Regenerate artifacts from biolink-model.yaml

biolink · Jan 6, 2025 · fe44b8d · fe44b8d
1 parent fb92180
commit fe44b8d
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Showing 9 changed files with 24,635 additions and 24,602 deletions.
diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2025-01-06T18:56:40",
+      "generation_date": "2025-01-06T20:02:56",
       "source": "biolink_model.yaml"
    },
    "@context": {
@@ -229,7 +229,8 @@
          "@id": "http://purl.obolibrary.org/obo/IAO_",
          "@prefix": true
       },
-      "ICD10": "https://icd.codes/icd9cm/",
+      "ICD10": "https://icd.who.int/browse10/2016/en#/",
+      "ICD11": "http://id.who.int/icd/entity/",
       "ICD9": {
          "@id": "http://translator.ncats.nih.gov/ICD9_",
          "@prefix": true
@@ -541,6 +542,8 @@
       "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#",
       "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#",
       "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#",
+      "icd11": "http://id.who.int/icd/entity/",
+      "icd11.foundation": "http://id.who.int/icd/entity/",
       "interpro": "https://www.ebi.ac.uk/interpro/entry/",
       "isbn": "https://www.isbn-international.org/identifier/",
       "isni": "https://isni.org/isni/",

diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld
@@ -214,12 +214,20 @@
     },
     {
       "prefix_prefix": "ICD10",
-      "prefix_reference": "https://icd.codes/icd9cm/"
+      "prefix_reference": "https://icd.who.int/browse10/2016/en#/"
     },
     {
       "prefix_prefix": "ICD9",
       "prefix_reference": "http://translator.ncats.nih.gov/ICD9_"
     },
+    {
+      "prefix_prefix": "icd11",
+      "prefix_reference": "http://id.who.int/icd/entity/"
+    },
+    {
+      "prefix_prefix": "icd11.foundation",
+      "prefix_reference": "http://id.who.int/icd/entity/"
+    },
     {
       "prefix_prefix": "interpro",
       "prefix_reference": "https://www.ebi.ac.uk/interpro/entry/"
@@ -27223,6 +27231,8 @@
         "NCIT",
         "SNOMEDCT",
         "medgen",
+        "ICD11",
+        "icd11.foundation",
         "ICD10",
         "ICD9",
         "KEGG.DISEASE",
@@ -35890,9 +35900,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2025-01-06T18:56:37",
-  "source_file_size": 403978,
-  "generation_date": "2025-01-06T18:56:43",
+  "source_file_date": "2025-01-06T20:02:53",
+  "source_file_size": 404123,
+  "generation_date": "2025-01-06T20:02:58",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",

diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl
diff --git a/project/prefixmap/biolink-model-prefix-map.json b/project/prefixmap/biolink-model-prefix-map.json
@@ -81,7 +81,8 @@
    "HP": "http://purl.obolibrary.org/obo/HP_",
    "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_",
    "IAO": "http://purl.obolibrary.org/obo/IAO_",
-   "ICD10": "https://icd.codes/icd9cm/",
+   "ICD10": "https://icd.who.int/browse10/2016/en#/",
+   "ICD11": "http://id.who.int/icd/entity/",
    "ICD9": "http://translator.ncats.nih.gov/ICD9_",
    "IDO": "http://purl.obolibrary.org/obo/IDO_",
    "INCHI": "http://identifiers.org/inchi/",
@@ -234,6 +235,8 @@
    "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#",
    "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#",
    "gtpo": "https://rdf.guidetopharmacology.org/ns/gtpo#",
+   "icd11": "http://id.who.int/icd/entity/",
+   "icd11.foundation": "http://id.who.int/icd/entity/",
    "interpro": "https://www.ebi.ac.uk/interpro/entry/",
    "isbn": "https://www.isbn-international.org/identifier/",
    "isni": "https://isni.org/isni/",

diff --git a/project/prefixmap/preferred_prefixes_per_class.json b/project/prefixmap/preferred_prefixes_per_class.json
@@ -2059,34 +2059,44 @@
           "order": 12
         },
         {
-          "prefix": "ICD10",
-          "base_uri": "https://icd.codes/icd9cm/",
+          "prefix": "ICD11",
+          "base_uri": "http://id.who.int/icd/entity/",
           "order": 13
         },
+        {
+          "prefix": "icd11.foundation",
+          "base_uri": "http://id.who.int/icd/entity/",
+          "order": 14
+        },
+        {
+          "prefix": "ICD10",
+          "base_uri": "https://icd.who.int/browse10/2016/en#/",
+          "order": 15
+        },
         {
           "prefix": "ICD9",
           "base_uri": "http://translator.ncats.nih.gov/ICD9_",
-          "order": 14
+          "order": 16
         },
         {
           "prefix": "KEGG.DISEASE",
           "base_uri": "http://identifiers.org/kegg.disease/",
-          "order": 15
+          "order": 17
         },
         {
           "prefix": "HP",
           "base_uri": "http://purl.obolibrary.org/obo/HP_",
-          "order": 16
+          "order": 18
         },
         {
           "prefix": "MP",
           "base_uri": "http://purl.obolibrary.org/obo/MP_",
-          "order": 17
+          "order": 19
         },
         {
           "prefix": "PHARMGKB.DISEASE",
           "base_uri": "https://www.pharmgkb.org/disease/",
-          "order": 18
+          "order": 20
         }
       ]
     },