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

Example 46 with OntologyTerm

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

the class DgaDatabaseImporter method findTermsWithParents.

// extra step to take out redundant terms, if a child term is more specific dont keep the parent, if 2 lines share
// same pubmed, gene and gene RIF take the most specific uri
// example: same pubed, same gene 1-leukemia 2-myeloid leukemia 3-acute myeloid leukemia, keep only 3-
private void findTermsWithParents() throws Exception {
    try (BufferedReader dgaReader = new BufferedReader(new FileReader(dgaFile))) {
        String line;
        while ((line = dgaReader.readLine()) != null) {
            // found a term
            if (line.contains("DOID")) {
                // this being of the url could change make sure its still correct if something doesn't work
                String valueUri = "http://purl.obolibrary.org/obo/DOID_" + this.findStringBetweenSpecialCharacter(line);
                String geneId = this.findStringBetweenSpecialCharacter(dgaReader.readLine(), "GeneID");
                String pubMedID = this.findStringBetweenSpecialCharacter(dgaReader.readLine(), "PubMedID");
                String geneRIF = this.findStringBetweenSpecialCharacter(dgaReader.readLine(), "GeneRIF");
                OntologyTerm o = this.findOntologyTermExistAndNotObsolote(valueUri);
                if (o != null) {
                    String key = geneId + pubMedID + geneRIF;
                    HashSet<OntologyTerm> valuesUri = new HashSet<>();
                    if (commonLines.get(key) != null) {
                        valuesUri = commonLines.get(key);
                    }
                    valuesUri.add(o);
                    commonLines.put(key, valuesUri);
                }
            }
        }
        dgaReader.close();
    }
    for (String key : commonLines.keySet()) {
        AbstractCLI.log.info("Checking for lines that are ontology duplicated: " + key);
        HashSet<OntologyTerm> ontologyTerms = commonLines.get(key);
        HashSet<String> allUri = new HashSet<>();
        for (OntologyTerm o : ontologyTerms) {
            allUri.add(o.getUri());
        }
        for (OntologyTerm o : ontologyTerms) {
            // get all kids terms
            Collection<OntologyTerm> childrenOntology = o.getChildren(false);
            for (OntologyTerm onChil : childrenOntology) {
                // then this line is a parent dont keep it there is more specific child term
                if (allUri.contains(onChil.getUri())) {
                    // result of this method, set of lines to exclude in the checkForDGAFile() step :
                    linesToExclude.add(key + o.getUri());
                }
            }
        }
    }
}

Example 47 with OntologyTerm

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

the class EvidenceImporterCLI method experiementTags2Ontology.

private Set<CharacteristicValueObject> experiementTags2Ontology(Set<String> values, String category, String categoryUri, AbstractOntologyService ontologyUsed) {
    Set<CharacteristicValueObject> experimentTags = new HashSet<>();
    for (String term : values) {
        String valueUri = "";
        if (ontologyUsed != null) {
            Collection<OntologyTerm> ontologyTerms = ontologyUsed.findTerm(term);
            OntologyTerm ot = this.findExactTerm(ontologyTerms, term);
            if (ot != null) {
                valueUri = ot.getUri();
            }
        }
        CharacteristicValueObject c = new CharacteristicValueObject(-1L, term, category, valueUri, categoryUri);
        experimentTags.add(c);
    }
    return experimentTags;
}

Example 48 with OntologyTerm

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

the class EvidenceImporterCLI method phenotype2Ontology.

// value or valueUri given changed to valueUri (even if valueUri is given in file we need to check)
private String phenotype2Ontology(String phenotypeToSearch) {
    OntologyTerm ot;
    // we got an uri, search by uri
    if (phenotypeToSearch.contains("http://purl.")) {
        AbstractCLI.log.info("Found an URI: " + phenotypeToSearch);
        ot = this.diseaseOntologyService.getTerm(phenotypeToSearch);
        if (ot == null) {
            ot = this.humanPhenotypeOntologyService.getTerm(phenotypeToSearch);
        }
        if (ot == null) {
            this.mammalianPhenotypeOntologyService.getTerm(phenotypeToSearch);
        }
    } else // value found
    {
        // search disease
        Collection<OntologyTerm> ontologyTerms = this.diseaseOntologyService.findTerm(phenotypeToSearch);
        ot = this.findExactTerm(ontologyTerms, phenotypeToSearch);
        if (ot == null) {
            // search hp
            ontologyTerms = this.humanPhenotypeOntologyService.findTerm(phenotypeToSearch);
            ot = this.findExactTerm(ontologyTerms, phenotypeToSearch);
        }
        if (ot == null) {
            // search mammalian
            ontologyTerms = this.mammalianPhenotypeOntologyService.findTerm(phenotypeToSearch);
            this.findExactTerm(ontologyTerms, phenotypeToSearch);
        }
    }
    return phenotypeToSearch;
}

Example 49 with OntologyTerm

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

the class EvidenceImporterAbstractCLI method findExactTerm.

/**
 * find the exact term of a search term in a Collection of Ontology terms
 *
 * @param ontologyTerms Collection of ontologyTerms
 * @param search        The value we are interested in finding
 * @return OntologyTerm the exact match value found
 */
OntologyTerm findExactTerm(Collection<OntologyTerm> ontologyTerms, String search) {
    // list of OntologyTerms found
    Collection<OntologyTerm> ontologyKept = new HashSet<>();
    OntologyTerm termFound = null;
    for (OntologyTerm ot : ontologyTerms) {
        if (ot.getLabel() != null) {
            if (ot.getLabel().equalsIgnoreCase(search)) {
                ontologyKept.add(ot);
                termFound = ot;
            }
        }
    }
    // if we have more than 1 result, hardcode the one to choose
    if (ontologyKept.size() > 1) {
        if (search.equalsIgnoreCase("juvenile")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://purl.org/obo/owl/PATO#PATO_0001190")) {
                    return ontologyTerm;
                }
            }
        } else if (search.equalsIgnoreCase("adult")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#birnlex_681")) {
                    return ontologyTerm;
                }
            }
        } else if (search.equalsIgnoreCase("newborn")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#birnlex_699")) {
                    return ontologyTerm;
                }
            }
        } else if (search.equalsIgnoreCase("prenatal")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#birnlex_7014")) {
                    return ontologyTerm;
                }
            }
        } else if (search.equalsIgnoreCase("infant")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#birnlex_695")) {
                    return ontologyTerm;
                }
            }
        } else if (search.equalsIgnoreCase("elderly")) {
            for (OntologyTerm ontologyTerm : ontologyKept) {
                if (ontologyTerm.getUri().equalsIgnoreCase("http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl#birnlex_691")) {
                    return ontologyTerm;
                }
            }
        }
    }
    if (ontologyKept.size() > 1) {
        if (search.equalsIgnoreCase("apraxia")) {
            for (OntologyTerm o : ontologyKept) {
                if (o.getLabel().equalsIgnoreCase("apraxia") && o.getUri().equalsIgnoreCase("http://purl.obolibrary.org/obo/DOID_4019")) {
                    return o;
                }
            }
        }
        this.writeError("More than 1 term found for : " + search + "   " + ontologyKept.size());
        for (OntologyTerm o : ontologyKept) {
            this.writeError(o.getLabel() + " " + o.getUri());
        }
    }
    return termFound;
}

Example 50 with OntologyTerm

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

the class ExternalDatabaseEvidenceImporterAbstractCLI method meshToDiseaseTerms.

private HashMap<String, Collection<OntologyTerm>> meshToDiseaseTerms(Collection<OntologyTerm> meshTerms) {
    HashMap<String, Collection<OntologyTerm>> diseaseTerms = new HashMap<>();
    for (OntologyTerm m : meshTerms) {
        String meshId = this.changeToId(m.getUri());
        Collection<OntologyTerm> onDisease = this.findOntologyTermsUriWithDiseaseId(meshId);
        if (!onDisease.isEmpty()) {
            diseaseTerms.put(meshId, onDisease);
        }
    }
    return diseaseTerms;
}