest.yaml index 78719f538..da96368ec 100644 --- a/model/schema/ingest.yaml +++ b/model/schema/ingest.yaml @@ -330,6 +330,20 @@ slots: mixins: - object_set + high_throughput_expression_dataset_annotation_ingest_set: + domain: Ingest + range: HighThroughputExpressionDatasetAnnotationDTO + multivalued: true + mixins: + - object_set + + high_throughput_expression_dataset_sample_annotation_ingest_set: + domain: Ingest + range: HighThroughputExpressionDatasetSampleAnnotationDTO + multivalued: true + mixins: + - object_set + object_set: mixin: true domain: Ingest @@ -384,3 +398,5 @@ classes: - chromosome_ingest_set - genome_assembly_ingest_set - assembly_component_ingest_set + - high_throughput_expression_dataset_annotation_ingest_set + - high_throughput_expression_dataset_sample_annotation_ingest_set diff --git a/model/schema/phenotypeAndDiseaseAnnotation.yaml b/model/schema/phenotypeAndDiseaseAnnotation.yaml index 19080fa7b..029fb2031 100644 --- a/model/schema/phenotypeAndDiseaseAnnotation.yaml +++ b/model/schema/phenotypeAndDiseaseAnnotation.yaml @@ -58,7 +58,7 @@ classes: slots: - curie - unique_id - - mod_entity_id + - primary_external_id - mod_internal_id - condition_relations - related_notes @@ -74,7 +74,7 @@ classes: Ingest class for an annotation slots: - mod_internal_id - - mod_entity_id + - primary_external_id - note_dtos - data_provider_dto - condition_relation_dtos @@ -265,9 +265,9 @@ classes: Unique identifier for the disease annotation. Will be generated at AGR if not submitted by the MOD. required: false - mod_entity_id: + primary_external_id: description: >- - The model organism database (MOD) identifier/curie for the disease annotation. Currently only + The primary external (non-AGRKB) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. "WBDOannot00000907" required: false mod_internal_id: @@ -396,7 +396,6 @@ classes: - inferred_gene_identifier - asserted_gene_identifiers - AGMDiseaseAnnotation: description: >- An annotation asserting an association between an AGM and a disease @@ -590,7 +589,7 @@ slots: asserted_allele_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the allele to which something is manually asserted to be + Identifier (curie/primary_external_id/mod_internal_id) of the allele to which something is manually asserted to be associated range: string @@ -603,7 +602,7 @@ slots: asserted_gene_identifiers: description: >- - Identifiers (curie/mod_entity_id/mod_internal_id) of the gene(s) to which something is manually asserted to be + Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated range: string multivalued: true @@ -744,7 +743,7 @@ slots: multivalued: true disease_genetic_modifier_identifiers: - description: Identifiers (curie/mod_entity_id/mod_internal_id) of BiologcalEntity that modifies the disease model + description: Identifiers (curie/primary_external_id/mod_internal_id) of BiologcalEntity that modifies the disease model domain: DiseaseAnnotationDTO range: string multivalued: true @@ -803,7 +802,7 @@ slots: inferred_gene_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of gene to which something is inferred to be associated via an + Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline range: string @@ -814,7 +813,7 @@ slots: inferred_allele_identifier: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of allele to which something is inferred to be associated via an + Identifier (curie/primary_external_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline range: string @@ -850,7 +849,7 @@ slots: range: AffectedGenomicModel sgd_strain_background_identifier: - description: Identifier (curie/mod_entity_id/mod_internal_id) of SGD strain background AGM + description: Identifier (curie/primary_external_id/mod_internal_id) of SGD strain background AGM domain: GeneDiseaseAnnotationDTO range: string @@ -862,7 +861,7 @@ slots: with_gene_identifiers: description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of genes + Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8 range: string multivalued: true diff --git a/model/schema/reagent.yaml b/model/schema/reagent.yaml index 336cae2d1..c43773ab6 100644 --- a/model/schema/reagent.yaml +++ b/model/schema/reagent.yaml @@ -57,7 +57,7 @@ classes: - secondary_identifiers slot_usage: mod_internal_id: - notes: This is required if mod_entity_id is not submitted + notes: This is required if primary_external_id is not submitted Antibody: is_a: Reagent @@ -325,7 +325,7 @@ slots: antibody_target_gene_identifiers: description: >- - Identifiers (curie/mod_entity_id/mod_internal_id) of the genes whose gene + Identifiers (curie/primary_external_id/mod_internal_id) of the genes whose gene products are recognized by the antibody. required: false multivalued: true diff --git a/model/schema/variantDTO.yaml b/model/schema/variantDTO.yaml index d0ebc6fc5..3d4f5a978 100644 --- a/model/schema/variantDTO.yaml +++ b/model/schema/variantDTO.yaml @@ -152,7 +152,7 @@ classes: slots: associated_transcript_identifiers: description: >- - Identifiers (curie/mod_entity_id/mod_internal_id) of transcript(s) associated + Identifiers (curie/primary_external_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned. required: false multivalued: true @@ -203,7 +203,7 @@ slots: variant_identifier: is_a: genomic_entity_identifier description: >- - Identifier (curie/mod_entity_id/mod_internal_id) of the variant + Identifier (curie/primary_external_id/mod_internal_id) of the variant required: true variant_status_name: diff --git a/test/data/agm_test.json b/test/data/agm_test.json index b5721b3b7..c44aa9119 100644 --- a/test/data/agm_test.json +++ b/test/data/agm_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "agm_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-FISH-200601-1", + "primary_external_id": "ZFIN:ZDB-FISH-200601-1", "taxon_curie": "NCBITaxon:7955", "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", @@ -35,7 +35,7 @@ } }, { - "mod_entity_id": "ZFIN:ZDB-FISH-150901-28778", + "primary_external_id": "ZFIN:ZDB-FISH-150901-28778", "taxon_curie": "NCBITaxon:7955", "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", diff --git a/test/data/allele_association_ingest_test.json b/test/data/allele_association_ingest_test.json index 3cc74b3cb..5f9e96335 100644 --- a/test/data/allele_association_ingest_test.json +++ b/test/data/allele_association_ingest_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "allele_ingest_set": [ { - "mod_entity_id": "WB:WBVar00000001", + "primary_external_id": "WB:WBVar00000001", "allele_symbol_dto": { "name_type_name": "nomenclature_symbol", "format_text": "a83", diff --git a/test/data/allele_slot_annotation_ingest_test.json b/test/data/allele_slot_annotation_ingest_test.json index 6b23fb68b..0a0501f75 100644 --- a/test/data/allele_slot_annotation_ingest_test.json +++ b/test/data/allele_slot_annotation_ingest_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "allele_ingest_set": [ { - "mod_entity_id": "WB:WBVar00000001", + "primary_external_id": "WB:WBVar00000001", "allele_symbol_dto": { "name_type_name": "nomenclature_symbol", "format_text": "wg1", diff --git a/test/data/allele_test.json b/test/data/allele_test.json index 3dfd504b1..e37f0d838 100644 --- a/test/data/allele_test.json +++ b/test/data/allele_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "allele_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-ALT-130621-1", + "primary_external_id": "ZFIN:ZDB-ALT-130621-1", "data_provider_dto": { "source_organization_abbreviation": "ZFIN", "cross_reference_dto": { @@ -51,7 +51,7 @@ ] }, { - "mod_entity_id": "ZFIN:ZDB-ALT-130411-947", + "primary_external_id": "ZFIN:ZDB-ALT-130411-947", "data_provider_dto": { "source_organization_abbreviation": "ZFIN", "cross_reference_dto": { @@ -91,7 +91,7 @@ } }, { - "mod_entity_id": "WB:WBTransgene00023682", + "primary_external_id": "WB:WBTransgene00023682", "data_provider_dto": { "source_organization_abbreviation": "WB", "cross_reference_dto": { diff --git a/test/data/antibody_test.json b/test/data/antibody_test.json index 595d407eb..ef5fd8879 100644 --- a/test/data/antibody_test.json +++ b/test/data/antibody_test.json @@ -6,7 +6,7 @@ "updated_by_curie": "WB:WBPerson123", "internal": false, "obsolete": false, - "mod_entity_id": "WB:WBAntibody123", + "primary_external_id": "WB:WBAntibody123", "cross_reference_dtos": [ { "internal": false, diff --git a/test/data/assembly_component_test.json b/test/data/assembly_component_test.json index 950a90366..d6b87c7bb 100644 --- a/test/data/assembly_component_test.json +++ b/test/data/assembly_component_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "assembly_component_ingest_set": [ { - "mod_entity_id": "WB:W02C12", + "primary_external_id": "WB:W02C12", "taxon_curie": "NCBITaxon:6239", "created_by_curie": "WB:WBPerson2987", "updated_by_curie": "WB:WBPerson2987", diff --git a/test/data/construct_test.json b/test/data/construct_test.json index f0f9a9e97..30ac57f31 100644 --- a/test/data/construct_test.json +++ b/test/data/construct_test.json @@ -6,7 +6,7 @@ "updated_by_curie": "WB:WBPerson123", "internal": false, "obsolete": false, - "mod_entity_id": "WB:WBConstruct123", + "primary_external_id": "WB:WBConstruct123", "construct_symbol_dto": { "name_type_name": "nomenclature_symbol", "format_text": "const123", diff --git a/test/data/gene_test.json b/test/data/gene_test.json index f7b1007e6..661ed9eae 100644 --- a/test/data/gene_test.json +++ b/test/data/gene_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "gene_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-GENE-010226-1", + "primary_external_id": "ZFIN:ZDB-GENE-010226-1", "data_provider_dto": { "source_organization_abbreviation": "ZFIN", "cross_reference_dto": { diff --git a/test/data/genome_assembly_test.json b/test/data/genome_assembly_test.json index bcce296be..cf9c3aa4b 100644 --- a/test/data/genome_assembly_test.json +++ b/test/data/genome_assembly_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "genome_assembly_ingest_set": [ { - "mod_entity_id": "WB:WBcel235", + "primary_external_id": "WB:WBcel235", "taxon_curie": "NCBITaxon:6239", "created_by_curie": "WB:WBPerson2987", "updated_by_curie": "WB:WBPerson2987", diff --git a/test/data/high_throughput_expression_test.json b/test/data/high_throughput_expression_test.json new file mode 100644 index 000000000..3c938b1a2 --- /dev/null +++ b/test/data/high_throughput_expression_test.json @@ -0,0 +1,9 @@ +{ + "linkml_version": "2.4.0", + "high_throughput_expression_dataset_annotation_ingest_set": [ + + ], + "high_throughput_expression_dataset_sample_annotation_ingest_set": [ + + ] +} \ No newline at end of file diff --git a/test/data/invalid/allele_invalid.json b/test/data/invalid/allele_invalid.json index 7f88809aa..a336ff465 100644 --- a/test/data/invalid/allele_invalid.json +++ b/test/data/invalid/allele_invalid.json @@ -3,7 +3,7 @@ "allele_ingest_set": [ { "additional_propertie": "this is invalid", - "mod_entity_id": "ZFIN:ZDB-ALT-123456-1", + "primary_external_id": "ZFIN:ZDB-ALT-123456-1", "taxon_curie": "NCBITaxon:7955", "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN" diff --git a/test/data/invalid/missing_version.json b/test/data/invalid/missing_version.json index c43800893..7034b377a 100644 --- a/test/data/invalid/missing_version.json +++ b/test/data/invalid/missing_version.json @@ -1,7 +1,7 @@ { "agm_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-FISH-200601-1", + "primary_external_id": "ZFIN:ZDB-FISH-200601-1", "taxon_curie": "NCBITaxon:7955", "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", diff --git a/test/data/protein_test.json b/test/data/protein_test.json index 0ce729596..bb123764c 100644 --- a/test/data/protein_test.json +++ b/test/data/protein_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "protein_ingest_set": [ { - "mod_entity_id": "WB:CE06191", + "primary_external_id": "WB:CE06191", "taxon_curie": "NCBITaxon:6239", "created_by_curie": "WB:WBPerson2987", "updated_by_curie": "WB:WBPerson2987", diff --git a/test/data/sqtr_test.json b/test/data/sqtr_test.json index d9b591c11..0b486eb8d 100644 --- a/test/data/sqtr_test.json +++ b/test/data/sqtr_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "sqtr_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-TALEN-200601-1", + "primary_external_id": "ZFIN:ZDB-TALEN-200601-1", "name": "TALEN2-eftud2", "synonyms" : [ "CXCR7mo1", "MO1-cxcr7b" ], "secondary_identifiers" : [ "ZFIN:ZDB-MRKRSEQ-071105-1" ], @@ -26,7 +26,7 @@ } }, { - "mod_entity_id": "ZFIN:ZDB-CRISPR-220422", + "primary_external_id": "ZFIN:ZDB-CRISPR-220422", "name": "CRISPR1-psma1", "taxon_curie": "NCBITaxon:7955", "data_provider_dto": { @@ -48,7 +48,7 @@ ] }, { - "mod_entity_id": "ZFIN:ZDB-MRPHLNO-220216-1", + "primary_external_id": "ZFIN:ZDB-MRPHLNO-220216-1", "name": "MO1-abcg2b", "taxon_curie": "NCBITaxon:7955", "data_provider_dto": { diff --git a/test/data/transcript_test.json b/test/data/transcript_test.json index eb0ca6aa2..991bc2ab5 100644 --- a/test/data/transcript_test.json +++ b/test/data/transcript_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "transcript_ingest_set": [ { - "mod_entity_id": "WB:M05B5.5a.1", + "primary_external_id": "WB:M05B5.5a.1", "taxon_curie": "NCBITaxon:6239", "transcript_type_curie": "SO:0000010", "created_by_curie": "WB:WBPerson2987", diff --git a/test/data/variant_test.json b/test/data/variant_test.json index 46ed58a86..d45ccca48 100644 --- a/test/data/variant_test.json +++ b/test/data/variant_test.json @@ -2,7 +2,7 @@ "linkml_version": "2.0.0", "variant_ingest_set": [ { - "mod_entity_id": "ZFIN:ZDB-ALT-000412-8", + "primary_external_id": "ZFIN:ZDB-ALT-000412-8", "data_provider_dto": { "source_organization_abbreviation": "ZFIN", "cross_reference_dto": { @@ -36,7 +36,7 @@ ] }, { - "mod_entity_id": "ZFIN:ZDB-ALT-000412-9", + "primary_external_id": "ZFIN:ZDB-ALT-000412-9", "data_provider_dto": { "source_organization_abbreviation": "ZFIN", "cross_reference_dto": { diff --git a/test/data/wb_disease_test.json b/test/data/wb_disease_test.json index b7cc4fd04..1a449e188 100644 --- a/test/data/wb_disease_test.json +++ b/test/data/wb_disease_test.json @@ -45,7 +45,7 @@ "ECO:0007013" ], "genetic_sex_name": "hermaphrodite", - "mod_entity_id": "WBDOannot00001032", + "primary_external_id": "WBDOannot00001032", "mod_internal_id": "MGI:diseaseannotation_239930183_295748146", "updated_by_curie": "WB:WBPerson324", "internal": false, @@ -98,7 +98,7 @@ "ECO:0007013" ], "genetic_sex_name": "hermaphrodite", - "mod_entity_id": "WBDOannot00001014", + "primary_external_id": "WBDOannot00001014", "updated_by_curie": "WB:WBPerson324", "negated": false, "internal": false, @@ -130,7 +130,7 @@ "ECO:0007013" ], "genetic_sex_name": "hermaphrodite", - "mod_entity_id": "WBDOannot00000109", + "primary_external_id": "WBDOannot00000109", "updated_by_curie": "WB:WBPerson324", "internal": false, "do_term_curie": "DOID:10652", @@ -183,7 +183,7 @@ "ECO:0007013" ], "genetic_sex_name": "hermaphrodite", - "mod_entity_id": "WBDOannot00000110", + "primary_external_id": "WBDOannot00000110", "updated_by_curie": "WB:WBPerson324", "internal": false, "do_term_curie": "DOID:11723",