Merge pull request #5 from biothings/bte_804_update_data

update ontology files and dependencies in README

README.md

@@ -8,6 +8,10 @@ Module for expanding terms to children.
 pnpm i @biothings-explorer/node-expansion
 ```
 
+### Dependencies
+1. Java 11+ (to run `robot.jar`)
+2. Download the script and JAR from [ROBOT](http://robot.obolibrary.org/). The script for Mac & Linux is already downloaded.
+
 ## Usage
 
 - by default, the module will expand terms to all descendants
@@ -62,3 +66,6 @@ console.log(getDescendants(['GO:0022010', 'DOID:0060524', 'DOID:4'], recursive=f
 node download.js
 ```
  - downloads, converts, and parses all the owl files listed in the config file
+
+## References
+R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019.

__test__/index.test.js

@@ -27,13 +27,12 @@ test('go', () => {
   expect(descendants['GO:0032553']).toContain('GO:0032559');
 });
 
-//HP:0003812 -> HP:0003829 -> HP:0003831
-//Phenotypic variability -> Incomplete penetrance -> Age-dependent penetrance
+//HP:0003812 -> HP:0003828
+//Phenotypic variability -> Variable expressivity
 test('hp', () => {
   let curies = ['HP:0003812'];
   let descendants = getDescendants(curies);
-  expect(descendants['HP:0003812']).toContain('HP:0003829');
-  expect(descendants['HP:0003812']).toContain('HP:0003831');
+  expect(descendants['HP:0003812']).toContain('HP:0003828');
 });
 
 //MONDO:0001517 -> MONDO:0001955 -> MONDO:0024275
@@ -57,8 +56,7 @@ test('umls', () => {
 test('multiple', () => {
   let curies = ['HP:0003812', 'MONDO:0001517'];
   let descendants = getDescendants(curies);
-  expect(descendants['HP:0003812']).toContain('HP:0003829');
-  expect(descendants['HP:0003812']).toContain('HP:0003831');
+  expect(descendants['HP:0003812']).toContain('HP:0003828');
   expect(descendants['MONDO:0001517']).toContain('MONDO:0001955');
   expect(descendants['MONDO:0001517']).toContain('MONDO:0024275');
 });

src/download.js

@@ -20,6 +20,7 @@ for (let ontology of Object.values(ONTOLOGIES)) {
     console.log(`Done downloading ${url} with code ${code}`);
 
     // use robot to convert owl to json
+    // http://robot.obolibrary.org/
     child_process.execSync(
       `../robot convert -i ../data/${ontology.name}.owl --format json -o ../data/${ontology.name}.json`,
     );