Examples with Locus uk.ac.ebi.spot.goci.model.Locus used on opensource projects

Example 1 with Locus

use of uk.ac.ebi.spot.goci.model.Locus in project goci by EBISPOT.

the class AssociationRowProcessor method createLoci.

private Collection<Locus> createLoci(AssociationUploadRow row, Boolean snpInteraction, Boolean multiSnpHaplotype) {
    String delimiter;
    Collection<Locus> loci = new ArrayList<>();
    if (snpInteraction) {
        delimiter = "x";
        // For SNP interaction studies we need to create a locus per risk allele
        // Handle curator entered risk allele
        Collection<RiskAllele> locusRiskAlleles = createLocusRiskAlleles(row.getStrongestAllele(), row.getSnp(), row.getProxy(), row.getRiskFrequency(), row.getSnpStatus(), delimiter);
        // Deal with genes for each interaction which should be
        // separated by 'x'
        String[] separatedGenes = row.getAuthorReportedGene().split(delimiter);
        int geneIndex = 0;
        for (RiskAllele riskAllele : locusRiskAlleles) {
            Locus locus = new Locus();
            // Set risk alleles, assume one locus per risk allele
            Collection<RiskAllele> currentLocusRiskAlleles = new ArrayList<>();
            currentLocusRiskAlleles.add(riskAllele);
            locus.setStrongestRiskAlleles(currentLocusRiskAlleles);
            // Set gene
            String interactionGene = separatedGenes[geneIndex];
            Collection<Gene> locusGenes = associationAttributeService.createLocusGenes(interactionGene, ",");
            locus.setAuthorReportedGenes(locusGenes);
            geneIndex++;
            // Set description
            locus.setDescription("SNP x SNP interaction");
            loci.add(locus);
        }
    } else // Handle multi-snp and standard snp
    {
        delimiter = ";";
        // For multi-snp and standard snps we assume their is only one locus
        Locus locus = new Locus();
        // Handle curator entered genes, for haplotype they are separated by a comma
        if (row.getAuthorReportedGene() != null && !row.getAuthorReportedGene().isEmpty()) {
            Collection<Gene> locusGenes = associationAttributeService.createLocusGenes(row.getAuthorReportedGene(), ",");
            locus.setAuthorReportedGenes(locusGenes);
        }
        // Handle curator entered risk allele
        Collection<RiskAllele> locusRiskAlleles = createLocusRiskAlleles(row.getStrongestAllele(), row.getSnp(), row.getProxy(), row.getRiskFrequency(), row.getSnpStatus(), delimiter);
        // For standard associations set the risk allele frequency to the
        // same value as the overall association frequency
        Collection<RiskAllele> locusRiskAllelesWithRiskFrequencyValues = new ArrayList<>();
        if (!multiSnpHaplotype) {
            for (RiskAllele riskAllele : locusRiskAlleles) {
                riskAllele.setRiskFrequency(row.getAssociationRiskFrequency());
                locusRiskAllelesWithRiskFrequencyValues.add(riskAllele);
            }
            locus.setStrongestRiskAlleles(locusRiskAllelesWithRiskFrequencyValues);
        } else {
            locus.setStrongestRiskAlleles(locusRiskAlleles);
        }
        // Set locus attributes
        Integer haplotypeCount = locusRiskAlleles.size();
        if (haplotypeCount > 1) {
            locus.setHaplotypeSnpCount(haplotypeCount);
            locus.setDescription(String.valueOf(haplotypeCount) + "-SNP haplotype");
        } else {
            locus.setDescription("Single variant");
        }
        loci.add(locus);
    }
    return loci;
}

Example 2 with Locus

use of uk.ac.ebi.spot.goci.model.Locus in project goci by EBISPOT.

the class ValidationChecksBuilder method runLociAttributeChecks.

/**
     * Run loci attributes checks on association
     *
     * @param association association to be checked
     */
public Collection<ValidationError> runLociAttributeChecks(Association association, String eRelease) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    if (association.getLoci() != null) {
        Set<String> associationGenes = new HashSet<>();
        Collection<ValidationError> geneErrors = new ArrayList<>();
        // Create a unique set of all locus genes
        for (Locus locus : association.getLoci()) {
            Set<String> locusGenes = new HashSet<>();
            if (!locus.getAuthorReportedGenes().isEmpty()) {
                locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
            }
            associationGenes.addAll(locusGenes);
        }
        // Check genes
        associationGenes.forEach(geneName -> {
            getLog().info("Checking gene: ".concat(geneName));
            ValidationError geneError = errorCreationService.checkGene(geneName, eRelease);
            if (geneError.getError() != null) {
                geneErrors.add(geneError);
            }
        });
        if (!geneErrors.isEmpty()) {
            validationErrors.addAll(geneErrors);
        }
        for (Locus locus : association.getLoci()) {
            Collection<RiskAllele> riskAlleles = locus.getStrongestRiskAlleles();
            // Check risk allele attributes
            riskAlleles.forEach(riskAllele -> {
                ValidationError riskAlleleError = errorCreationService.checkRiskAllele(riskAllele.getRiskAlleleName());
                validationErrors.add(riskAlleleError);
                if (geneErrors.isEmpty()) {
                    Set<String> locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
                    locusGenes.forEach(geneName -> {
                        getLog().info("Checking snp/gene location: ".concat(geneName).concat(" ").concat(riskAllele.getSnp().getRsId()));
                        ValidationError snpGeneLocationError = errorCreationService.checkSnpGeneLocation(riskAllele.getSnp().getRsId(), geneName, eRelease);
                        validationErrors.add(snpGeneLocationError);
                    });
                } else {
                    ValidationError snpError = errorCreationService.checkSnp(riskAllele.getSnp().getRsId(), eRelease);
                    validationErrors.add(snpError);
                }
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 3 with Locus

use of uk.ac.ebi.spot.goci.model.Locus in project goci by EBISPOT.

the class DefaultGWASOWLConverter method convertAssociation.

protected void convertAssociation(Association association, OWLOntology ontology, Set<String> issuedWarnings) {
    // get the trait association class
    OWLClass taClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.TRAIT_ASSOCIATION_CLASS_IRI));
    IRI taIndIRI = getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, association);
    // create a new trait association instance
    OWLNamedIndividual taIndiv = getDataFactory().getOWLNamedIndividual(taIndIRI);
    // assert class membership
    OWLClassAssertionAxiom classAssertion = getDataFactory().getOWLClassAssertionAxiom(taClass, taIndiv);
    getManager().addAxiom(ontology, classAssertion);
    // get datatype relations
    OWLDataProperty has_p_value = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_P_VALUE_PROPERTY_IRI));
    // get annotation relations
    OWLAnnotationProperty rdfsLabel = getDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
    //pvalue but says it was less then 10-6. So if we have no pvalue we just don't add it.
    if (association.getPvalueMantissa() != null && association.getPvalueExponent() != null) {
        double pval = association.getPvalueMantissa() * Math.pow(10, association.getPvalueExponent());
        OWLLiteral pValue = getDataFactory().getOWLLiteral(pval);
        //            OWLLiteral pValue = getDataFactory().getOWLLiteral(association.getPvalueMantissa()+"e"+association.getPvalueExponent());
        OWLDataPropertyAssertionAxiom p_value_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_p_value, taIndiv, pValue);
        AddAxiom add_p_value = new AddAxiom(ontology, p_value_relation);
        getManager().applyChange(add_p_value);
    }
    // get the snp instance for this association
    OWLNamedIndividual snpIndiv;
    String rsId = null;
    for (Locus locus : association.getLoci()) {
        for (RiskAllele riskAllele : locus.getStrongestRiskAlleles()) {
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            rsId = snp.getRsId();
            snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, snp));
            if (snpIndiv == null) {
                String warning = "A new SNP with the given RSID only will be created";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                snpIndiv = getDataFactory().getOWLNamedIndividual(getMinter().mint(OntologyConstants.GWAS_ONTOLOGY_BASE_IRI, "SingleNucleotidePolymorphism", snp.getRsId(), true));
                // assert class membership
                OWLClass snpClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.SNP_CLASS_IRI));
                OWLClassAssertionAxiom snpClassAssertion = getDataFactory().getOWLClassAssertionAxiom(snpClass, snpIndiv);
                getManager().addAxiom(ontology, snpClassAssertion);
                // assert rsid relation
                OWLDataProperty has_snp_rsid = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_SNP_REFERENCE_ID_PROPERTY_IRI));
                OWLLiteral rsid = getDataFactory().getOWLLiteral(snp.getRsId());
                OWLDataPropertyAssertionAxiom rsid_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_snp_rsid, snpIndiv, rsid);
                AddAxiom add_rsid = new AddAxiom(ontology, rsid_relation);
                getManager().applyChange(add_rsid);
                // assert label
                OWLAnnotationAssertionAxiom snp_label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, snpIndiv.getIRI(), rsid);
                AddAxiom add_snp_label = new AddAxiom(ontology, snp_label_annotation);
                getManager().applyChange(add_snp_label);
            }
            // get object properties
            OWLObjectProperty has_subject = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_SUBJECT_IRI));
            OWLObjectProperty is_subject_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_SUBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_subject_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_subject, taIndiv, snpIndiv);
            AddAxiom add_has_subject_snp = new AddAxiom(ontology, has_subject_snp_relation);
            getManager().applyChange(add_has_subject_snp);
            OWLObjectPropertyAssertionAxiom is_subject_of_snp_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_subject_of, snpIndiv, taIndiv);
            AddAxiom add_is_subject_of_snp = new AddAxiom(ontology, is_subject_of_snp_relation);
            getManager().applyChange(add_is_subject_of_snp);
        }
        // get the EFO class for the trait
        for (EfoTrait efoTrait : association.getEfoTraits()) {
            OWLClass traitClass;
            traitClass = getDataFactory().getOWLClass(IRI.create(efoTrait.getUri()));
            if (traitClass == null) {
                String warning = "This trait will be mapped to Experimental Factor";
                if (!issuedWarnings.contains(warning)) {
                    getLog().warn(warning);
                    issuedWarnings.add(warning);
                }
                traitClass = getDataFactory().getOWLClass(IRI.create(OntologyConstants.EXPERIMENTAL_FACTOR_CLASS_IRI));
            }
            // create a new trait instance (puns the class)
            IRI traitIRI = traitClass.getIRI();
            OWLNamedIndividual traitIndiv = getDataFactory().getOWLNamedIndividual(traitIRI);
            if (ontology.containsIndividualInSignature(traitIRI)) {
                getLog().trace("Trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ") already exists");
            } else {
                getLog().trace("Creating trait individual '" + traitIRI.toString() + "' (type: " + traitClass + ")");
            }
            // and also add the gwas label to the individual so we don't lose curated data
            OWLDataProperty has_gwas_trait_name = getDataFactory().getOWLDataProperty(IRI.create(OntologyConstants.HAS_GWAS_TRAIT_NAME_PROPERTY_IRI));
            OWLLiteral gwasTrait = getDataFactory().getOWLLiteral(association.getStudy().getDiseaseTrait().getTrait());
            OWLDataPropertyAssertionAxiom gwas_trait_relation = getDataFactory().getOWLDataPropertyAssertionAxiom(has_gwas_trait_name, taIndiv, gwasTrait);
            AddAxiom add_gwas_trait_name = new AddAxiom(ontology, gwas_trait_relation);
            getManager().applyChange(add_gwas_trait_name);
            // assert class membership
            OWLClassAssertionAxiom traitClassAssertion = getDataFactory().getOWLClassAssertionAxiom(traitClass, traitIndiv);
            getManager().addAxiom(ontology, traitClassAssertion);
            // get object properties
            OWLObjectProperty has_object = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.HAS_OBJECT_IRI));
            OWLObjectProperty is_object_of = getDataFactory().getOWLObjectProperty(IRI.create(OntologyConstants.IS_OBJECT_OF_IRI));
            // assert relations
            OWLObjectPropertyAssertionAxiom has_object_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(has_object, taIndiv, traitIndiv);
            AddAxiom add_has_object_trait = new AddAxiom(ontology, has_object_trait_relation);
            getManager().applyChange(add_has_object_trait);
            OWLObjectPropertyAssertionAxiom is_object_of_trait_relation = getDataFactory().getOWLObjectPropertyAssertionAxiom(is_object_of, traitIndiv, taIndiv);
            AddAxiom add_is_object_of_trait = new AddAxiom(ontology, is_object_of_trait_relation);
            getManager().applyChange(add_is_object_of_trait);
        }
        // finally, assert label for this association
        OWLLiteral label = getDataFactory().getOWLLiteral("Association between " + rsId + " and " + association.getStudy().getDiseaseTrait().getTrait());
        OWLAnnotationAssertionAxiom label_annotation = getDataFactory().getOWLAnnotationAssertionAxiom(rdfsLabel, taIndiv.getIRI(), label);
        AddAxiom add_band_label = new AddAxiom(ontology, label_annotation);
        getManager().applyChange(add_band_label);
    }
}

Example 4 with Locus

use of uk.ac.ebi.spot.goci.model.Locus in project goci by EBISPOT.

the class DefaultGWASOWLPublisher method validateGWASData.

/**
     * Validates the data obtained from the GWAS catalog (prior to converting to OWL)
     *
     * @param studies the set of studies to validate
     */
protected void validateGWASData(Collection<Study> studies) {
    // now check a random assortment of 5 studies for trait associations, abandoning broken ones
    int count = 0;
    int noAssocCount = 0;
    int termMismatches = 0;
    for (Study study : studies) {
        //            try {
        Collection<Association> associations = study.getAssociations();
        getLog().debug("Study (PubMed ID '" + study.getPubmedId() + "') had " + associations.size() + " associations");
        if (associations.size() > 0) {
            for (Association association : associations) {
                String efoTraitsDashSepList = "";
                for (EfoTrait efoTrait : association.getEfoTraits()) {
                    if ("".equals(efoTraitsDashSepList)) {
                        efoTraitsDashSepList.concat(efoTrait.getTrait());
                    } else {
                        efoTraitsDashSepList.concat(", " + efoTrait.getTrait());
                    }
                }
                for (Locus locus : association.getLoci()) {
                    for (RiskAllele riskAllele : locus.getStrongestRiskAlleles()) {
                        getLog().debug(//                                "    Association: SNP '" + association.getAssociatedSNP().getRSID() +
                        "    Association: SNP '" + riskAllele.getSnp().getRsId() + "' <-> Trait '" + efoTraitsDashSepList.toString() + "'");
                    }
                }
            }
            count++;
        } else {
            noAssocCount++;
        }
    }
    int eligCount = studies.size() - noAssocCount;
    int correctCount = count + termMismatches;
    getLog().info("\n\nREPORT:\n" + eligCount + "/" + studies.size() + " declared associations and therefore could usefully be mapped.\n" + (eligCount - count - termMismatches) + "/" + eligCount + " failed due to data integrity concerns.\n" + count + "/" + correctCount + " studies could be completely mapped after passing all checks.\n" + termMismatches + "/" + correctCount + " failed due to missing or duplicated terms in EFO");
}

Example 5 with Locus

use of uk.ac.ebi.spot.goci.model.Locus in project goci by EBISPOT.

the class DefaultGWASOWLPublisher method filterAndPublishGWASData.

private OWLOntology filterAndPublishGWASData(OWLOntology conversion, Collection<Study> studies) throws OWLConversionException {
    //TODO : check with tony : Discard studies which are not yet associated with a trait.
    //Discard studies which are not associated with a disease trait and those which haven't been published yet
    //by the GWAS catalog.
    //        Iterator<Study> iterator = studies.iterator();
    //        while(iterator.hasNext()){
    //            Study study = iterator.next();
    //            if(study.getDiseaseTrait() == null) {
    //                iterator.remove();
    //            }
    //            else if( study.getHousekeeping().getCatalogPublishDate() == null) {
    //                iterator.remove();
    //            }
    //            else if(study.getHousekeeping().getCatalogUnpublishDate() != null){
    //                iterator.remove();
    //            }
    //        }
    Collection<Study> filteredStudies = new ArrayList<Study>();
    Collection<Association> filteredTraitAssociations = new ArrayList<Association>();
    Collection<SingleNucleotidePolymorphism> filteredSNPs = new ArrayList<SingleNucleotidePolymorphism>();
    int count = 0;
    int studyLimit = getStudiesLimit() == -1 ? Integer.MAX_VALUE : getStudiesLimit();
    Iterator<Study> studyIterator = studies.iterator();
    while (count < studyLimit && studyIterator.hasNext()) {
        Study nextStudy = studyIterator.next();
        //only process a study if no date filter has been provided or if the study's publication date is smaller than the filter date
        if (FilterProperties.getDateFilter() == null || nextStudy.getPublicationDate().before(FilterProperties.getDateFilter())) {
            System.out.println("Qualifying study");
            for (Association nextTA : nextStudy.getAssociations()) {
                float filter = 0;
                float pval = 0;
                if (FilterProperties.getPvalueFilter() != null) {
                    filter = (float) (FilterProperties.getPvalueMant() * Math.pow(10, FilterProperties.getPvalueExp()));
                    pval = (float) (nextTA.getPvalueMantissa() * Math.pow(10, nextTA.getPvalueExponent()));
                    System.out.println("Your comparators are " + filter + " and " + pval);
                }
                if (FilterProperties.getPvalueFilter() == null || pval < filter) {
                    System.out.println("Qualifying association");
                    filteredTraitAssociations.add(nextTA);
                    for (Locus locus : nextTA.getLoci()) {
                        for (RiskAllele riskAllele : locus.getStrongestRiskAlleles()) {
                            filteredSNPs.add(riskAllele.getSnp());
                        }
                    }
                }
            }
            filteredStudies.add(nextStudy);
            count++;
        }
    }
    // convert this data, starting with SNPs (no dependencies) and working up to studies
    getLog().debug("Starting conversion to OWL...");
    getLog().debug("Converting " + filteredSNPs.size() + " filtered SNPs...");
    getConverter().addSNPsToOntology(filteredSNPs, conversion);
    getLog().debug("Converting " + filteredTraitAssociations.size() + " filtered Trait Associations...");
    getConverter().addAssociationsToOntology(filteredTraitAssociations, conversion);
    getLog().debug("Converting " + filteredStudies.size() + " filtered Studies...");
    getConverter().addStudiesToOntology(filteredStudies, conversion);
    getLog().debug("All conversion done!");
    return conversion;
}