Examples with OntologyIndividual ubic.basecode.ontology.model.OntologyIndividual used on opensource projects

Example 1 with OntologyIndividual

use of ubic.basecode.ontology.model.OntologyIndividual in project Gemma by PavlidisLab.

the class SearchServiceImpl method characteristicSearchTerm.

/**
 * Perform a search on a query - it does not have to be one word, it could be "parkinson's disease"
 */
private Collection<SearchResult> characteristicSearchTerm(Collection<Class<?>> classes, String query) {
    if (SearchServiceImpl.log.isDebugEnabled())
        SearchServiceImpl.log.debug("Starting search for " + query);
    StopWatch watch = this.startTiming();
    Collection<Characteristic> cs = new HashSet<>();
    Collection<OntologyIndividual> individuals = ontologyService.findIndividuals(query);
    for (Collection<OntologyIndividual> individualbatch : BatchIterator.batches(individuals, 10)) {
        Collection<String> uris = new HashSet<>();
        for (OntologyIndividual individual : individualbatch) {
            uris.add(individual.getUri());
        }
        Collection<SearchResult> dbhits = this.dbHitsToSearchResult(characteristicService.findByUri(classes, uris), null);
        for (SearchResult crs : dbhits) {
            cs.add((Characteristic) crs.getResultObject());
        }
        if (cs.size() >= SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
            break;
        }
    }
    if (individuals.size() > 0 && watch.getTime() > 1000) {
        SearchServiceImpl.log.info("Found " + individuals.size() + " individuals matching '" + query + "' in " + watch.getTime() + "ms");
    }
    /*
         * Add characteristics that have values matching the query; this pulls in items not associated with ontology
         * terms (free text). We do this here so we can apply the query logic to the matches.
         */
    if (cs.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        // note I changed the order of search operations so
        String dbQueryString = query.replaceAll("\\*", "");
        // this might not be wanted.
        Collection<Characteristic> valueMatches = characteristicService.findByValue(classes, dbQueryString);
        if (valueMatches != null && !valueMatches.isEmpty()) {
            cs.addAll(valueMatches);
            if (watch.getTime() > 1000) {
                SearchServiceImpl.log.info("Found " + valueMatches.size() + " characteristics matching value '" + query + "' in " + watch.getTime() + "ms");
            }
            watch.reset();
            watch.start();
        }
    }
    if (cs.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        /*
             * Identify initial set of matches to the query.
             */
        Collection<OntologyTerm> matchingTerms = ontologyService.findTerms(query);
        if (watch.getTime() > 1000) {
            SearchServiceImpl.log.info("Found " + matchingTerms.size() + " ontology classes matching '" + query + "' in " + watch.getTime() + "ms");
        }
        /*
             * Search for child terms.
             */
        if (!matchingTerms.isEmpty()) {
            for (OntologyTerm term : matchingTerms) {
                /*
                     * In this loop, each term is a match directly to our query, and we do a depth-first fetch of the
                     * children.
                     */
                String uri = term.getUri();
                if (StringUtils.isBlank(uri))
                    continue;
                int sizeBefore = cs.size();
                this.getCharacteristicsAnnotatedToChildren(classes, term, cs);
                if (SearchServiceImpl.log.isDebugEnabled() && cs.size() > sizeBefore) {
                    SearchServiceImpl.log.debug((cs.size() - sizeBefore) + " characteristics matching children term of " + term);
                }
                if (cs.size() >= SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
                    break;
                }
            }
            if (watch.getTime() > 1000) {
                SearchServiceImpl.log.info("Found " + cs.size() + " characteristics for '" + query + "' including child terms in " + watch.getTime() + "ms");
            }
            watch.reset();
            watch.start();
        }
    }
    /*
         * Retrieve the owner objects
         */
    watch.reset();
    watch.start();
    Collection<SearchResult> matchingEntities = this.getAnnotatedEntities(classes, cs);
    if (watch.getTime() > 1000) {
        SearchServiceImpl.log.info("Retrieved " + matchingEntities.size() + " entities via characteristics for '" + query + "' in " + watch.getTime() + "ms");
    }
    if (SearchServiceImpl.log.isDebugEnabled())
        SearchServiceImpl.log.debug("End search for " + query);
    return matchingEntities;
}

Example 2 with OntologyIndividual

use of ubic.basecode.ontology.model.OntologyIndividual in project Gemma by PavlidisLab.

the class OntologyServiceImpl method termsToCharacteristics.

/**
 * Convert raw ontology resources into VocabCharacteristics.
 */
@Override
public Collection<VocabCharacteristic> termsToCharacteristics(final Collection<? extends OntologyResource> terms) {
    Collection<VocabCharacteristic> results = new HashSet<>();
    if ((terms == null) || (terms.isEmpty()))
        return results;
    for (OntologyResource res : terms) {
        if (res == null)
            continue;
        VocabCharacteristic vc = VocabCharacteristic.Factory.newInstance();
        if (res instanceof OntologyTerm) {
            OntologyTerm term = (OntologyTerm) res;
            vc.setValue(term.getTerm());
            vc.setValueUri(term.getUri());
            vc.setDescription(term.getComment());
        } else if (res instanceof OntologyIndividual) {
            OntologyIndividual indi = (OntologyIndividual) res;
            vc.setValue(indi.getLabel());
            vc.setValueUri(indi.getUri());
            vc.setDescription("Individual");
        } else {
            OntologyServiceImpl.log.warn("What is it? " + res);
            continue;
        }
        if (vc.getValue() == null)
            continue;
        results.add(vc);
    }
    OntologyServiceImpl.log.debug("returning " + results.size() + " terms after filter");
    return results;
}

Example 3 with OntologyIndividual

use of ubic.basecode.ontology.model.OntologyIndividual in project Gemma by PavlidisLab.

the class OntologyServiceImpl method convert.

/**
 * Given a collection of ontology terms converts them to a collection of VocabCharacteristics
 */
private Collection<VocabCharacteristic> convert(final Collection<OntologyResource> resources) {
    Collection<VocabCharacteristic> converted = new HashSet<>();
    if ((resources == null) || (resources.isEmpty()))
        return converted;
    for (OntologyResource res : resources) {
        VocabCharacteristic vc = VocabCharacteristic.Factory.newInstance();
        // If there is no URI we don't want to send it back (ie useless)
        if ((res.getUri() == null) || StringUtils.isEmpty(res.getUri()))
            continue;
        if (res instanceof OntologyTerm) {
            OntologyTerm term = (OntologyTerm) res;
            vc.setValue(term.getTerm());
            vc.setValueUri(term.getUri());
            vc.setDescription(term.getComment());
        }
        if (res instanceof OntologyIndividual) {
            OntologyIndividual indi = (OntologyIndividual) res;
            vc.setValue(indi.getLabel());
            vc.setValueUri(indi.getUri());
            vc.setDescription("Individual");
        }
        converted.add(vc);
    }
    return converted;
}