update mappings, semantic types (without update to biolink v2)

README.md

@@ -1,10 +1,10 @@
-![Test Coveralls](https://github.com/kevinxin90/biomedical_id_resolver.js/workflows/Test%20Coveralls/badge.svg)
-[![Coverage Status](https://coveralls.io/repos/github/kevinxin90/biomedical_id_resolver.js/badge.svg?branch=master)](https://coveralls.io/github/kevinxin90/biomedical_id_resolver.js?branch=master)
+![Test Coveralls](https://github.com/biothings/biomedical_id_resolver.js/workflows/Test%20Coveralls/badge.svg)
+[![Coverage Status](https://coveralls.io/repos/github/biothings/biomedical_id_resolver.js/badge.svg?branch=master)](https://coveralls.io/github/kevinxin90/biomedical_id_resolver.js?branch=master)
 ![npm](https://img.shields.io/npm/dw/biomedical_id_resolver)
-![GitHub issues](https://img.shields.io/github/issues/kevinxin90/biomedical_id_resolver.js)
+![GitHub issues](https://img.shields.io/github/issues/biothings/biomedical_id_resolver.js)
 ![NPM](https://img.shields.io/npm/l/biomedical_id_resolver)
 ![npm](https://img.shields.io/npm/v/biomedical_id_resolver?style=plastic)
-![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/kevinxin90/biomedical_id_resolver.js)
+![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/biothings/biomedical_id_resolver.js)
 
 
 
@@ -114,7 +114,24 @@ let input = {
   5. OMIM
   6. UniProtKB
   7. UMLS
-  8. name
+  8. MGI
+  9. name
+
+  > Transcript ID resolution is done through MyGene.info API
+
+- Transcript
+  1. ENSEMBL
+  2. SYMBOL
+  3. name
+
+  > Protein ID resolution is done through MyGene.info API
+
+- Protein
+  1. UniProtKB
+  2. ENSEMBL
+  3. SYMBOL
+  4. UMLS
+  5. name
 
 > Variant ID resolution is done through MyVariant.info API
 
@@ -130,15 +147,35 @@ let input = {
     1. CHEBI
     2. CHEMBL.COMPOUND
     3. DRUGBANK
-    4. PUBCHEM
+    4. PUBCHEM.COMPOUND
+    5. MESH
+    6. INCHI
+    7. INCHIKEY
+    8. UNII
+    9. UMLS
+    10. CAS
+    11. HMDB
+    12. LINCS
+    13. name
+
+> Drug ID resolution is done through MyChem.info API
+
+- Drug
+    1. CHEBI
+    2. CHEMBL.COMPOUND
+    3. DRUGBANK
+    4. PUBCHEM.COMPOUND
     5. MESH
     6. INCHI
     7. INCHIKEY
     8. UNII
-    9. KEGG
-    10. UMLS
-    11. name
-    12. id
+    9. UMLS
+    10. CAS
+    11. HMDB
+    12. LINCS
+    13. RXCUI
+    14. NDC
+    15. name
 
 > Disease ID Resolution is done through MyDisease.info API
 
@@ -151,17 +188,23 @@ let input = {
   5. EFO
   6. UMLS
   7. MESH
-  8. GARD
-  9. name
+  8. HP
+  9. GARD
+  10. SNOMEDCT
+  11. NCIT
+  12. name
 
 > Pathway ID Resolution is done through biothings.ncats.io/geneset API
 
 - Pathway
-  1. Reactome
+  1. REACT
   2. KEGG
-  3. PHARMGKB
+  3. PHARMGKB.PATHWAYS
   4. WIKIPATHWAYS
-  5. name
+  5. BIOCARTA
+  6. GO
+  7. SMPDB
+  8. name
 
 > MolecularActivity ID Resolution is done through BioThings Gene Ontology Molecular Activity API
 
@@ -170,37 +213,31 @@ let input = {
   2. MetaCyc
   3. RHEA
   4. KEGG.REACTION
-  5. Reactome
+  5. REACT
+  6. name
 
 > CellularComponent ID Resolution is done through BioThings Gene Ontology Cellular Component API
 
 - CellularComponent
   1. GO
-  2. MESH
-  3. UMLS
-  4. NCIT
-  5. SNOMEDCT
-  6. UBERON
-  7. CL
-  8. name
+  2. name
 
 > BiologicalProcess ID Resolution is done through BioThings Gene Ontology Biological Process API
 
 - BiologicalProcess
 
   1. GO
   2. MetaCyc
-  3. Reactome
+  3. REACT
   4. name
 
 > AnatomicalEntity ID Resolution is done through BioThings UBERON API
 
 - AnatomicalEntity
   1. UBERON
   2. UMLS
-  3. NCIT
-  4. MESH
-  5. name
+  3. MESH
+  4. name
 
 > PhenotypicFeature ID Resolution is done through BioThings HPO API
 
@@ -215,16 +252,21 @@ let input = {
   8. MP
   9. name
 
-> Cell ID Resolution is done through nodenormalization API
+> ClinicalFinding ID Resolution is done through MyDisease.info API
+
+- ClinicalFinding
+  1. LOINC
+  2. NCIT
+  3. EFO
+  4. name
+
+> Cell ID Resolution is done through Biothings Cell Ontology API
 
 - Cell
   1. CL
-  2. UMLS
-  3. NCIT
-  4. MESH
-  5. UBERON
-  6. SNOMEDCT
-  7. name
+  2. NCIT
+  3. MESH
+  4. name
 
 ## Development
 
@@ -234,9 +276,9 @@ let input = {
 3. Run `npm ci` to install the dependencies.
 4. scripts are stored in `/src` folder
 5. Add test to `/__tests__` folder
-6. run `npm run release` to bump version and generte change log
+6. run `npm run release` to bump version and generate change log
 7. run `npx depcheck` to check for unused packages in package.json
 
 ## CHANGELOG
 
-See [CHANGELOG.md](https://github.com/kevinxin90/biomedical_id_resolver.js/blob/master/CHANGELOG.md)
+See [CHANGELOG.md](https://github.com/biothings/biomedical_id_resolver.js/blob/master/CHANGELOG.md)

__tests__/integration/default_resolver.test.ts

@@ -232,20 +232,20 @@ describe("Test ID Resolver", () => {
         expect(res["NCIT:C116936"][0]).toBeInstanceOf(ResolvableBioEntity);
     })
 
-    // skip RHEA test below per https://github.com/biothings/biomedical_id_resolver.js/pull/56
-    test.skip("Test chemical ids can be resolved as RHEA ids", async () => {
+    // update RHEA test to use MolecularActivity semantic type
+    test("Test molecular activity ids can be resolved as RHEA ids", async () => {
         const resolver = new DefaultIDResolver();
-        const res = await resolver.resolve({ "ChemicalSubstance": ["PUBCHEM.COMPOUND:5460389"] });
-        expect(res["PUBCHEM.COMPOUND:5460389"][0]).toBeInstanceOf(ResolvableBioEntity);
-        expect(res["PUBCHEM.COMPOUND:5460389"][0].dbIDs).toHaveProperty("RHEA");
-        expect(res["PUBCHEM.COMPOUND:5460389"][0].dbIDs.RHEA).toContain("RHEA:37975")
+        const res = await resolver.resolve({ "MolecularActivity": ["GO:0010176"] });
+        expect(res["GO:0010176"][0]).toBeInstanceOf(ResolvableBioEntity);
+        expect(res["GO:0010176"][0].dbIDs).toHaveProperty("RHEA");
+        expect(res["GO:0010176"][0].dbIDs.RHEA).toContain("RHEA:37975")
     })
 
-    // skip RHEA test below per https://github.com/biothings/biomedical_id_resolver.js/pull/56
-    test.skip("Test RHEA ids can be correctly resolved", async () => {
+    // update RHEA test to use MolecularActivity semantic type
+    test("Test RHEA ids can be correctly resolved", async () => {
         const resolver = new DefaultIDResolver();
-        const res = await resolver.resolve({ "ChemicalSubstance": ["RHEA:37975"] });
+        const res = await resolver.resolve({ "MolecularActivity": ["RHEA:37975"] });
         expect(res["RHEA:37975"][0]).toBeInstanceOf(ResolvableBioEntity);
-        expect(res["RHEA:37975"][0].primaryID).toEqual("CHEBI:16169")
+        expect(res["RHEA:37975"][0].primaryID).toEqual("GO:0010176")
     })
-})
+})

__tests__/unittest/bioentity.test.ts

@@ -11,7 +11,7 @@ const CDK2_DB_IDs = {
 const RILUZOLE_DB_IDS = {
     "CHEMBL.COMPOUND": ["CHEMBL744"],
     "name": ["Riluzole", "RILUZOLE"],
-    "PUBCHEM": ["5070"],
+    "PUBCHEM.COMPOUND": ["5070"],
 }
 
 const DB_ID_WITH_NO_PRIMARY = {
@@ -22,7 +22,11 @@ const DISEASE_DB_IDS = {
     "MONDO": ["MONDO:12345"]
 }
 
-const CHEMBL7512_DB_IDS = { "CHEMBL.COMPOUND": ["CHEMBL7512"], "PUBCHEM": ["53428"] }
+const CHEMBL7512_DB_IDS = {
+    "CHEMBL.COMPOUND": ["CHEMBL7512"],
+    "PUBCHEM.COMPOUND": ["53428"]
+}
+
 describe("Test ResolvableBioEntity Class", () => {
     test("return semanticType when called semanticType property", () => {
         const entity = new ResolvableBioEntity("Gene", CDK2_DB_IDs, {});
@@ -147,4 +151,4 @@ describe("Test IrresolvableBioEntity Class", () => {
 
     })
 
-})
+})

src/common/types.ts

@@ -13,11 +13,15 @@ export interface BioThingsAPIFailedQueryResponse extends BioThingsAPIQueryRespon
 
 export type ResolvableSemanticTypes =
   | 'Gene'
+  | 'Transcript'
+  | 'Protein'
   | 'SequenceVariant'
   | 'ChemicalSubstance'
+  | 'Drug'
   | 'Disease'
   | 'DiseaseOrPhenotypicFeature'
   | 'PhenotypicFeature'
+  | 'ClinicalFinding'
   | 'MolecularActivity'
   | 'BiologicalProcess'
   | 'CellularComponent'
@@ -27,11 +31,15 @@ export type ResolvableSemanticTypes =
 
 export enum ResolvableTypes {
   Gene = 'Gene',
+  Transcript = 'Transcript',
+  Protein = 'Protein',
   SequenceVariant = 'SequenceVariant',
   ChemicalSubstance = 'ChemicalSubstance',
+  Drug = 'Drug',
   Disease = 'Disease',
   DiseaseOrPhenotypicFeature = 'DiseaseOrPhenotypicFeature',
   PhenotypicFeature = 'PhenotypicFeature',
+  ClinicalFinding = 'ClinicalFinding',
   MolecularActivity = 'MolecularActivity',
   BiologicalProcess = 'BiologicalProcess',
   CellularComponent = 'CellularComponent',