simple: fast fixes

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=main)](https://coveralls.io/github/biothings/biomedical_id_resolver.js?branch=main)
 ![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)
 
 
 
@@ -104,7 +104,7 @@ let input = {
 
 ## Available Semantic Types & prefixes
 
-> Gene ID resolution is done through MyGene.info API
+> Gene, Transcript, Protein ID resolution is done through MyGene.info API
 
 - Gene
   1. NCBIGene
@@ -114,7 +114,20 @@ let input = {
   5. OMIM
   6. UniProtKB
   7. UMLS
-  8. name
+  8. MGI
+  9. name
+
+- Transcript
+  1. ENSEMBL
+  2. SYMBOL
+  3. name
+
+- Protein
+  1. UniProtKB
+  2. ENSEMBL
+  3. SYMBOL
+  4. UMLS
+  5. name
 
 > Variant ID resolution is done through MyVariant.info API
 
@@ -124,21 +137,35 @@ let input = {
   3. MYVARIANT_HG19
   4. ClinVar
 
-> ChemicalSubstance ID resolution is done through MyChem.info API
+> ChemicalSubstance, Drug ID resolution is done through MyChem.info API
 
 - ChemicalSubstance
     1. CHEBI
     2. CHEMBL.COMPOUND
     3. DRUGBANK
-    4. PUBCHEM
+    4. PUBCHEM.COMPOUND
     5. MESH
     6. INCHI
     7. INCHIKEY
     8. UNII
-    9. KEGG
+    9. KEGG.COMPOUND
     10. UMLS
-    11. name
-    12. id
+    11. LINCS
+    12. name
+
+- Drug
+    1. CHEBI
+    2. CHEMBL.COMPOUND
+    3. DRUGBANK
+    4. PUBCHEM.COMPOUND
+    5. MESH
+    6. INCHI
+    7. INCHIKEY
+    8. UNII
+    9. KEGG.COMPOUND
+    10. UMLS
+    11. LINCS
+    12. name
 
 > Disease ID Resolution is done through MyDisease.info API
 
@@ -148,20 +175,24 @@ let input = {
   2. DOID
   3. OMIM
   4. ORPHANET
-  5. EFO
-  6. UMLS
-  7. MESH
-  8. GARD
-  9. name
+  5. SNOMEDCT
+  6. NCIT
+  7. EFO
+  8. UMLS
+  9. MESH
+  10. HP
+  11. GARD
+  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. name
 
 > MolecularActivity ID Resolution is done through BioThings Gene Ontology Molecular Activity API
 
@@ -170,37 +201,31 @@ 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 +240,13 @@ let input = {
   8. MP
   9. name
 
-> Cell ID Resolution is done through nodenormalization API
+> 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 +256,9 @@ 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/main/CHANGELOG.md)

__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, {});

src/common/types.ts

@@ -13,8 +13,11 @@ export interface BioThingsAPIFailedQueryResponse extends BioThingsAPIQueryRespon
 
 export type ResolvableSemanticTypes =
   | 'Gene'
+  | 'Transcript'
+  | 'Protein'
   | 'SequenceVariant'
   | 'ChemicalSubstance'
+  | 'Drug'
   | 'Disease'
   | 'DiseaseOrPhenotypicFeature'
   | 'PhenotypicFeature'
@@ -27,8 +30,11 @@ export type ResolvableSemanticTypes =
 
 export enum ResolvableTypes {
   Gene = 'Gene',
+  Transcript = 'Transcript',
+  Protein = 'Protein',
   SequenceVariant = 'SequenceVariant',
   ChemicalSubstance = 'ChemicalSubstance',
+  Drug = 'Drug',
   Disease = 'Disease',
   DiseaseOrPhenotypicFeature = 'DiseaseOrPhenotypicFeature',
   PhenotypicFeature = 'PhenotypicFeature',