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org.obolibrary.obo2owl.Obo2OWLConstants Maven / Gradle / Ivy
package org.obolibrary.obo2owl;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
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 {
/** default iri */
@Nonnull
public static final String DEFAULT_IRI_PREFIX = "http://purl.obolibrary.org/obo/";
/** OIO vocabulary prefix */
@Nonnull
public static final String OIOVOCAB_IRI_PREFIX =
"http://www.geneontology.org/formats/oboInOwl#";
/** IRI for the 'has obsolescence reason' annotation property */
@Nonnull
public static final IRI IRI_IAO_0000231 = IRI.create(DEFAULT_IRI_PREFIX + "IAO_0000231");
/** IRI for the 'terms merged' individual */
@Nonnull
public static final IRI IRI_IAO_0000227 = IRI.create(DEFAULT_IRI_PREFIX + "IAO_0000227");
/**
* @param d date to format
* @return formatted string
*/
@Nonnull
public static synchronized String format(@Nonnull Date d) {
return FORMATTER.format(d);
}
private static final SimpleDateFormat FORMATTER =
new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
/** 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_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
@Nonnull
final IRI iri;
@Nonnull
final String namespace;
@Nonnull
final String shortName;
@Nonnull
final String label;
@Nonnull
final String mappedTag;
Obo2OWLVocabulary(@Nonnull String namespce, @Nonnull String shortName,
@Nonnull String label, @Nonnull String mappedTag) {
iri = IRI.create(namespce + shortName);
this.shortName = shortName;
namespace = namespce;
this.label = label;
this.mappedTag = mappedTag;
}
/**
* @return short name
*/
@Nonnull
public String getShortName() {
return shortName;
}
/**
* @return namespace
*/
@Nonnull
public String getNamespace() {
return namespace;
}
@Override
public IRI getIRI() {
return iri;
}
/**
* @return label
*/
@Nonnull
public String getLabel() {
return label;
}
/**
* @return mapped tag
*/
@Nonnull
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());
}
}
private static final Map TAGSTOVOCAB = initTagsToVocab();
static Map initTagsToVocab() {
Map tags = new HashMap<>();
for (Obo2OWLVocabulary vocab : Obo2OWLVocabulary.values()) {
tags.put(vocab.mappedTag, vocab);
}
return tags;
}
/**
* @param tag tag
* @return Obo2OWLVocabulary for tag
*/
public static Obo2OWLVocabulary getVocabularyObj(String tag) {
return TAGSTOVOCAB.get(tag);
}
}
