Add new providers (#1323)

These support automated generation of pyobo database
biopragmatics · Dec 12, 2024 · 2c97dcb · 2c97dcb
1 parent d934420
commit 2c97dcb
Showing 1 changed file with 92 additions and 2 deletions.
diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
@@ -32233,6 +32233,15 @@
       }
     ],
     "preferred_prefix": "EFO",
+    "providers": [
+      {
+        "code": "ols.curie",
+        "description": "OLS via CURIE",
+        "homepage": "https://www.ebi.ac.uk/ols",
+        "name": "OLS",
+        "uri_format": "http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_$1"
+      }
+    ],
     "publications": [
       {
         "doi": "10.1093/bioinformatics/btq099",
@@ -42430,6 +42439,15 @@
     },
     "name": "General Multilingual Environmental Thesaurus",
     "pattern": "^\\d+$",
+    "providers": [
+      {
+        "code": "gemet.multilingual",
+        "description": "An alternate URI that doesn't have the language encoded in it",
+        "homepage": "https://www.eionet.europa.eu/gemet",
+        "name": "GEMET Multilingual",
+        "uri_format": "http://www.eionet.europa.eu/gemet/concept/$1"
+      }
+    ],
     "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1"
   },
   "genatlas": {
@@ -59999,7 +60017,20 @@
       "pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
       "prefix": "jcsd",
       "uri_format": "http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp?CONTENT=syosai&SN=$1"
-    }
+    },
+    "providers": [
+      {
+        "code": "stirdf",
+        "description": "Appears in iobc",
+        "homepage": "http://stirdf.jst.go.jp",
+        "name": "Unknown",
+        "uri_format": "http://stirdf.jst.go.jp/cde/nikkaji/$1"
+      }
+    ],
+    "synonyms": [
+      "Nikkaji number",
+      "nikkaji"
+    ]
   },
   "jecfa": {
     "contact": {
@@ -66404,6 +66435,13 @@
         "homepage": "http://id.nlm.nih.gov/mesh/",
         "name": "Medical Subject Headings (N3)",
         "uri_format": "https://id.nlm.nih.gov/mesh/$1.n3"
+      },
+      {
+        "code": "mesh.2008",
+        "description": "Appears in birnlex",
+        "homepage": "http://id.nlm.nih.gov/mesh/",
+        "name": "Legacy 2008 MeSH URL",
+        "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$1"
       }
     ],
     "publications": [
@@ -71869,6 +71907,15 @@
       "prefix": "MONDO"
     },
     "pattern": "^\\d{7}$",
+    "providers": [
+      {
+        "code": "clinicalgenome",
+        "description": "Clinical genome condition",
+        "homepage": "https://search.clinicalgenome.org",
+        "name": "Clinical Genome",
+        "uri_format": "https://search.clinicalgenome.org/kb/conditions/MONDO:$1"
+      }
+    ],
     "publications": [
       {
         "doi": "10.1101/2022.04.13.22273750",
@@ -72872,10 +72919,19 @@
     },
     "name": "Molecular Signatures Database",
     "pattern": "^M\\d+$",
+    "providers": [
+      {
+        "code": "biopragmatics",
+        "description": "An OBO to Website of MMSigDB",
+        "homepage": "https://biopragmatics.github.io/providers/msigdb/",
+        "name": "MMSigDB from Biopragmatics",
+        "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1"
+      }
+    ],
     "synonyms": [
       "msig"
     ],
-    "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1",
+    "uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1",
     "wikidata": {
       "paper": "Q34509167"
     }
@@ -76376,6 +76432,15 @@
     },
     "name": "NeuroNames",
     "pattern": "^\\d+$",
+    "providers": [
+      {
+        "code": "neuronames.alt1",
+        "description": "Alternate URI inside neuronames, appearning in birnlex",
+        "homepage": "http://braininfo.rprc.washington.edu",
+        "name": "Neuronames Alternate 1",
+        "uri_format": "http://braininfo.rprc.washington.edu/Scripts/hiercentraldirectory.aspx?ID=$1"
+      }
+    ],
     "references": [
       "https://en.wikipedia.org/wiki/NeuroNames"
     ],
@@ -84356,6 +84421,15 @@
       "version.iri": "https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl"
     },
     "pattern": "^C?\\d+$",
+    "providers": [
+      {
+        "code": "legacy",
+        "description": "This link is no longer live",
+        "homepage": "https://www.orpha.net",
+        "name": "Legacy Orphanet Expert",
+        "uri_format": "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=en&Expert=$1"
+      }
+    ],
     "publications": [
       {
         "pubmed": "22874158",
@@ -106801,6 +106875,15 @@
         "snomedct_2013_01_31"
       ]
     },
+    "providers": [
+      {
+        "code": "bioportal.purl",
+        "description": "BioPortal PURL",
+        "homepage": "https://bioontology.org",
+        "name": "BioPortal PURL",
+        "uri_format": "http://purl.bioontology.org/ontology/SNOMEDCT/$1"
+      }
+    ],
     "publications": [
       {
         "doi": "10.1097/00024665-200609000-00011",
@@ -115248,6 +115331,13 @@
         "name": "OmniPathDB",
         "uri_format": "https://omnipathdb.org/interactions/?fields=sources,references&partners=$1"
       },
+      {
+        "code": "pharos",
+        "description": "Part of the Illuminating the Druggable Genome project",
+        "homepage": "https://pharos.nih.gov/idg",
+        "name": "Pharos",
+        "uri_format": "https://pharos.nih.gov/idg/targets/$1"
+      },
       {
         "code": "iptmnet",
         "description": "Protein post translational modification information",