source: trunk/grails-app/domain/dbnp/data/Ontology.groovy @ 558

Last change on this file since 558 was 558, checked in by roberth, 11 years ago

Improved template editor , stringlists and ontologyfields can be edited and extra checks are built in.

  • Property svn:keywords set to Date Rev Author
File size: 2.6 KB
Line 
1package dbnp.data
2
3/**
4 * This class describes an existing ontology, of which terms can be stored (actually 'cached' would be a better description)
5 * in the (global) Term store.
6 * This information is mapped from the BioPortal NCBO REST service, e.g.: http://rest.bioontology.org/bioportal/ontologies/38802
7 * @see http://www.bioontology.org/wiki/index.php/NCBO_REST_services
8 *
9 * Revision information:
10 * $Rev: 558 $
11 * $Author: roberth $
12 * $Date: 2010-06-11 14:00:10 +0000 (vr, 11 jun 2010) $
13 */
14class Ontology implements Serializable {
15        String name             // BioPortal: displayLabel
16        String description      // BioPortal: description
17        String url              // BioPortal: homepage
18        String versionNumber    // BioPortal: versionNumber
19        int ncboId              // BioPortal: ontologyId
20        int ncboVersionedId     // BioPortal: id
21
22        /**
23         * Find child terms
24         * @return A set containing all terms that reside under this ontology
25         */
26        Set<Term> giveTerms() {
27                Term.findAllByOntology(this)
28        }
29
30        Object giveTermByName(String name) {
31                giveTerms().find {
32                        it.name == name
33                }
34
35                /* TODO: find out why the following doesn't work (probably more efficient):
36                Term.find {
37                        it.name == name
38                        it.ontology == this
39                }
40                }*/
41        }
42
43        static Ontology getBioPortalOntology(String ncboId) {
44                // Get ontology from BioPortal via Ontocat
45                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
46                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
47                uk.ac.ebi.ontocat.Ontology o = os.getOntology(ncboId)
48
49                // Instantiate and return Ontology object
50                new dbnp.data.Ontology(
51                        name: o.label,
52                        description: o.description,
53                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
54                        versionNumber: o.versionNumber,
55                        ncboId: o.ontologyAccession,
56                        ncboVersionedId: o.id
57                );
58        }
59
60        static Ontology getBioPortalOntologyByTerm(String termId) {
61                // Get ontology from BioPortal via Ontocat
62                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
63                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
64                uk.ac.ebi.ontocat.OntologyTerm term = os.getTerm( termId );
65                println( term );
66                uk.ac.ebi.ontocat.Ontology o = os.getOntology( term.getOntologyAccession() );
67                println( o );
68
69                // Instantiate and return Ontology object
70                new dbnp.data.Ontology(
71                        name: o.label,
72                        description: o.description,
73                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
74                        versionNumber: o.versionNumber,
75                        ncboId: o.ontologyAccession,
76                        ncboVersionedId: o.id
77                );
78        }
79}
Note: See TracBrowser for help on using the repository browser.