org.coode.owlapi.obo12.parser.OBOVocabulary Maven / Gradle / Ivy
/*
* This file is part of the OWL API.
*
* The contents of this file are subject to the LGPL License, Version 3.0.
*
* Copyright (C) 2011, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see http://www.gnu.org/licenses/.
*
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
* in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
*
* Copyright 2011, University of Manchester
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.coode.owlapi.obo12.parser;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.annotation.Nonnull;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.vocab.DublinCoreVocabulary;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
/**
* Author: Matthew Horridge
* The University Of Manchester
* Bio-Health Informatics Group
* Date: 10-Jan-2007
*
*/
@SuppressWarnings("javadoc")
public enum OBOVocabulary {
DATA_VERSION("data-version"), VERSION("version"), DATE("date", DublinCoreVocabulary.DATE.getIRI()), SAVED_BY(
"saved-by"), AUTO_GENERATED_BY("auto-generated-by"), ONTOLOGY("ontology"), SUBSETDEF("subsetdef",
OBOPrefix.OBO_IN_OWL, "SubsetProperty"), IMPORT("import"), SYNONYM_TYPE_DEF("synonymtypedef",
OBOPrefix.OBO_IN_OWL, "SynonymTypeProperty"), SYNONYM_TYPE("synonym-type", OBOPrefix.OBO_IN_OWL,
"hasSynonymType"), ID_SPACE("id_space"), DEFAULT_RELATIONSHIP_ID_PREFIX(
"default-relationship-id-prefix"), ID_MAPPING("id-mapping"), REMARK("remark"), ID("id"), NAME(
"name", OWLRDFVocabulary.RDFS_LABEL.getIRI()), FORMAT_VERSION("format-version"), TYPEDEF(
"Typedef"), ALT_ID("alt_id", OBOPrefix.OBO_IN_OWL, "hasAlternativeId"), SHORT_HAND(
"shorthand", OBOPrefix.OBO_IN_OWL, "shorthand"), ALT_NAME("alt_name"), NAMESPACE(
"namespace"), DEFAULT_NAMESPACE("default-namespace"), DEF("def"), COMMENT(
"comment", OWLRDFVocabulary.RDFS_COMMENT.getIRI()), SUBSET("subset",
OBOPrefix.OBO_IN_OWL, "inSubset"), SYNONYM("synonym"), HAS_SCOPE(
"hasScope", OBOPrefix.OBO_IN_OWL), RELATED_SYNONYM("relatedSynonym",
OBOPrefix.OBO_IN_OWL, "hasRelatedSynonym"), EXACT_SYNONYM(
"exactSynonym", OBOPrefix.OBO_IN_OWL,
"hasExactSynonym"), BROAD_SYNONYM("broadSynonym",
OBOPrefix.OBO_IN_OWL,
"hasBroadSynonym"), NARROW_SYNONYM("narrowSynonym",
OBOPrefix.OBO_IN_OWL, "hasNarrowSynonym"), XREF(
"xref", OBOPrefix.OBO_IN_OWL), XREF_ANALOGUE(
"xref_analogue"), XREF_UNKNOWN(
"xref_unk"), IS_A("is_a"), IS_OBSOLETE(
"is_obsolete",
OWLRDFVocabulary.OWL_DEPRECATED
.getIRI()), PART_OF(
"part_of"), RELATIONSHIP(
"relationship"), REPLACED_BY(
"replaced_by"), CONSIDER(
"consider",
OBOPrefix.OBO_IN_OWL,
"consider"), USE_TERM(
"use_term"), DOMAIN(
"domain"), RANGE(
"range"), IS_CYCLIC(
"is_cyclic"), IS_TRANSITIVE(
"is_transitive"), IS_SYMMETRIC(
"is_symmetric"), IS_ASYMMETRIC(
"is_asymmetric"), IS_REFLEXIVE(
"is_reflexive"), INVERSE(
"inverse"), TRANSITIVE_OVER(
"transitive_over"), INTERSECTION_OF(
"intersection_of"), UNION_OF(
"union_of"), DISJOINT_FROM(
"disjoint_from"), TERM(
"Term"), BUILTIN(
"builtin"), IS_METADATA_TAG(
"is_metadata_tag"), CARDINALITY(
"cardinality"), MAX_CARDINALITY(
"maxCardinality"), MIN_CARDINALITY(
"minCardinality"), INSTANCE(
"Instance"), INSTANCE_OF(
"instance_of"), PROPERTY_VALUE(
"property_value"), IS_ANONYMOUS(
"is_anonymous");
/**
* @deprecated Use {@link #OBO_IRI_BASE}
*/
@Deprecated
public static final String ONTOLOGY_URI_BASE = "http://purl.org/obo/owl";
/**
* @deprecated Use {@link #OBO_IRI_BASE}
*/
@Deprecated
public static final String ANNOTATION_URI_BASE = OBOPrefix.OBO_IN_OWL.getPrefix();
public static final String OBO_IRI_BASE = OBOPrefix.OBO.getPrefix();
public static final String LEGACY_OBO_IRI_BASE = "http://purl.org/obo/owl/";//
/**
* The pattern for OBO IDs. Specified at
* http://www.
* obofoundry.org/id-policy.shtml
*/
public static final Pattern OBO_ID_PATTERN = Pattern.compile("(([^:]+):)?(.+)");
private static final String bases = Pattern.quote(OBO_IRI_BASE) + "|" + Pattern.quote(ONTOLOGY_URI_BASE + "/") + "|"
+ Pattern.quote(LEGACY_OBO_IRI_BASE) + "|" + Pattern.quote(ANNOTATION_URI_BASE);
public static final Pattern OBO_IRI_PATTERN = Pattern.compile("(" + bases + ")"
+ "(([^\\_]*)\\_)?([A-Za-z0-9\\_\\-]*)");
private static final IDSpaceManager DEFAULT_ID_SPACE_MANAGER = new IDSpaceManager() {
@Override
public void setIRIPrefix(String idPrefix, String iriPrefix) {
throw new RuntimeException("The default id space manager must not be used for custom prefixes.");
}
};
/**
* Converts OBO Ids to IRIs. The conversion is defined at
* http://www.
* obofoundry.org/id-policy.shtml
*
* @param oboId
* The Id to convert
* @return The IRI of the converted Id
*/
public static IRI ID2IRI(@Nonnull String oboId) {
return ID2IRI(oboId, DEFAULT_ID_SPACE_MANAGER);
}
/**
* Converts OBO Ids to IRIs. The conversion is defined at
* http://www.
* obofoundry.org/id-policy.shtml.
*
* @param oboId
* The OBO Id to convert.
* @param idSpaceManager
* An {@link IDSpaceManager} which can be used to customise the IRI
* prefixes used in the conversion.
* @return The IRI of the converted Id.
*/
public static IRI ID2IRI(@Nonnull String oboId, IDSpaceManager idSpaceManager) {
Matcher matcher = OBO_ID_PATTERN.matcher(oboId);
if (matcher.matches()) {
String idSpace = matcher.group(2);
String localId = matcher.group(3);
StringBuilder sb = new StringBuilder();
String iriPrefix = idSpaceManager.getIRIPrefix(idSpace);
sb.append(iriPrefix);
if (idSpace != null) {
sb.append(idSpace);
sb.append("_");
}
sb.append(localId);
return IRI.create(sb.toString());
} else {
return IRI.create(oboId);
}
}
// Format of Foundry-compliant URIs
// FOUNDRY_OBO_URI ::= "http://purl.obolibrary.org/obo/" IDSPACE "_" LOCALID
// Format of OBO legacy URIs
// Those are found in documents that were natively authored using the OBO
// format and which were converted using the NCBOoboInOwl script before this
// policy was put in place.
// LEGACY_OBO_URI ::= "http://purl.org/obo/owl/" IDSPACE "#" IDSPACE "_"
// LOCALID
public static String IRI2ID(IRI oboIRI) {
Matcher matcher = OBO_IRI_PATTERN.matcher(oboIRI.toString());
if (matcher.matches()) {
String idSpace = matcher.group(3);
String localId = matcher.group(4);
StringBuilder sb = new StringBuilder();
if (idSpace != null) {
sb.append(idSpace);
sb.append(":");
}
sb.append(localId);
return sb.toString();
} else {
throw new RuntimeException("Not an OBO IRI");
}
}
public static boolean isOBOIRI(IRI oboIRI) {
return OBO_ID_PATTERN.matcher(oboIRI.toString()).matches();
}
private static final List headerTags = Arrays.asList(FORMAT_VERSION, DATA_VERSION, DATE, SAVED_BY,
AUTO_GENERATED_BY, SUBSETDEF, IMPORT, SYNONYM_TYPE_DEF, ID_SPACE, DEFAULT_RELATIONSHIP_ID_PREFIX, ID_MAPPING,
REMARK);
private static final List termStanzaTags = Arrays.asList(ID, NAME, NAMESPACE, ALT_ID, DEF, COMMENT,
SUBSET, SYNONYM, XREF, IS_A, INTERSECTION_OF, UNION_OF, DISJOINT_FROM, RELATIONSHIP, IS_OBSOLETE, REPLACED_BY,
CONSIDER);
private static final List typeDefStanzaTags = Arrays.asList(ID, NAME, NAMESPACE, ALT_ID, DEF,
COMMENT, SUBSET, SYNONYM, XREF, DOMAIN, RANGE, IS_ASYMMETRIC, IS_CYCLIC, IS_REFLEXIVE, IS_SYMMETRIC,
IS_TRANSITIVE, IS_A, INVERSE, TRANSITIVE_OVER, RELATIONSHIP, IS_METADATA_TAG, IS_OBSOLETE, REPLACED_BY,
CONSIDER);
private static final List instanceStanzaTags = Arrays.asList(ID, NAME, NAMESPACE, ALT_ID, DEF,
COMMENT, SYNONYM, XREF, INSTANCE_OF, PROPERTY_VALUE, IS_OBSOLETE, REPLACED_BY, CONSIDER);
OBOVocabulary(@Nonnull String name) {
this.name = name;
iri = IRI.create(OBOPrefix.OBO.getPrefix() + name);
}
OBOVocabulary(@Nonnull String name, @Nonnull OBOPrefix prefix) {
this.name = name;
iri = IRI.create(prefix.getPrefix() + name);
}
OBOVocabulary(@Nonnull String name, OBOPrefix prefix, String localName) {
this.name = name;
iri = IRI.create(prefix.getPrefix() + localName);
}
OBOVocabulary(@Nonnull String name, @Nonnull IRI iri) {
this.name = name;
this.iri = iri;
}
@Nonnull
private String name;
@Nonnull
private IRI iri;
@Nonnull
public String getName() {
return name;
}
@Nonnull
public IRI getIRI() {
return iri;
}
@Override
@Nonnull
public String toString() {
return name;
}
public static List getHeaderTags() {
return new ArrayList<>(headerTags);
}
public static List getTermStanzaTags() {
return new ArrayList<>(termStanzaTags);
}
public static List getTypeDefStanzaTags() {
return new ArrayList<>(typeDefStanzaTags);
}
public static List getInstanceStanzaTags() {
return new ArrayList<>(instanceStanzaTags);
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy