Enrich antibody with external data from SciCrunch database

src/enrichment/enrich-omap.js

@@ -1,7 +1,10 @@
+import { readFileSync } from 'fs';
 import { error } from 'console';
 import { resolve } from 'path';
 import { getRawData } from '../normalization/normalize-omap.js';
 import { info, more } from '../utils/logging.js';
+import { RdfBuilder, iri, literal } from '../utils/rdf-builder.js';
+import { retrieveAntibody } from '../utils/scicrunch-client.js';
 import { convert, merge } from '../utils/robot.js';
 import { enrichBasicData } from './enrich-basic.js';
 import {
@@ -29,7 +32,6 @@ export async function enrichOmapData(context) {
   } else {
     try {
       const { selectedDigitalObject: obj } = context;
-
       const normalizedPath = resolve(obj.path, 'normalized/normalized.yaml');
       const baseInputPath = resolve(obj.path, 'enriched/base-input.ttl');
       convertNormalizedDataToOwl(context, normalizedPath, baseInputPath);
@@ -39,6 +41,38 @@ export async function enrichOmapData(context) {
       const ontologyExtractionPaths = [];
       ontologyExtractionPaths.push(baseInputPath); // Set the base input path as the initial
 
+      const rridEntitiesPath = collectEntities(context, 'rrid', baseInputPath);
+      if (!isFileEmpty(rridEntitiesPath)) {
+        const rridExtractPath = resolve(obj.path, `enriched/rrid-extract.ttl`);
+        const rrids = readFileSync(rridEntitiesPath).toString()
+          .split(/[\n\r]/)
+          .filter((str) => str)
+          .map((str) => /.*RRID:(?<rrid>.*)/.exec(str).groups.rrid)
+          .map((str) => str.toLowerCase());
+        const builder = await retrieveAntibody(rrids).then((response) => {
+          return response.reduce((accum, item) => {
+            const antibody = item["_source"]["item"];
+            const antibodyIri = `http://identifiers.org/rrid/RRID:${antibody.identifier}`;
+            return accum
+              .add(
+                iri(antibodyIri),
+                iri("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"),
+                iri("http://www.w3.org/2002/07/owl#Class"))
+              .add(
+                iri(antibodyIri), 
+                iri("http://www.w3.org/2000/01/rdf-schema#label"),
+                literal(antibody.name))
+              .add(
+                iri(antibodyIri), 
+                iri("http://www.w3.org/2000/01/rdf-schema#comment"),
+                literal(antibody.description));
+          }, new RdfBuilder(`${context.purlIri}/rrid/antibody`));
+        });
+        builder.save(rridExtractPath);
+        logOutput(rridExtractPath);
+        ontologyExtractionPaths.push(rridExtractPath);
+      }
+
       const uberonEntitiesPath = collectEntities(context, 'uberon', baseInputPath);
       if (!isFileEmpty(uberonEntitiesPath)) {
         info('Extracting UBERON.');

src/utils/get-rrid-terms.sparql

@@ -0,0 +1,16 @@
+SELECT DISTINCT ?entity
+WHERE {
+   {
+      SELECT (?s AS ?entity) WHERE { 
+         ?s ?p ?o .
+         FILTER(STRSTARTS(STR(?s),"http://identifiers.org/rrid/RRID:"))
+      }
+   }
+   UNION
+   {
+      SELECT (?o AS ?entity) WHERE {
+         ?s ?p ?o .
+         FILTER(STRSTARTS(STR(?o),"http://identifiers.org/rrid/RRID:"))
+      }
+   }
+}

src/utils/rdf-builder.js

@@ -0,0 +1,38 @@
+import { writeFileSync } from 'fs';
+import { graph, sym, lit, serialize } from 'rdflib';
+
+
+export function RdfBuilder(iri) {
+  const store = graph();
+  store.add(
+    sym(iri), 
+    sym("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"), 
+    sym("http://www.w3.org/2002/07/owl#Ontology"));
+
+  this.add = function (subject, predicate, object) {
+    if (subject && predicate && object) {
+      store.add(subject, predicate, object);
+    }
+    return this;
+  }
+
+  this.build = function () {
+    return serialize(null, store, null, null, (err, result) => {
+      return result;
+    })
+  }
+
+  this.save = function(filePath) {
+    serialize(null, store, null, null, (err, result) => {
+      writeFileSync(filePath, result);
+    })
+  }
+}
+
+export function iri(text) {
+  return sym(text);
+}
+
+export function literal(text) {
+  return lit(text);
+}

src/utils/scicrunch-client.js

@@ -0,0 +1,40 @@
+import fetch from 'node-fetch';
+
+const API_BASE = "https://api.scicrunch.io/elastic/v1";
+const ANTIBODY_INDEX = "RIN_Antibody_pr";
+const TOOL_INDEX = "RIN_Tool_pr";
+
+export function retrieveAntibody(rrids) {
+  const url = `${API_BASE}/${ANTIBODY_INDEX}/_search`;
+  const options = {
+    method: "POST",
+    headers: {
+      'Content-Type': "application/json",
+      apikey: process.env.SCICRUNCH_API_KEY
+    },
+    body: JSON.stringify(createQuery(rrids))
+  };
+  return fetch(url, options).then((response) => {
+    return response.json().then((data) => {
+      return data.hits.hits;
+    });
+  }).catch((err) => { console.log(err); });
+}
+
+function createQuery(rrids) {
+  return {
+    size: 1000,
+    query: {
+      terms: {
+        "rrid.curie": rrids
+      }
+    },
+    "_source": {
+      includes: [
+        "item.identifier",
+        "item.name",
+        "item.description"
+      ]
+    }
+  }
+}