Merge branch 'idPriorities' into main

biothings · Aug 16, 2021 · 6a9f225 · 6a9f225
2 parents 87068f8 + aae97c5
commit 6a9f225
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diff --git a/README.md b/README.md
@@ -110,11 +110,11 @@ let input = {
   1. NCBIGene
   2. ENSEMBL
   3. HGNC
-  4. SYMBOL
+  4. MGI
   5. OMIM
-  6. UniProtKB
-  7. UMLS
-  8. MGI
+  6. UMLS
+  7. SYMBOL
+  8. UniProtKB
   9. name
 
 - Transcript
@@ -125,52 +125,52 @@ let input = {
 - Protein
   1. UniProtKB
   2. ENSEMBL
-  3. SYMBOL
-  4. UMLS
+  3. UMLS
+  4. SYMBOL
   5. name
 
 > Variant ID resolution is done through MyVariant.info API
 
 - SequenceVariant
-  1. HGVS
+  1. CLINVAR
   2. DBSNP
-  3. MYVARIANT_HG19
-  4. ClinVar
+  3. HGVS
+  4. MYVARIANT_HG19
 
 > SmallMolecule, Drug ID resolution is done through MyChem.info API
 
 - SmallMolecule
-    1. CHEBI
+    1. PUBCHEM.COMPOUND
     2. CHEMBL.COMPOUND
-    3. DRUGBANK
-    4. PUBCHEM.COMPOUND
-    5. MESH
-    6. INCHI
-    7. INCHIKEY
-    8. UNII
+    3. UNII
+    4. CHEBI
+    5. DRUGBANK
+    6. MESH
+    7. CAS
+    8. HMDB
     9. KEGG.COMPOUND
-    10. UMLS
-    11. LINCS
-    12. CAS
-    13. HMDB
+    10. INCHI
+    11. INCHIKEY
+    12. UMLS
+    13. LINCS
     14. name
 
 - Drug
-    1. CHEBI
-    2. CHEMBL.COMPOUND
+    1. RXCUI
+    2. NDC
     3. DRUGBANK
     4. PUBCHEM.COMPOUND
-    5. MESH
-    6. INCHI
-    7. INCHIKEY
-    8. UNII
-    9. KEGG.COMPOUND
-    10. UMLS
-    11. LINCS
-    12. CAS
-    13. HMDB
-    14. RXCUI
-    15. NDC
+    5. CHEMBL.COMPOUND
+    6. UNII
+    7. CHEBI
+    8. MESH
+    9. CAS
+    10. HMDB
+    11. KEGG.COMPOUND
+    12. INCHI
+    13. INCHIKEY
+    14. UMLS
+    15. LINCS
     16. name
 
 > Disease, ClinicalFinding ID Resolution is done through MyDisease.info API
@@ -181,14 +181,14 @@ let input = {
   2. DOID
   3. OMIM
   4. ORPHANET
-  5. SNOMEDCT
-  6. NCIT
-  7. EFO
-  8. UMLS
-  9. MESH
-  10. HP
-  11. GARD
-  12. MEDDRA
+  5. EFO
+  6. UMLS
+  7. MESH
+  8. MEDDRA
+  9. NCIT
+  10. SNOMEDCT
+  11. HP
+  12. GARD
   13. name
 
 - ClinicalFinding
@@ -200,23 +200,23 @@ let input = {
 > Pathway ID Resolution is done through biothings.ncats.io/geneset API
 
 - Pathway
-  1. REACT
-  2. KEGG
-  3. PHARMGKB.PATHWAYS
-  4. WIKIPATHWAYS
-  5. BIOCARTA
-  6. GO
-  7. SMPDB
+  1. GO
+  2. REACT
+  3. KEGG
+  4. SMPDB
+  5. PHARMGKB.PATHWAYS
+  6. WIKIPATHWAYS
+  7. BIOCARTA
   8. name
 
 > MolecularActivity ID Resolution is done through BioThings Gene Ontology Molecular Activity API
 
 - MolecularActivity
   1. GO
-  2. MetaCyc
+  2. REACT
   3. RHEA
-  4. KEGG.REACTION
-  5. REACT
+  4. MetaCyc
+  5. KEGG.REACTION
   6. name
 
 > CellularComponent ID Resolution is done through BioThings Gene Ontology Cellular Component API
@@ -231,8 +231,8 @@ let input = {
 - BiologicalProcess
 
   1. GO
-  2. MetaCyc
-  3. REACT
+  2. REACT
+  3. MetaCyc
   4. KEGG
   5. name
 
@@ -248,14 +248,14 @@ let input = {
 > PhenotypicFeature ID Resolution is done through BioThings HPO API
 
 - PhenotypicFeature
-  1. UMLS
-  2. SNOMEDCT
-  3. HP
-  4. MEDDRA
-  5. EFO
-  6. NCIT
-  7. MESH
-  8. MP
+  1. HP
+  2. EFO
+  3. NCIT
+  4. UMLS
+  5. MEDDRA
+  6. MP
+  7. SNOMEDCT
+  8. MESH
   9. name
 
 > Cell ID Resolution is done through Biothings Cell Ontology API

diff --git a/__tests__/integration/default_resolver.test.ts b/__tests__/integration/default_resolver.test.ts
@@ -30,7 +30,7 @@ describe("Test ID Resolver", () => {
         expect(res).toHaveProperty("LINCS:LSM-2471");
         expect(res['LINCS:LSM-2471']).toHaveLength(1);
         expect(res['LINCS:LSM-2471'][0]).toBeInstanceOf(ResolvableBioEntity);
-        expect(res['LINCS:LSM-2471'][0].primaryID).toEqual("CHEBI:8863");
+        expect(res['LINCS:LSM-2471'][0].primaryID).toEqual("PUBCHEM.COMPOUND:5070");
         expect(res['LINCS:LSM-2471'][0].dbIDs.LINCS).toEqual(["LSM-2471"]);
     })
 

diff --git a/__tests__/unittest/bioentity.test.ts b/__tests__/unittest/bioentity.test.ts
@@ -69,7 +69,7 @@ describe("Test ResolvableBioEntity Class", () => {
         test("if both SYMBOL and name are not provided in db ids, should return primary id", () => {
             const entity = new ResolvableBioEntity("SmallMolecule", CHEMBL7512_DB_IDS, {});
             const label = entity.label;
-            expect(label).toBe("CHEMBL.COMPOUND:CHEMBL7512");
+            expect(label).toBe("PUBCHEM.COMPOUND:53428");
         })
     });
 

diff --git a/src/config.ts b/src/config.ts
@@ -12,7 +12,7 @@ export const MAX_CONCURRENT_QUERIES = 3;
 
 export const APIMETA: MetaDataItemsObject = {
   Gene: {
-    id_ranks: ['NCBIGene', 'ENSEMBL', 'HGNC', 'SYMBOL', 'OMIM', 'UniProtKB', 'UMLS', 'MGI', 'name'],
+    id_ranks: ['NCBIGene', 'ENSEMBL', 'HGNC', 'MGI', 'OMIM', 'UMLS', 'SYMBOL', 'UniProtKB', 'name'],
     semantic: 'Gene',
     api_name: 'mygene.info',
     url: 'https://mygene.info/v3/query',
@@ -47,7 +47,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   Protein: {
-    id_ranks: ['UniProtKB', 'ENSEMBL', 'SYMBOL', 'UMLS', 'name'],
+    id_ranks: ['UniProtKB', 'ENSEMBL', 'UMLS', 'SYMBOL', 'name'],
     semantic: 'Protein',
     api_name: 'mygene.info',
     url: 'https://mygene.info/v3/query',
@@ -63,7 +63,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   SequenceVariant: {
-    id_ranks: ['HGVS', 'DBSNP', 'MYVARIANT_HG19', 'CLINVAR'],
+    id_ranks: ['CLINVAR', 'DBSNP', 'HGVS', 'MYVARIANT_HG19'],
     api_name: 'myvariant.info',
     semantic: 'SequenceVariant',
     url: 'https://myvariant.info/v1/query',
@@ -82,22 +82,8 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   SmallMolecule: {
-    id_ranks: [
-      'CHEBI',
-      'CHEMBL.COMPOUND',
-      'DRUGBANK',
-      'PUBCHEM.COMPOUND',
-      'MESH',
-      'INCHI',
-      'INCHIKEY',
-      'UNII',
-      'KEGG.COMPOUND',
-      'UMLS',
-      'LINCS',
-      'CAS',
-      'HMDB',
-      'name',
-    ],
+    id_ranks: ['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'HMDB', 'KEGG.COMPOUND', 
+    'INCHI', 'INCHIKEY', 'UMLS', 'LINCS', 'name'], 
     semantic: 'SmallMolecule',
     api_name: 'mychem.info',
     url: 'https://mychem.info/v1/query',
@@ -164,24 +150,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   Drug: {
-    id_ranks: [
-      'CHEBI',
-      'CHEMBL.COMPOUND',
-      'DRUGBANK',
-      'PUBCHEM.COMPOUND',
-      'MESH',
-      'INCHI',
-      'INCHIKEY',
-      'UNII',
-      'KEGG.COMPOUND',
-      'UMLS',
-      'LINCS',
-      'CAS',
-      'HMDB',
-      'RXCUI',
-      'NDC',
-      'name',
-    ],
+    id_ranks: ['RXCUI', 'NDC', 'DRUGBANK', 'PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI',  'MESH', 'CAS', 'HMDB', 'KEGG.COMPOUND', 'INCHI', 'INCHIKEY', 'UMLS', 'LINCS', 'name'],
     semantic: 'Drug',
     api_name: 'mychem.info',
     url: 'https://mychem.info/v1/query',
@@ -250,7 +219,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   PhenotypicFeature: {
-    id_ranks: ['UMLS', 'SNOMEDCT', 'HP', 'MEDDRA', 'EFO', 'NCIT', 'MESH', 'MP', 'name'],
+    id_ranks: ['HP', 'EFO', 'NCIT', 'UMLS', 'MEDDRA', 'MP', 'SNOMEDCT', 'MESH', 'name'],
     semantic: 'PhenotypicFeature',
     api_name: 'HPO API',
     url: 'https://biothings.ncats.io/hpo/query',
@@ -267,21 +236,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   Disease: {
-    id_ranks: [
-      'MONDO',
-      'DOID',
-      'OMIM',
-      'ORPHANET',
-      'SNOMEDCT',
-      'NCIT',
-      'EFO',
-      'UMLS',
-      'MESH',
-      'HP',
-      'GARD',
-      'MEDDRA',
-      'name',
-    ],
+    id_ranks: ['MONDO', 'DOID', 'OMIM', 'ORPHANET', 'EFO', 'UMLS', 'MESH', 'MEDDRA', 'NCIT', 'SNOMEDCT', 'HP', 'GARD', 'name'],
     semantic: 'Disease',
     api_name: 'mydisease.info',
     url: 'https://mydisease.info/v1/query',
@@ -320,7 +275,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   MolecularActivity: {
-    id_ranks: ['GO', 'MetaCyc', 'RHEA', 'KEGG.REACTION', 'REACT', 'name'],
+    id_ranks: ['GO', 'REACT', 'RHEA', 'MetaCyc', 'KEGG.REACTION', 'name'],
     semantic: 'MolecularActivity',
     api_name: 'Gene Ontology Molecular Function API',
     url: 'https://biothings.ncats.io/go_mf/query',
@@ -334,7 +289,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   BiologicalProcess: {
-    id_ranks: ['GO', 'MetaCyc', 'REACT', 'KEGG', 'name'],
+    id_ranks: ['GO', 'REACT', 'MetaCyc', 'KEGG', 'name'],
     semantic: 'BiologicalProcess',
     api_name: 'Gene Ontology Biological Process API',
     url: 'https://biothings.ncats.io/go_bp/query',
@@ -358,7 +313,7 @@ export const APIMETA: MetaDataItemsObject = {
     },
   },
   Pathway: {
-    id_ranks: ['REACT', 'KEGG', 'PHARMGKB.PATHWAYS', 'WIKIPATHWAYS', 'BIOCARTA', 'GO', 'SMPDB', 'name'],
+    id_ranks: ['GO', 'REACT', 'KEGG', 'SMPDB', 'PHARMGKB.PATHWAYS', 'WIKIPATHWAYS', 'BIOCARTA', 'name'],
     semantic: 'Pathway',
     api_name: 'Geneset API',
     url: 'https://biothings.ncats.io/geneset/query',