From ba6f0cc305182bdd0feb212b9cb44fb785e44956 Mon Sep 17 00:00:00 2001 From: Chris Grove Date: Tue, 12 Jul 2022 22:40:02 -0400 Subject: [PATCH 1/6] Add children, parents, ancestors, and descendants to OntologyTerm --- model/schema/ontologyTerm.yaml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/model/schema/ontologyTerm.yaml b/model/schema/ontologyTerm.yaml index 832609012..d763a1fb2 100644 --- a/model/schema/ontologyTerm.yaml +++ b/model/schema/ontologyTerm.yaml @@ -84,6 +84,32 @@ slots: domain: Molecule range: string + is_a_children: + description: >- + Direct is_a relationship children, a.k.a. direct subclasses, of an ontology term + domain: OntologyTerm + range: OntologyTerm + multivalued: true + + is_a_parents: + description: Direct is_a relationship parents, a.k.a. direct superclasses, of an ontology term + domain: OntologyTerm + range: OntologyTerm + multivalued: true + + is_a_ancestors: + description: All is_a relationship ancestors (all superclasses) of an ontology term + domain: OntologyTerm + range: OntologyTerm + multivalued: true + + is_a_descendants: + description: All is_a relationship descendants (all subclasses) of an ontology term + domain: OntologyTerm + range: OntologyTerm + multivalued: true + + classes: OntologyTerm: @@ -106,6 +132,10 @@ classes: - namespace - subsets - secondary_identifiers + - is_a_children + - is_a_parents + - is_a_ancestors + - is_a_descendants defining_slots: - curie - namespace From 850f952ad40a60afbca129ec5a442e837fee7644 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 19 Sep 2022 16:26:50 -0700 Subject: [PATCH 2/6] refactor according to discussions in DQM and DevCoordination --- model/schema/ontologyTerm.yaml | 58 ++++++++++++++++++++-------------- 1 file changed, 34 insertions(+), 24 deletions(-) diff --git a/model/schema/ontologyTerm.yaml b/model/schema/ontologyTerm.yaml index d763a1fb2..217d3bf44 100644 --- a/model/schema/ontologyTerm.yaml +++ b/model/schema/ontologyTerm.yaml @@ -84,31 +84,29 @@ slots: domain: Molecule range: string - is_a_children: - description: >- - Direct is_a relationship children, a.k.a. direct subclasses, of an ontology term - domain: OntologyTerm - range: OntologyTerm - multivalued: true - - is_a_parents: - description: Direct is_a relationship parents, a.k.a. direct superclasses, of an ontology term - domain: OntologyTerm - range: OntologyTerm + ancestors: + range: OntologyTermClosure multivalued: true + description: >- + The ancestors of this term in the ontology, including the term itself. + This language works well for the majority of use cases, however for a relationship + like "develops_from", ancestors are the terms from which this term develops (not a true + parent/child or ancestor/descendant relationship). - is_a_ancestors: - description: All is_a relationship ancestors (all superclasses) of an ontology term - domain: OntologyTerm - range: OntologyTerm + descendants: + range: OntologyTermClosure multivalued: true + description: >- + The descendants of this term in the ontology, including the term itself. + This language works well for the majority of use cases, however for a relationship + like "develops_from", ancestors are the terms to which this term develops into (not a true + parent/child or ancestor/descendant relationship). - is_a_descendants: - description: All is_a relationship descendants (all subclasses) of an ontology term - domain: OntologyTerm - range: OntologyTerm - multivalued: true + relationship_type: + range: ROTerm + distance_between: + range: integer classes: @@ -132,10 +130,8 @@ classes: - namespace - subsets - secondary_identifiers - - is_a_children - - is_a_parents - - is_a_ancestors - - is_a_descendants + - ancestors + - descendents defining_slots: - curie - namespace @@ -146,6 +142,20 @@ classes: the text description of the term and a collection of URLs that further define the term. +OntologyTermClosure: + is_a: Association + slots: + - relationship_type + - distance_between + slot_usage: + subject: + range: OntologyTerm + object: + range: OntologyTerm + distance_between: + description: >- + distance_between = 0 for reflexive–transitive closure + each node has an ancestor or descendant of itself DOTerm: is_a: OntologyTerm From 0e3ae714d1d620d129f2946c412f36c564246050 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 19 Sep 2022 16:28:05 -0700 Subject: [PATCH 3/6] adding test data --- Makefile | 1 + model/schema/ingest.yaml | 9 +++++++++ test/data/ontology_closure_test.json | 24 ++++++++++++++++++++++++ 3 files changed, 34 insertions(+) create mode 100644 test/data/ontology_closure_test.json diff --git a/Makefile b/Makefile index c8470bd1c..8800eebbc 100644 --- a/Makefile +++ b/Makefile @@ -195,6 +195,7 @@ SCHEMA_TEST_EXAMPLES := \ variant_test \ agm_test \ sqtr_test \ + ontology_closure_test \ SCHEMA_TEST_EXAMPLES_INVALID := \ diff --git a/model/schema/ingest.yaml b/model/schema/ingest.yaml index 8967b991d..7369eec06 100644 --- a/model/schema/ingest.yaml +++ b/model/schema/ingest.yaml @@ -108,6 +108,14 @@ slots: mixins: - object_set + ontology_closure_ingest_set: + description: >- + domain: Ingest + range: OntologyClosure + multivalued: true + mixins: + - object_set + gene_ingest_set: description: >- domain: Ingest @@ -139,4 +147,5 @@ classes: - allele_variant_association_ingest_set - agm_ingest_set - sqtr_ingest_set + - ontology_closure_ingest_set diff --git a/test/data/ontology_closure_test.json b/test/data/ontology_closure_test.json new file mode 100644 index 000000000..8a6ed0f28 --- /dev/null +++ b/test/data/ontology_closure_test.json @@ -0,0 +1,24 @@ +{ + "ontology_closure_ingest_set": [ + { + "curie": "ZFIN:ZDB-ALT-000412-8", + "taxon": "NCBITaxon:7955", + "created_by": "ZFIN", + "updated_by": "ZFIN", + "internal": false, + "variant_genome_locations": [ + { + "assembly": "GRCz11", + "chromosome": "7", + "start_position": 30341642, + "end_position": 30341642, + "reference_sequence": "C", + "variant_sequence": "T", + "internal": false + } + ], + "variant_status": "public", + "variant_type": "SO:1000008" + } + ] +} \ No newline at end of file From 55d663cd878a332b853b48505ee949d230eda581 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 19 Sep 2022 16:58:29 -0700 Subject: [PATCH 4/6] add test data examples --- test/data/ontology_closure_test.json | 46 +++++++++++++++++----------- 1 file changed, 28 insertions(+), 18 deletions(-) diff --git a/test/data/ontology_closure_test.json b/test/data/ontology_closure_test.json index 8a6ed0f28..91468d013 100644 --- a/test/data/ontology_closure_test.json +++ b/test/data/ontology_closure_test.json @@ -1,24 +1,34 @@ { "ontology_closure_ingest_set": [ { - "curie": "ZFIN:ZDB-ALT-000412-8", - "taxon": "NCBITaxon:7955", - "created_by": "ZFIN", - "updated_by": "ZFIN", - "internal": false, - "variant_genome_locations": [ - { - "assembly": "GRCz11", - "chromosome": "7", - "start_position": 30341642, - "end_position": 30341642, - "reference_sequence": "C", - "variant_sequence": "T", - "internal": false - } - ], - "variant_status": "public", - "variant_type": "SO:1000008" + "subject": "ZFA:brain", + "object": "ZFA:cavitated_compound_organ", # direct + "relationship_type": ["RO:is_a"] + }, + { + "subject": "ZFA:brain", + "object": "ZFA:compound_organ", # via cavitated_compound_organ isa compound_organ + "relationship_type": ["RO:is_a"] + }, + { + "subject": "ZFA:brain", + "object": "ZFA:anatomical_structure", # via cavitated_compound_organ isa compound_organ isa anatomical_structure + "relationship_type": ["RO:is_a"] + }, + { + "subject": "ZFA:brain", + "object": "ZFA:zebrafish_anatomical_entity", # via cavitated_compound_organ isa compound_organ isa anatomical_structure isa zebrafish_anatomical_entity + "relationship_type": ["RO:is_a"] + }, + { + "subject": "ZFA:brain", + "object": "ZFA:whole_organism", # ??? + "relationship_type": ["RO:is_a", "RO:part_of"] + }, + { + "subject": "ZFA:brain", + "object": "ZFA:whole_organism", # makes more sense? + "relationship_type": ["is_a_part_of"] } ] } \ No newline at end of file From 7420770aa739ec4c1f6c7d907bffa90f8f0849ef Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 20 Sep 2022 16:47:59 -0700 Subject: [PATCH 5/6] keeping this simple for now, just a list of strings to support is_a and part_of --- model/schema/ontologyTerm.yaml | 5 ++--- test/data/ontology_closure_test.json | 14 +++++++------- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/model/schema/ontologyTerm.yaml b/model/schema/ontologyTerm.yaml index 217d3bf44..70a4f85e5 100644 --- a/model/schema/ontologyTerm.yaml +++ b/model/schema/ontologyTerm.yaml @@ -103,7 +103,8 @@ slots: parent/child or ancestor/descendant relationship). relationship_type: - range: ROTerm + range: string + multivalued: true distance_between: range: integer @@ -196,8 +197,6 @@ OntologyTermClosure: XBEDTerm: is_a: OntologyTerm - - CHEBITerm: is_a: ChemicalTerm diff --git a/test/data/ontology_closure_test.json b/test/data/ontology_closure_test.json index 91468d013..81beab1f1 100644 --- a/test/data/ontology_closure_test.json +++ b/test/data/ontology_closure_test.json @@ -2,33 +2,33 @@ "ontology_closure_ingest_set": [ { "subject": "ZFA:brain", - "object": "ZFA:cavitated_compound_organ", # direct + "object": "ZFA:cavitated_compound_organ", "relationship_type": ["RO:is_a"] }, { "subject": "ZFA:brain", - "object": "ZFA:compound_organ", # via cavitated_compound_organ isa compound_organ + "object": "ZFA:compound_organ", "relationship_type": ["RO:is_a"] }, { "subject": "ZFA:brain", - "object": "ZFA:anatomical_structure", # via cavitated_compound_organ isa compound_organ isa anatomical_structure + "object": "ZFA:anatomical_structure", "relationship_type": ["RO:is_a"] }, { "subject": "ZFA:brain", - "object": "ZFA:zebrafish_anatomical_entity", # via cavitated_compound_organ isa compound_organ isa anatomical_structure isa zebrafish_anatomical_entity + "object": "ZFA:zebrafish_anatomical_entity", "relationship_type": ["RO:is_a"] }, { "subject": "ZFA:brain", - "object": "ZFA:whole_organism", # ??? + "object": "ZFA:whole_organism", "relationship_type": ["RO:is_a", "RO:part_of"] }, { "subject": "ZFA:brain", - "object": "ZFA:whole_organism", # makes more sense? - "relationship_type": ["is_a_part_of"] + "object": "ZFA:whole_organism", + "relationship_type": ["RO:is_a", "RO:part_of"] } ] } \ No newline at end of file From 509cc0feb4dfb21c2bbca6336a8e09f651378110 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 20 Sep 2022 16:54:31 -0700 Subject: [PATCH 6/6] fix up ontology closure tests --- jsonschema/allianceModel.schema.json | 1990 +++++++++++++++++++++++++- model/schema/ingest.yaml | 2 +- model/schema/ontologyTerm.yaml | 22 +- test/data/ontology_closure_test.json | 18 +- 4 files changed, 1998 insertions(+), 34 deletions(-) diff --git a/jsonschema/allianceModel.schema.json b/jsonschema/allianceModel.schema.json index 125b2083d..d84133477 100644 --- a/jsonschema/allianceModel.schema.json +++ b/jsonschema/allianceModel.schema.json @@ -44,6 +44,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "disease_genetic_modifier": { "description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.", "type": "string" @@ -191,6 +201,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -252,6 +272,13 @@ "additionalProperties": false, "description": "An ontology term from the Alliance Tags for Papers ontology (ATP)", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -277,6 +304,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -291,6 +328,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -381,6 +425,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -468,6 +522,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "has_allele": { "type": "string" }, @@ -512,6 +576,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -572,6 +646,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -666,6 +750,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -724,6 +818,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -797,6 +901,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -862,6 +976,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "disease_genetic_modifier": { "description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.", "type": "string" @@ -990,6 +1114,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1040,6 +1174,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1106,6 +1250,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1171,6 +1325,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1218,6 +1382,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1283,6 +1457,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1336,6 +1520,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1386,6 +1580,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1433,6 +1637,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1491,6 +1705,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1567,6 +1791,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1638,6 +1872,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1707,6 +1951,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1756,6 +2010,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1799,6 +2063,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1861,6 +2135,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -1927,6 +2211,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -2002,6 +2296,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -2069,6 +2373,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "generated_by": { "description": "Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory.", "items": { @@ -2188,6 +2502,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -2226,6 +2550,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -2284,6 +2618,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -2332,6 +2676,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "first_author": { "description": "Indicates if the author is a first author.", "type": "boolean" @@ -2367,6 +2721,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -2392,6 +2753,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -2406,6 +2777,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "formula": { "description": "Formula of the molecule", "type": "string" @@ -2480,6 +2858,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -2505,6 +2890,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -2519,6 +2914,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -2598,6 +3000,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -2668,6 +3080,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -2706,10 +3128,20 @@ "format": "date", "type": "string" }, - "internal": { - "description": "Classifies the entity as private (for internal use) or not (for public use).", - "type": "boolean" - }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -2753,6 +3185,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "handle": { "description": "A slot pointing to a free-text alias or 'handle' for a data object, such as a reference-specific alias for a data object used while curating.", "type": "string" @@ -2820,6 +3262,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -2905,6 +3357,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -2975,6 +3437,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -3047,6 +3519,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "display_name": { "type": "string" }, @@ -3087,6 +3569,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -3112,6 +3601,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -3126,6 +3625,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -3198,6 +3704,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "generated_by": { "description": "Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory.", "items": { @@ -3241,6 +3757,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -3266,6 +3789,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -3280,6 +3813,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -3536,6 +4076,13 @@ "description": "Letter code used by curators to refer to the ECO term.", "type": "string" }, + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -3561,6 +4108,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -3575,6 +4132,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -3629,6 +4193,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -3654,6 +4225,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -3668,6 +4249,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -3736,6 +4324,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -3850,6 +4448,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -3904,6 +4512,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "expression_qualifiers": { "$ref": "#/$defs/ExpressionQualifierSet", "description": "Qualifiers that describe additional characteristics of gene expression. For example: aint, intense, restricted." @@ -3969,6 +4587,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -4054,6 +4682,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4159,6 +4797,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -4207,6 +4855,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -4232,6 +4887,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -4246,6 +4911,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4300,6 +4972,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -4325,6 +5004,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -4339,6 +5028,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4415,6 +5111,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4468,6 +5174,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4509,6 +5225,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genes": { "items": { "type": "string" @@ -4548,6 +5274,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -4573,6 +5306,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -4587,6 +5330,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -4680,6 +5430,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "designating_laboratories": { "description": "A laboratory, rarely laboratories, which designated this gene", "items": { @@ -4812,6 +5572,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genes": { "items": { "type": "string" @@ -4869,6 +5639,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "experiment_type": { "description": "Type of experiment by which these genes were collated eg chip-seq, interaction, expression", "items": { @@ -4947,6 +5727,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "disease_genetic_modifier": { "description": "Specifies a genetic object that modifies the disease model. May be a gene, allele, AGM.", "type": "string" @@ -5082,6 +5872,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -5208,6 +6008,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -5281,6 +6091,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "detection_method": { "$ref": "#/$defs/DetectionMethodsEnum", "description": "The experimental method used to identify the physical interaction between two molecules" @@ -5385,6 +6205,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "designating_laboratory": { "$ref": "#/$defs/Laboratory", "description": "A laboratory which designated this gene class" @@ -5459,6 +6289,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -5529,10 +6369,20 @@ "format": "date", "type": "string" }, - "evidence": { - "items": { - "type": "string" - }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, + "evidence": { + "items": { + "type": "string" + }, "type": "array" }, "internal": { @@ -5595,6 +6445,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -5643,6 +6503,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genetic_map_band": { "description": "Genetic map predicted chromosome location eg 10q12", "type": "string" @@ -5749,6 +6619,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -5815,6 +6695,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "end": { "description": "The end of the feature in positive 1-based integer coordinates", "type": "string" @@ -5961,6 +6851,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "height": { "description": "The height of the image (pixels).", "type": "integer" @@ -6043,6 +6943,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "from_image": { "description": "Holds between an ImagePane and an Image.", "type": "string" @@ -6111,6 +7021,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6261,6 +7181,12 @@ }, "type": "array" }, + "ontology_closure_ingest_set": { + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "sqtr_ingest_set": { "items": { "$ref": "#/$defs/SequenceTargetingReagent" @@ -6458,6 +7384,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6501,6 +7437,10 @@ "additionalProperties": false, "description": "", "properties": { + "api_token": { + "description": "The API token of the LoggedInPerson for the curation system", + "type": "string" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -6515,6 +7455,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "emails": { "description": "list of emails for a person", "items": { @@ -6591,6 +7541,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -6616,6 +7573,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -6630,6 +7597,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6684,6 +7658,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -6709,6 +7690,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -6723,6 +7714,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6777,6 +7775,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -6802,6 +7807,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -6816,6 +7831,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6870,6 +7892,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -6895,6 +7924,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -6909,6 +7948,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -6959,6 +8005,123 @@ "title": "MMUSDVTerm", "type": "object" }, + "MPTerm": { + "additionalProperties": false, + "description": "", + "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "cross_references": { + "description": "Holds between an object and its CrossReferences.", + "items": { + "$ref": "#/$defs/CrossReference" + }, + "type": "array" + }, + "curie": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" + }, + "definition": { + "description": "The definition of the ontology term. This is a reference to an object that holds the text description of the term and a collection of URLs that further define the term.", + "type": "string" + }, + "definition_urls": { + "items": { + "type": "string" + }, + "type": "array" + }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "name": { + "description": "a human-readable name for an entity", + "type": "string" + }, + "namespace": { + "description": "the namespace of the ontology.", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "secondary_identifiers": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subsets": { + "items": { + "type": "string" + }, + "type": "array" + }, + "synonyms": { + "description": "holds between a named thing and a synonym", + "items": { + "$ref": "#/$defs/Synonym" + }, + "type": "array" + }, + "type": { + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal", + "curie" + ], + "title": "MPTerm", + "type": "object" + }, "MeshDetail": { "additionalProperties": false, "description": "Medical Subject Headings information coming from PubMed.", @@ -6977,6 +8140,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "heading_term": { "description": "The MeSH term description or definition from PubMed. e.g. Measles in a Measles/epidemiology term.", "type": "string" @@ -7019,6 +8192,13 @@ "additionalProperties": false, "description": "Molecules as described by WormBase", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -7044,6 +8224,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -7058,6 +8248,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "formula": { "description": "Formula of the molecule", "type": "string" @@ -7132,6 +8329,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -7157,6 +8361,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -7171,6 +8385,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7248,6 +8469,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -7287,6 +8518,13 @@ "additionalProperties": false, "description": "A concept or class in an ontology, vocabulary or thesaurus. Note, ontology terms can be found in multiple ontologies (ie: mireoting). defining_slots helps define an alternative key for ontology terms.", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -7312,6 +8550,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -7326,6 +8574,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7376,6 +8631,73 @@ "title": "OntologyTerm", "type": "object" }, + "OntologyTermClosure": { + "additionalProperties": false, + "description": "", + "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", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, + "distance_between": { + "description": "distance_between is zero for reflexive\u2013transitive closure each node has an ancestor or descendant of itself ", + "type": "integer" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "object": { + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "type": "string" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "relationship_type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "subject": { + "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "internal", + "subject", + "object" + ], + "title": "OntologyTermClosure", + "type": "object" + }, "Operon": { "additionalProperties": false, "description": "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.", @@ -7398,6 +8720,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genes": { "items": { "type": "string" @@ -7451,6 +8783,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7492,6 +8834,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7535,6 +8887,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "emails": { "description": "list of emails for a person", "items": { @@ -7615,6 +8977,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7663,6 +9035,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -7716,6 +9098,13 @@ "additionalProperties": false, "description": "An ontology term representing a characteristic of an organism. This may or may not be expressed as a difference in comparison to a reference organism.", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -7741,6 +9130,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -7755,6 +9154,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -7844,6 +9250,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -7914,6 +9330,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -8063,6 +9489,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "generated_by": { "description": "Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory.", "items": { @@ -8106,6 +9542,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -8131,6 +9574,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -8145,6 +9598,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -8217,6 +9677,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "generated_by": { "description": "Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory.", "items": { @@ -8308,6 +9778,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -8449,6 +9929,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "editors": { "description": "holds between a resource and a editor_resource", "items": { @@ -8518,6 +10008,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -8543,6 +10040,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -8557,6 +10064,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -8636,6 +10150,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -8710,6 +10234,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "evidence": { "items": { "type": "string" @@ -8774,13 +10308,23 @@ "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.", + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", "format": "date", "type": "string" }, - "date_updated": { - "description": "Date on which an entity was last modified.", + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", "format": "date", "type": "string" }, @@ -8821,6 +10365,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -8910,18 +10464,28 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" }, + "name": { + "description": "a human-readable name for an entity", + "type": "string" + }, "obsolete": { "description": "Entity is no longer current.", "type": "boolean" }, - "synonym": { - "description": "the text string of the synonym", - "type": "string" - }, "updated_by": { "description": "The individual that last modified the entity.", "type": "string" @@ -8966,6 +10530,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "developmental_stage_start": { "description": "The beginning developmental stage at which an annotated event was observed.", "type": "string" @@ -9035,6 +10609,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -9087,6 +10671,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -9112,6 +10703,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -9126,6 +10727,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -9205,6 +10813,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "genomic_locations": { "items": { "$ref": "#/$defs/GenomicLocation" @@ -9319,6 +10937,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -9402,6 +11030,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "end_position": { "description": "End position of variant on genomic entity.", "type": "integer" @@ -9473,6 +11111,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "end_position": { "description": "End position of variant on genomic entity.", "type": "integer" @@ -9579,6 +11227,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "hgvs_coding_nomenclature": { "description": "HGVS coding sequence (HGVSc) name", "type": "string" @@ -9670,6 +11328,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "end_position": { "description": "End position of variant on genomic entity.", "type": "integer" @@ -9745,6 +11413,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -9801,6 +11479,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "type": "string" + }, "definition": { "description": "The explanation of the meaning of a term.", "type": "string" @@ -9840,6 +11528,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -9865,6 +11560,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -9879,6 +11584,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -9933,6 +11645,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -9958,6 +11677,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -9972,6 +11701,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10026,6 +11762,13 @@ "additionalProperties": false, "description": "The Xenbase anatomy ontology XAO is home to Xenopus anatomy terms as well as Xenopus developmental life stage terms, differentiated by namespace. The anatomy term class in LinkML will be named 'XBATerm' for Xenbase Anatomy Term and life stage terms will be named 'XBSTerm' for Xenbase Stage Term.", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10051,6 +11794,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10065,6 +11818,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10119,6 +11879,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10144,6 +11911,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10158,6 +11935,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10212,6 +11996,13 @@ "additionalProperties": false, "description": "The Xenbase anatomy ontology XAO is home to Xenopus anatomy terms as well as Xenopus developmental life stage terms, differentiated by namespace. The anatomy term class in LinkML will be named 'XBATerm' for Xenbase Anatomy Term and life stage terms will be named 'XBSTerm' for Xenbase Stage Term.", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10237,6 +12028,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10251,6 +12052,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10305,6 +12113,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10330,6 +12145,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10344,6 +12169,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10398,6 +12230,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10423,6 +12262,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10437,6 +12286,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10491,6 +12347,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10516,6 +12379,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10530,6 +12403,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "formula": { "description": "Formula of the molecule", "type": "string" @@ -10604,6 +12484,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10629,6 +12516,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10643,6 +12540,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10697,6 +12601,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10722,6 +12633,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10736,6 +12657,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -10790,6 +12718,13 @@ "additionalProperties": false, "description": "", "properties": { + "ancestors": { + "description": "The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "created_by": { "description": "The individual that created the entity.", "type": "string" @@ -10815,6 +12750,16 @@ "format": "date", "type": "string" }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date", + "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" @@ -10829,6 +12774,13 @@ }, "type": "array" }, + "descendants": { + "description": "The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like \"develops_from\", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).", + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "internal": { "description": "Classifies the entity as private (for internal use) or not (for public use).", "type": "boolean" @@ -11027,6 +12979,12 @@ }, "type": "array" }, + "ontology_closure_ingest_set": { + "items": { + "$ref": "#/$defs/OntologyTermClosure" + }, + "type": "array" + }, "sqtr_ingest_set": { "items": { "$ref": "#/$defs/SequenceTargetingReagent" diff --git a/model/schema/ingest.yaml b/model/schema/ingest.yaml index 8748b3bca..ab28bd2d2 100644 --- a/model/schema/ingest.yaml +++ b/model/schema/ingest.yaml @@ -160,7 +160,7 @@ slots: ontology_closure_ingest_set: description: >- domain: Ingest - range: OntologyClosure + range: OntologyTermClosure multivalued: true mixins: - object_set diff --git a/model/schema/ontologyTerm.yaml b/model/schema/ontologyTerm.yaml index a0f931c52..b2ff2e36b 100644 --- a/model/schema/ontologyTerm.yaml +++ b/model/schema/ontologyTerm.yaml @@ -132,7 +132,7 @@ classes: - subsets - secondary_identifiers - ancestors - - descendents + - descendants defining_slots: - curie - namespace @@ -146,20 +146,20 @@ classes: required: true identifier: true -OntologyTermClosure: - is_a: Association - slots: + OntologyTermClosure: + is_a: AuditedObject + slots: - relationship_type - distance_between - slot_usage: - subject: + slot_usage: + subject: range: OntologyTerm - object: + object: range: OntologyTerm - distance_between: - description: >- - distance_between = 0 for reflexive–transitive closure - each node has an ancestor or descendant of itself + distance_between: + description: >- + distance_between is zero for reflexive–transitive closure + each node has an ancestor or descendant of itself DOTerm: is_a: OntologyTerm diff --git a/test/data/ontology_closure_test.json b/test/data/ontology_closure_test.json index 81beab1f1..0520c4bbd 100644 --- a/test/data/ontology_closure_test.json +++ b/test/data/ontology_closure_test.json @@ -3,32 +3,38 @@ { "subject": "ZFA:brain", "object": "ZFA:cavitated_compound_organ", - "relationship_type": ["RO:is_a"] + "relationship_type": ["RO:is_a"], + "internal": false }, { "subject": "ZFA:brain", "object": "ZFA:compound_organ", - "relationship_type": ["RO:is_a"] + "relationship_type": ["RO:is_a"], + "internal": false }, { "subject": "ZFA:brain", "object": "ZFA:anatomical_structure", - "relationship_type": ["RO:is_a"] + "relationship_type": ["RO:is_a"], + "internal": false }, { "subject": "ZFA:brain", "object": "ZFA:zebrafish_anatomical_entity", - "relationship_type": ["RO:is_a"] + "relationship_type": ["RO:is_a"], + "internal": false }, { "subject": "ZFA:brain", "object": "ZFA:whole_organism", - "relationship_type": ["RO:is_a", "RO:part_of"] + "relationship_type": ["RO:is_a", "RO:part_of"], + "internal": false }, { "subject": "ZFA:brain", "object": "ZFA:whole_organism", - "relationship_type": ["RO:is_a", "RO:part_of"] + "relationship_type": ["RO:is_a", "RO:part_of"], + "internal": false } ] } \ No newline at end of file