Merge pull request #199 from togoid/main

release 2023-11-21
togoid · Nov 21, 2023 · a72eed4 · a72eed4
2 parents 4c58917 + 6bea600
commit a72eed4
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Showing 7 changed files with 2,647 additions and 2,705 deletions.
diff --git a/config/dataset.yaml b/config/dataset.yaml
@@ -85,7 +85,7 @@ chebi:
   category: Compound
   regex: '^(?:CHEBI[:_])?(?<id>\d+)$'
   prefix: 'http://purl.obolibrary.org/obo/CHEBI_'
-  format: ["%s","CHEBI:%s","CHEBI_%"]
+  format: ["CHEBI:%s","CHEBI_%"]
   examples:
     - ["84824","40167","32807","87666","57524","64860","94440","18005","4806","50158"]
     - ["CHEBI:84824","CHEBI:40167","CHEBI:32807","CHEBI:87666","CHEBI:57524","CHEBI:64860","CHEBI:94440","CHEBI:18005","CHEBI:4806","CHEBI:50158"]
@@ -113,7 +113,7 @@ clinvar:
   category: Variant
   regex: '^(VCV0*)?(?<id>(\d{1,9}))$'
   prefix: 'http://identifiers.org/clinvar/'
-  format: ["%s","VCV%09d"]
+  format: ["VCV%09d"]
   examples:
     - ["658761","619209","745342","11955","731668","724289","725734","743127","789913","5302"]
     - ["VCV000658761","VCV000619209","VCV000745342","VCV000011955","VCV000731668","VCV000724289","VCV000725734","VCV000743127","VCV000789913","VCV000005302"]
@@ -150,7 +150,7 @@ ec:
   category: Function
   regex: '^(?:EC:)?(?<id>\d+\.(?:(?:-\.-\.-)|\d+\.(?:(?:-\.-)|\d+\.(?:-|n?\d+))))$'
   prefix: 'http://identifiers.org/ec-code/'
-  format: ["%s","EC:%s"]
+  format: ["EC:%s"]
   examples:
     - ["1.6.3.1","2.4.1.353","1.1.1.288","1.5.1.2","3.1.1.71","1.3.1.31","3.5.1.29","1.16.1.1","3.1.3.48","2.3.1.138"]
     - ["EC:1.6.3.1","EC:2.4.1.353","EC:1.1.1.288","EC:1.5.1.2","EC:3.1.1.71","EC:1.3.1.31","EC:3.5.1.29","EC:1.16.1.1","EC:3.1.3.48","EC:2.3.1.138"]
@@ -228,7 +228,7 @@ hgnc:
   category: Gene
   regex: '^(?:(?:HGNC|hgnc):)?(?<id>\d{1,5})$'
   prefix: 'http://identifiers.org/hgnc/'
-  format: ["%s","HGNC:%s","hgnc:%s"]
+  format: ["HGNC:%s","hgnc:%s"]
   examples:
     - ["26199","38937","14027","21498","18185","1314","25960","2206","22224","19741"]
     - ["HGNC:26199","HGNC:38937","HGNC:14027","HGNC:21498","HGNC:18185","HGNC:1314","HGNC:25960","HGNC:2206","HGNC:22224","HGNC:19741"]
@@ -247,7 +247,7 @@ hmdb:
   category: Compound
   regex: '^(?:hmdb:)?(?<id>HMDB\d+)$'
   prefix: 'http://identifiers.org/hmdb/'
-  format: ["%s","hmdb:%s"]
+  format: ["hmdb:%s"]
   examples:
     - ["HMDB0029433","HMDB0015609","HMDB0000042","HMDB0002360","HMDB0003345","HMDB0003550","HMDB0036769","HMDB0000935","HMDB0002755","HMDB0004369"]
     - ["hmdb:HMDB0029433","hmdb:HMDB0015609","hmdb:HMDB0000042","hmdb:HMDB0002360","hmdb:HMDB0003345","hmdb:HMDB0003550","hmdb:HMDB0036769","hmdb:HMDB0000935","hmdb:HMDB0002755","hmdb:HMDB0004369"]
@@ -394,7 +394,7 @@ meddra:
   category: Phenotype
   regex: '^(?:(?:MedDRA|meddra):)?(?<id>\d+)$'
   prefix: 'http://identifiers.org/meddra/'
-  format: ["%s","MedDRA:%s","meddra:%s"]
+  format: ["MedDRA:%s","meddra:%s"]
   examples:
     - ["10008033","10027710","10062506","10040493","10013611","10065857","10063143","10022599","10042342","10047883"]
     - ["MedDRA:10008033","MedDRA:10027710","MedDRA:10062506","MedDRA:10040493","MedDRA:10013611","MedDRA:10065857","MedDRA:10063143","MedDRA:10022599","MedDRA:10042342","MedDRA:10047883"]
@@ -473,6 +473,7 @@ mp:
   category: Phenotype
   regex: '^MP[:_](?<id>\d{7})$'
   prefix: 'http://identifiers.org/mp/MP:'
+  format: ["MP:%s","MP_%s"]
   examples:
     - ["MP:0000600","MP:0001716","MP:0001698","MP:0001092","MP:0000961","MP:0000245","MP:0000828","MP:0000826","MP:0005039","MP:0002840"]
     - ["MP_0000600","MP_0001716","MP_0001698","MP_0001092","MP_0000961","MP_0000245","MP_0000828","MP_0000826","MP_0005039","MP_0002840"]
@@ -549,7 +550,7 @@ omim_gene:
   category: Gene
   regex: '^(?:O?MIM:)?(?<id>\d{6})$'
   prefix: 'http://identifiers.org/mim/'
-  format: ["%s","OMIM:%s","MIM:%s"]
+  format: ["OMIM:%s","MIM:%s"]
   examples:
     - ["604810","115460","608706","300181","102575","601280","602832","601604","177075","608977"]
     - ["OMIM:604810","OMIM:115460","OMIM:608706","OMIM:300181","OMIM:102575","OMIM:601280","OMIM:602832","OMIM:601604","OMIM:177075","OMIM:608977"]
@@ -560,7 +561,7 @@ omim_phenotype:
   category: Phenotype
   regex: '^(?:O?MIM:)?(?<id>\d{6})$'
   prefix: 'http://identifiers.org/mim/'
-  format: ["%s","OMIM:%s","MIM:%s"]
+  format: ["OMIM:%s","MIM:%s"]
   examples:
     - ["207780","236100","237500","300716","125310","165199","617175","137600","600089","601317"]
     - ["OMIM:207780","OMIM:236100","OMIM:237500","OMIM:300716","OMIM:125310","OMIM:165199","OMIM:617175","OMIM:137600","OMIM:600089","OMIM:601317"]
@@ -646,7 +647,7 @@ pubchem_compound:
   category: Compound
   regex: '^(?:CID)?(?<id>\d+)$'
   prefix: 'http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID'
-  format: ["%s","CID%s"]
+  format: ["CID%s"]
   examples:
     - ["9548669","160419","9869929","76333303","9868491","27854","76329169","3448","296","10371227"]
     - ["CID9548669","CID160419","CID9869929","CID76333303","CID9868491","CID27854","CID76329169","CID3448","CID296","CID10371227"]
@@ -656,7 +657,7 @@ pubchem_substance:
   category: Compound
   regex: '^(?:SID)?(?<id>\d+)$'
   prefix: 'http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID'
-  format: ["%s","SID%s"]
+  format: ["SID%s"]
   examples:
     - ["15229855","15277848","15782795","16076657","16035895","12012900","15378994","14850434","14847540","15271473"]
     - ["SID15229855","SID15277848","SID15782795","SID16076657","SID16035895","SID12012900","SID15378994","SID14850434","SID14847540","SID15271473"]
@@ -666,7 +667,7 @@ pubchem_pathway:
   category: Pathway
   regex: '^(?:PWID)?(?<id>\d+)$'
   prefix: 'http://rdf.ncbi.nlm.nih.gov/pubchem/pathway/PWID'
-  format: ["%s","PWID%s"]
+  format: ["PWID%s"]
   examples:
     - ["10572","1","10576","10577","10579","10573","10582","10574","10575","10581"]
     - ["PWID10572","PWID1","PWID10576","PWID10577","PWID10579","PWID10573","PWID10582","PWID10574","PWID10575","PWID10581"]
@@ -677,7 +678,7 @@ pubmed:
   category: Literature
   regex: '^(?:pmid:|PMID:)?(?<id>\d+)$'
   prefix: 'http://rdf.ncbi.nlm.nih.gov/pubmed/'
-  format: ["%s","pmid:%s","PMID:%s"]
+  format: ["pmid:%s","PMID:%s"]
   examples:
     - ["19281226","19879151","20858243","10773016","16527252","28499733","10397770","15149666","23861362","10577920"]
     - ["pmid:19281226","pmid:19879151","pmid:20858243","pmid:10773016","pmid:16527252","pmid:28499733","pmid:10397770","pmid:15149666","pmid:23861362","pmid:10577920"]
@@ -735,7 +736,7 @@ rgd:
   category: Gene
   regex: '^(?:(?:RGD|rgd):)?(?<id>\d{4,})$'
   prefix: 'http://identifiers.org/rgd/'
-  format: ["%s","RGD:%s","rgd:%s"]
+  format: ["RGD:%s","rgd:%s"]
   examples:
     - ["1308312","1311120","1309724","1565514","7683241","1307957","71036","1307876","1308965","1305482"]
     - ["RGD:1308312","RGD:1311120","RGD:1309724","RGD:1565514","RGD:7683241","RGD:1307957","RGD:71036","RGD:1307876","RGD:1308965","RGD:1305482"]
@@ -820,6 +821,7 @@ swisslipids:
   category: Lipid
   regex: '^SLM[:_](?<id>\d+)$'
   prefix: 'http://identifiers.org/slm/SLM:'
+  format: ["SLM:%s","SLM_%s"]
   examples:
     - ["SLM:000000002","SLM:000000003","SLM:000000006","SLM:000000007","SLM:000000035", "SLM:000000042","SLM:000000043","SLM:000000044", "SLM:000000047","SLM:000000048"]
     - ["SLM_000000002","SLM_000000003","SLM_000000006","SLM_000000007","SLM_000000035", "SLM_000000042","SLM_000000043","SLM_000000044", "SLM_000000047","SLM_000000048"]
@@ -890,7 +892,7 @@ vgnc:
   catalog: nbdc02624
   category: Gene
   regex: '^((VGNC|vgnc):)?(?<id>\d{1,9})$'
-  format: ["%s","VGNC:%s","vgnc:%s"]
+  format: ["VGNC:%s","vgnc:%s"]
   prefix: 'http://identifiers.org/vgnc/'
   examples:
     - ["39230","49608","85188","76040","72808","73601","9436","78821","74596","5304"]

diff --git a/docs/help.md b/docs/help.md
@@ -1,5 +1,5 @@
 # TogoID ver. 1.1
-Datasets last updated: 2023-11-14
+Datasets last updated: 2023-11-20
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID currently supports 89 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an [ontology](https://togoid.dbcls.jp/ontology) that defines the semantics of the dataset relations.
@@ -22,7 +22,7 @@ Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya,
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## Statistics (as of 2023-11-14)
+## Statistics (as of 2023-11-20)
 - Number of target datasets 
     - 102 (from 72 databases)
 - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. 

diff --git a/docs/help_ja.md b/docs/help_ja.md
@@ -1,5 +1,5 @@
 # TogoID ver. 1.1
-Datasets last updated: 2023-11-14
+Datasets last updated: 2023-11-20
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) は、直感的なインターフェースにより生命科学系データベース(DB)間のつながりを探索的に確認しながらID変換を行うことができるウェブアプリケーションです。同一の実体を指すID間の変換だけでなく、関連する別のカテゴリーのIDへの変換も可能です。また、直接リンクされていないDBのID間でも、他のDBを経由した変換を探索することができます。
@@ -28,7 +28,7 @@ Datasets last updated: 2023-11-14
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## 統計 (2023-11-14)
+## 統計 (2023-11-20)
 - 対象データセット数 
     - 102 (72のデータベースに由来)
 - 対象DBの詳細やID例については、"DATASETS" タブ からご覧いただけます。