org.coode.owlapi.obo.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.obo.parser;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
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 {
//@formatter:off
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");
//@formatter:on
/** @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(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(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(String name) {
this.name = name;
iri = IRI.create(OBOPrefix.OBO.getPrefix() + name);
}
OBOVocabulary(String name, OBOPrefix prefix) {
this.name = name;
iri = IRI.create(prefix.getPrefix() + name);
}
OBOVocabulary(String name, OBOPrefix prefix, String localName) {
this.name = name;
iri = IRI.create(prefix.getPrefix() + localName);
}
OBOVocabulary(String name, IRI iri) {
this.name = name;
this.iri = iri;
}
private String name;
private IRI iri;
public String getName() {
return name;
}
public IRI getIRI() {
return iri;
}
@Override
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