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

package dbnp.data

/**
 * This class describes an existing ontology, of which terms can be stored (actually 'cached' would be a better description)
 * in the (global) Term store.
 * This information is mapped from the BioPortal NCBO REST service, e.g.: http://rest.bioontology.org/bioportal/ontologies/38802
 * @see http://www.bioontology.org/wiki/index.php/NCBO_REST_services
 *
 * Revision information:
 * $Rev: 558 $
 * $Author: roberth $
 * $Date: 2010-06-11 14:00:10 +0000 (vr, 11 jun 2010) $
 */
class Ontology implements Serializable {
        String name             // BioPortal: displayLabel
        String description      // BioPortal: description
        String url              // BioPortal: homepage
        String versionNumber    // BioPortal: versionNumber
        int ncboId              // BioPortal: ontologyId
        int ncboVersionedId     // BioPortal: id

        /**
         * Find child terms
         * @return A set containing all terms that reside under this ontology
         */
        Set<Term> giveTerms() {
                Term.findAllByOntology(this)
        }

        Object giveTermByName(String name) {
                giveTerms().find {
                        it.name == name
                }

                /* TODO: find out why the following doesn't work (probably more efficient):
                Term.find {
                        it.name == name
                        it.ontology == this
                }
                }*/
        }

        static Ontology getBioPortalOntology(String ncboId) {
                // Get ontology from BioPortal via Ontocat
                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
                uk.ac.ebi.ontocat.Ontology o = os.getOntology(ncboId)

                // Instantiate and return Ontology object
                new dbnp.data.Ontology(
                        name: o.label,
                        description: o.description,
                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
                        versionNumber: o.versionNumber,
                        ncboId: o.ontologyAccession,
                        ncboVersionedId: o.id
                );
        }

        static Ontology getBioPortalOntologyByTerm(String termId) {
                // Get ontology from BioPortal via Ontocat
                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
                uk.ac.ebi.ontocat.OntologyTerm term = os.getTerm( termId );
                println( term );
                uk.ac.ebi.ontocat.Ontology o = os.getOntology( term.getOntologyAccession() );
                println( o );

                // Instantiate and return Ontology object
                new dbnp.data.Ontology(
                        name: o.label,
                        description: o.description,
                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
                        versionNumber: o.versionNumber,
                        ncboId: o.ontologyAccession,
                        ncboVersionedId: o.id
                );
        }
}