jamesamcl
commented
2 years ago In OLS3 this seems to be based on "related from" relations.
String relatedGraphQuery = "MATCH path = (n:Class)-[r:SUBCLASSOF|Related]-(parent)\n"+
"WHERE n.ontology_name = {0} AND n.iri = {1}\n"+
"UNWIND nodes(path) as p\n" +
"UNWIND rels(path) as r1\n" +
"RETURN {nodes: collect( distinct {iri: p.iri, label: p.label})[0..200], " +
"edges: collect (distinct {source: startNode(r1).iri, target: endNode(r1).iri, label: r1.label, uri: r1.uri} )[0..200]} as result";
String relatedFromQuery = "MATCH (x)-[r:Related]->(n:Class) WHERE n.ontology_name = {0} AND n.iri = {1} RETURN r.label as relation, collect( {iri: x.iri, label: x.label})[0..99] as terms limit 100";
String usageQuery = "MATCH (n:Resource)<-[r:REFERSTO]-(x) WHERE n.iri = {0} RETURN distinct ({name: x.ontology_name, prefix: x.ontology_prefix}) as usage";
private Collection<Individual> instances;
public Object getGraphJson(String ontologyName, String iri, int distance) {
Map<String, Object> paramt = new HashMap<>();
paramt.put("0", ontologyName);
paramt.put("1", iri);
Result res = graphDatabaseService.execute(relatedGraphQuery, paramt);
return res.next().get("result");
}
public Map<String, Collection<Map<String, String>>> getRelatedFrom(String ontologyId, String iri) {
Map<String, Object> paramt = new HashMap<>();
paramt.put("0", ontologyId);
paramt.put("1", iri);
Result res = graphDatabaseService.execute(relatedFromQuery, paramt);
Map<String, Collection<Map<String, String>>> relatedFromMap = new HashMap<>();
while (res.hasNext()) {
Map<String, Object> r = res.next();
String relationLabel = r.get("relation").toString();
relatedFromMap.put(relationLabel, (Collection<Map<String, String>>) r.get("terms"));
}
return relatedFromMap;
}
public Collection<Map<String, String>> getOntologyUsage (String iri) {
Map<String, Object> paramt = new HashMap<>();
paramt.put("0", iri);
Result res = graphDatabaseService.execute(usageQuery,paramt);
Collection<Map<String, String>> usageInfo = new HashSet<>();
while (res.hasNext()) {
Map<String, Object> r = res.next();
usageInfo.add((Map<String, String>) r.get("usage"));
}
return usageInfo;
}Everything else just uses the termRepository methods which should already be implemented.
For legacy plugins
https://www.ebi.ac.uk/ols/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000400/graph