Regenerate artifacts from biolink-model.yaml

biolink · Sep 23, 2024 · c6e38d0 · c6e38d0
1 parent 67beb24
commit c6e38d0
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Showing 12 changed files with 31,134 additions and 52,588 deletions.
diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -1,5 +1,3 @@
-# metamodel_version: 1.7.0
-# version: 4.2.2
 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass
   {
     id: String!

diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld
@@ -1,11 +1,10 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-09-23T16:44:56",
+      "generation_date": "2024-09-23T23:51:05",
       "source": "biolink_model.yaml"
    },
    "@context": {
-      "xsd": "http://www.w3.org/2001/XMLSchema#",
       "AGRKB": "https://www.alliancegenome.org/",
       "APO": {
          "@id": "http://purl.obolibrary.org/obo/APO_",
@@ -579,6 +578,7 @@
          "@id": "http://www.w3.org/2003/01/geo/wgs84_pos",
          "@prefix": true
       },
+      "xsd": "http://www.w3.org/2001/XMLSchema#",
       "@vocab": "https://w3id.org/biolink/vocab/",
       "active_in": {
          "@type": "@id",
@@ -644,11 +644,12 @@
          "@id": "affects_response_to"
       },
       "affiliation": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "affiliation"
       },
       "agent_type": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -732,6 +733,7 @@
       },
       "available_from": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -788,11 +790,12 @@
          "@id": "catalyzes"
       },
       "category": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "category"
       },
       "causal_mechanism_qualifier": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -826,6 +829,7 @@
       },
       "clinical_approval_status": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1022,6 +1026,7 @@
       },
       "drug_regulatory_status_world_wide": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1087,6 +1092,7 @@
       },
       "FDA_adverse_event_level": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1140,6 +1146,7 @@
       },
       "genome_build": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1459,6 +1466,7 @@
       },
       "highest_FDA_approval_status": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1632,6 +1640,7 @@
       },
       "knowledge_level": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1690,6 +1699,7 @@
       },
       "logical_interpretation": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1709,6 +1719,7 @@
       },
       "max_research_phase": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1735,7 +1746,7 @@
          "@id": "mentions"
       },
       "mesh_terms": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "mesh_terms"
       },
       "missing_from": {
@@ -1816,6 +1827,7 @@
       },
       "object_direction_qualifier": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1862,7 +1874,7 @@
          "@id": "original_object"
       },
       "original_predicate": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "original_predicate"
       },
       "original_subject": {
@@ -1900,6 +1912,7 @@
       },
       "phase": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1987,7 +2000,7 @@
          "@id": "publications"
       },
       "published_in": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "published_in"
       },
       "publisher": {
@@ -2014,6 +2027,7 @@
       },
       "reaction_direction": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2022,6 +2036,7 @@
       },
       "reaction_side": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2076,11 +2091,12 @@
          "@id": "resistance_associated_with"
       },
       "resource_id": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "resource_id"
       },
       "resource_role": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2112,6 +2128,7 @@
       },
       "routes_of_delivery": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2184,6 +2201,7 @@
       },
       "strand": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2224,6 +2242,7 @@
       },
       "subject_direction_qualifier": {
          "@context": {
+            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2274,7 +2293,7 @@
          "@id": "supporting_document_year"
       },
       "supporting_documents": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "supporting_documents"
       },
       "supporting_study_cohort": {
@@ -2290,11 +2309,11 @@
          "@id": "supporting_study_metadata"
       },
       "supporting_study_method_description": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "supporting_study_method_description"
       },
       "supporting_study_method_type": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "supporting_study_method_type"
       },
       "supporting_study_size": {
@@ -2399,7 +2418,7 @@
          "@id": "update_date"
       },
       "upstream_resource_ids": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "upstream_resource_ids"
       },
       "url": {
@@ -2424,7 +2443,7 @@
          "@id": "xenologous_to"
       },
       "xref": {
-         "@type": "xsd:anyURI",
+         "@type": "@id",
          "@id": "xref"
       },
       "AccessibleDnaRegion": {