org.obolibrary.obo2owl.Obo2OWLConstants Maven / Gradle / Ivy

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A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This version has been slightly modified to be included directly in the OWL API. The upstream code for this module and its authors can be found at https://code.google.com/p/oboformat/.
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package org.obolibrary.obo2owl;

import java.util.Date;
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;

import javax.annotation.Nullable;

import org.obolibrary.oboformat.parser.OBOFormatConstants;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.semanticweb.owlapi.model.HasIRI;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLEntity;

/**
 * @author Shahid Manzoor
 */
public class Obo2OWLConstants {
    //@formatter:off
    /** Default iri. */
    public static final String DEFAULT_IRI_PREFIX = "http://purl.obolibrary.org/obo/";
    /** OIO vocabulary prefix. */
    public static final String OIOVOCAB_IRI_PREFIX = "http://www.geneontology.org/formats/oboInOwl#";
    /** IRI for the 'has obsolescence reason' annotation property */
    public static final IRI IRI_IAO_0000231 = IRI.create(DEFAULT_IRI_PREFIX, "IAO_0000231");
    /** IRI for the 'terms merged' individual */
    public static final IRI IRI_IAO_0000227 = IRI.create(DEFAULT_IRI_PREFIX, "IAO_0000227");
    //@formatter:on
    private static final Map TAGSTOVOCAB =
        Stream.of(Obo2OWLVocabulary.values())
            .collect(Collectors.toMap(Obo2OWLVocabulary::getMappedTag, Function.identity()));

    /**
     * @param tag tag
     * @return object for tag
     */
    @Nullable
    public static Obo2OWLVocabulary getVocabularyObj(String tag) {
        return TAGSTOVOCAB.get(tag);
    }

    /** OBO to OWL vocabulary. */
    public enum Obo2OWLVocabulary implements HasIRI {
        //@formatter:off
        /**IRI_IAO_0000424. */    IRI_IAO_0000424(DEFAULT_IRI_PREFIX, "IAO_0000424", "expand expression to", OboFormatTag.TAG_EXPAND_EXPRESSION_TO.getTag()),
        /**IRI_IAO_0000425. */    IRI_IAO_0000425(DEFAULT_IRI_PREFIX, "IAO_0000425", "expand assertion to", OboFormatTag.TAG_EXPAND_ASSERTION_TO.getTag()),
        /**IRI_IAO_0000115. */    IRI_IAO_0000115(DEFAULT_IRI_PREFIX, "IAO_0000115", "definition", OboFormatTag.TAG_DEF.getTag()),
        //                      IRI_IAO_0000118(DEFAULT_IRI_PREFIX, "IAO_0000118", "alternative term", OboFormatTag.TAG_SYNONYM.getTag()),
        /**IRI_IAO_0000427. */    IRI_IAO_0000427(DEFAULT_IRI_PREFIX, "IAO_0000427", "antisymmetric property", OboFormatTag.TAG_IS_ANTI_SYMMETRIC.getTag()),
        /**IRI_IAO_0100001. */    IRI_IAO_0100001(DEFAULT_IRI_PREFIX, "IAO_0100001", "term replaced by", OboFormatTag.TAG_REPLACED_BY.getTag()),
        /**IRI_OIO_shorthand. */  IRI_OIO_shorthand(OIOVOCAB_IRI_PREFIX, "shorthand", "shorthand", "shorthand"),
        /**IRI_OIO_consider. */   IRI_OIO_consider(OIOVOCAB_IRI_PREFIX, "consider", "consider", OboFormatTag.TAG_CONSIDER.getTag()),
        /**IRI_OIO_id*/   IRI_OIO_id(OIOVOCAB_IRI_PREFIX, "id", "id", OboFormatTag.TAG_ID.getTag()),
        /**IRI_OIO_created_by*/   IRI_OIO_created_by(OIOVOCAB_IRI_PREFIX, "created_by", "created by", OboFormatTag.TAG_CREATED_BY.getTag()),
        /**IRI_OIO_creation_date*/   IRI_OIO_creation_date(OIOVOCAB_IRI_PREFIX, "creation_date", "creation date", OboFormatTag.TAG_CREATION_DATE.getTag()),
        /**IRI_OIO_hasOBOFormatVersion. */        IRI_OIO_hasOBOFormatVersion(OIOVOCAB_IRI_PREFIX, "hasOBOFormatVersion", "has_obo_format_version", OboFormatTag.TAG_FORMAT_VERSION.getTag()),
        /**IRI_OIO_treatXrefsAsIsA. */            IRI_OIO_treatXrefsAsIsA(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-is_a", "treat-xrefs-as-is_a", OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.getTag()),
        /**IRI_OIO_treatXrefsAsHasSubClass. */    IRI_OIO_treatXrefsAsHasSubClass(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-has-subclass", "treat-xrefs-as-has-subclass", OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.getTag()),
        /**IRI_OIO_treatXrefsAsRelationship. */   IRI_OIO_treatXrefsAsRelationship(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-relationship", "treat-xrefs-as-relationship", OboFormatTag.TAG_TREAT_XREFS_AS_RELATIONSHIP.getTag()),
        /**IRI_OIO_treatXrefsAsGenusDifferentia. */           IRI_OIO_treatXrefsAsGenusDifferentia(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-genus-differentia", "treat-xrefs-as-genus-differentia", OboFormatTag.TAG_TREAT_XREFS_AS_GENUS_DIFFERENTIA.getTag()),
        /**IRI_OIO_treatXrefsAsReverseGenusDifferentia. */    IRI_OIO_treatXrefsAsReverseGenusDifferentia(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-reverse-genus-differentia", "treat-xrefs-as-reverse-genus-differentia", OboFormatTag.TAG_TREAT_XREFS_AS_REVERSE_GENUS_DIFFERENTIA.getTag()),
        /**IRI_OIO_treatXrefsAsEquivalent. */                 IRI_OIO_treatXrefsAsEquivalent(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-equivalent", "treat-xrefs-as-equivalent", OboFormatTag.TAG_TREAT_XREFS_AS_EQUIVALENT.getTag()),
        /**IRI_OIO_hasOboNamespace. */    IRI_OIO_hasOboNamespace(OIOVOCAB_IRI_PREFIX, "hasOBONamespace", "has_obo_namespace", OboFormatTag.TAG_NAMESPACE.getTag()),
        /**IRI_OIO_hasDbXref. */          IRI_OIO_hasDbXref(OIOVOCAB_IRI_PREFIX, "hasDbXref", "database_cross_reference", OboFormatTag.TAG_XREF.getTag()),
        /**hasAlternativeId. */           hasAlternativeId(OIOVOCAB_IRI_PREFIX, "hasAlternativeId", "has_alternative_id", OboFormatTag.TAG_ALT_ID.getTag()),
        /**IRI_OIO_inSubset. */           IRI_OIO_inSubset(OIOVOCAB_IRI_PREFIX, "inSubset", "in_subset", OboFormatTag.TAG_SUBSET.getTag()),
        /**IRI_OIO_hasScope. */           IRI_OIO_hasScope(OIOVOCAB_IRI_PREFIX, "hasScope", "has_scope", OboFormatTag.TAG_SCOPE.getTag()),
        /**IRI_OIO_hasBroadSynonym. */    IRI_OIO_hasBroadSynonym(OIOVOCAB_IRI_PREFIX, "hasBroadSynonym", "has_broad_synonym", OboFormatTag.TAG_BROAD.getTag()),
        /**IRI_OIO_hasNarrowSynonym. */   IRI_OIO_hasNarrowSynonym(OIOVOCAB_IRI_PREFIX, "hasNarrowSynonym", "has_narrow_synonym", OboFormatTag.TAG_NARROW.getTag()),
        /**IRI_OIO_hasExactSynonym. */    IRI_OIO_hasExactSynonym(OIOVOCAB_IRI_PREFIX, "hasExactSynonym", "has_exact_synonym", OboFormatTag.TAG_EXACT.getTag()),
        /**IRI_OIO_hasRelatedSynonym. */  IRI_OIO_hasRelatedSynonym(OIOVOCAB_IRI_PREFIX, "hasRelatedSynonym", "has_related_synonym", OboFormatTag.TAG_RELATED.getTag()),
        /**hasSynonymType. */             hasSynonymType(OIOVOCAB_IRI_PREFIX, "hasSynonymType", "has_synonym_type", OboFormatTag.TAG_HAS_SYNONYM_TYPE.getTag()),
        /**IRI_OIO_Subset. */             IRI_OIO_Subset(OIOVOCAB_IRI_PREFIX, "SubsetProperty", "subset_property", OboFormatTag.TAG_SUBSETDEF.getTag()),
        /**IRI_OIO_SynonymType. */        IRI_OIO_SynonymType(OIOVOCAB_IRI_PREFIX, "SynonymTypeProperty", "synonym_type_property", OboFormatTag.TAG_SYNONYMTYPEDEF.getTag()),
        /**IRI_OIO_NamespaceIdRule. */    IRI_OIO_NamespaceIdRule(OIOVOCAB_IRI_PREFIX, "NamespaceIdRule", "namespace-id-rule", OboFormatTag.TAG_NAMESPACE_ID_RULE.getTag()),
        /**IRI_OIO_LogicalDefinitionViewRelation. */          IRI_OIO_LogicalDefinitionViewRelation(OIOVOCAB_IRI_PREFIX, "logical-definition-view-relation", "logical-definition-view-relation", OboFormatTag.TAG_LOGICAL_DEFINITION_VIEW_RELATION.getTag());
        //@formatter:on
        final IRI iri;
        final String namespace;
        final String shortName;
        final String label;
        final String mappedTag;

        Obo2OWLVocabulary(String namespce, String shortName, String label, String mappedTag) {
            iri = IRI.create(namespce, shortName);
            this.shortName = shortName;
            namespace = namespce;
            this.label = label;
            this.mappedTag = mappedTag;
        }

        /**
         * @param d date to format
         * @return formatted string
         */
        public static String format(Date d) {
            return OBOFormatConstants.headerDateFormat().format(d);
        }

        /**
         * @return short name
         */
        public String getShortName() {
            return shortName;
        }

        /**
         * @return namespace
         */
        public String getNamespace() {
            return namespace;
        }

        @Override
        public IRI getIRI() {
            return iri;
        }

        /**
         * @return label
         */
        public String getLabel() {
            return label;
        }

        /**
         * @return mapped tag
         */
        public String getMappedTag() {
            return mappedTag;
        }

        /**
         * @param e entity to check
         * @return true if e has the same iri as the enum value, false if e is null or has a
         *         different iri
         */
        public boolean sameIRI(@Nullable OWLEntity e) {
            // if a null value is passed in, then no match
            if (e == null) {
                return false;
            }
            return iri.equals(e.getIRI());
        }
    }
}