/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework 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 Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.tools.rdf;
import static org.openbel.framework.common.BELUtilities.constrainedHashMap;
import java.util.Map;
import org.openbel.framework.common.enums.FunctionEnum;
import org.openbel.framework.common.enums.RelationshipType;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;
/**
* Defines the KAM Vocabulary (RDF-based).
*
* TODO Convert to Owl2-based Vocabulary.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class KAMVocabulary {
/**
* Holds {@link FunctionEnum} to RDF {@link Resource}
*/
private static final Map<FunctionEnum, Resource> F_TO_R;
/**
* Holds {@link RelationshipType} to RDF {@link Resource}
*/
private static final Map<RelationshipType, Resource> R_TO_R;
/**
* <p>
* The RDF model that holds the vocabulary terms
* </p>
*/
private static Model m_model = ModelFactory.createDefaultModel();
/**
* <p>
* The namespace of the vocabulary as a string
* </p>
*/
public static final String NS =
"http://resource.belframework.org/belframework/1.0/schema/1.0/kam#";
/**
* <p>
* The namespace of the vocabulary as a string
* </p>
*
* @see #NS
*/
public static String getURI() {
return NS;
}
/**
* <p>
* The namespace of the vocabulary as a resource
* </p>
*/
public static final Resource NAMESPACE = m_model.createResource(NS);
public static final Property composedOf =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#composedOf");
public static final Property definedBy =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#definedBy");
public static final Property defines =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#defines");
public static final Property hasAnnotation =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasAnnotation");
public static final Property hasArguments =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasArguments");
public static final Property hasAuthor =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasAuthor");
public static final Property hasContactInfo =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasContactInfo");
public static final Property hasCopyright =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasCopyright");
public static final Property hasDescription =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasDescription");
public static final Property hasDisclaimer =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasDisclaimer");
public static final Property hasFunction =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasFunction");
public static final Property hasId =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasId");
public static final Property hasLabel =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasLabel");
public static final Property hasLicense =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasLicense");
public static final Property hasList =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasList");
public static final Property hasName =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasName");
public static final Property hasNamespace =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasNamespace");
public static final Property hasObjectNode =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasObjectNode");
public static final Property hasObjectTerm =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasObjectTerm");
public static final Property hasPattern =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasPattern");
public static final Property hasPrefix =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasPrefix");
public static final Property hasRelationship =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasRelationship");
public static final Property hasResourceLocation =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasResourceLocation");
public static final Property hasSubjectNode =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasSubjectNode");
public static final Property hasSubjectTerm =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasSubjectTerm");
public static final Property hasType =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasType");
public static final Property hasURL =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasURL");
public static final Property hasUsage =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasUsage");
public static final Property hasValue =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasValue");
public static final Property hasVersion =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#hasVersion");
public static final Property isRepresentedBy =
m_model
.createProperty("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#isRepresentedBy");
/**
* <p>
* An abundance in BEL.
* </p>
*/
public static final Resource Abundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Abundance");
/**
* <p>
* A actsIn relationship in BEL.
* </p>
*/
public static final Resource ActsIn =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ActsIn");
/**
* <p>
* A analogous relationship in BEL.
* </p>
*/
public static final Resource Analogous =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Analogous");
/**
* <p>
* An annotation.
* </p>
*/
public static final Resource Annotation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Annotation");
/**
* <p>
* An annotation definition.
* </p>
*/
public static final Resource AnnotationDefinition =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#AnnotationDefinition");
/**
* <p>
* A association relationship in BEL.
* </p>
*/
public static final Resource Association =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Association");
/**
* <p>
* A biological process in BEL.
* </p>
*/
public static final Resource BiologicalProcess =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#BiologicalProcess");
/**
* <p>
* A biomarkerFor relationship in BEL.
* </p>
*/
public static final Resource BiomarkerFor =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#BiomarkerFor");
/**
* <p>
* A catalytic activity in BEL.
* </p>
*/
public static final Resource CatalyticActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#CatalyticActivity");
/**
* <p>
* A causesNoChange relationship in BEL.
* </p>
*/
public static final Resource CausesNoChange =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#CausesNoChange");
/**
* <p>
* A cell secretion in BEL.
* </p>
*/
public static final Resource CellSecretion =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#CellSecretion");
/**
* <p>
* A cell surface expression in BEL.
* </p>
*/
public static final Resource CellSurfaceExpression =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#CellSurfaceExpression");
/**
* <p>
* A chaperone activity in BEL.
* </p>
*/
public static final Resource ChaperoneActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ChaperoneActivity");
/**
* <p>
* A complex abundance in BEL.
* </p>
*/
public static final Resource ComplexAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ComplexAbundance");
/**
* <p>
* A composite abundance in BEL.
* </p>
*/
public static final Resource CompositeAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#CompositeAbundance");
/**
* <p>
* A decreases relationship in BEL.
* </p>
*/
public static final Resource Decreases =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Decreases");
/**
* <p>
* A degredation in BEL.
* </p>
*/
public static final Resource Degradation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Degradation");
/**
* <p>
* A directlyDecreases relationship in BEL.
* </p>
*/
public static final Resource DirectlyDecreases =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#DirectlyDecreases");
/**
* <p>
* A directlyIncreases relationship in BEL.
* </p>
*/
public static final Resource DirectlyIncreases =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#DirectlyIncreases");
/**
* <p>
* A document that provides BEL knowledge that this KAM is composed of.
* </p>
*/
public static final Resource BelDocument =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#BelDocument");
/**
* <p>
* A function in the KAM.
* </p>
*/
public static final Resource Function =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Function");
/**
* <p>
* A fusion in BEL.
* </p>
*/
public static final Resource Fusion =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Fusion");
/**
* <p>
* A gene abundance in BEL.
* </p>
*/
public static final Resource GeneAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#GeneAbundance");
/**
* <p>
* A gtp bound activity in BEL.
* </p>
*/
public static final Resource GtpBoundActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#GtpBoundActivity");
/**
* <p>
* A hasComponent relationship in BEL.
* </p>
*/
public static final Resource HasComponent =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasComponent");
/**
* <p>
* A hasComponents relationship in BEL.
* </p>
*/
public static final Resource HasComponents =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasComponents");
/**
* <p>
* A hasMember relationship in BEL.
* </p>
*/
public static final Resource HasMember =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasMember");
/**
* <p>
* A hasMembers relationship in BEL.
* </p>
*/
//public static final Resource HasMembers = m_model
// .createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasMembers");
/**
* <p>
* A hasModification relationship in BEL.
* </p>
*/
public static final Resource HasModification =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasModification");
/**
* <p>
* A hasProduct relationship in BEL.
* </p>
*/
public static final Resource HasProduct =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasProduct");
/**
* <p>
* A hasVariant relationship in BEL.
* </p>
*/
public static final Resource HasVariant =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#HasVariant");
/**
* <p>
* A includes relationship in BEL.
* </p>
*/
public static final Resource Includes =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Includes");
/**
* <p>
* A increases relationship in BEL.
* </p>
*/
public static final Resource Increases =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Increases");
/**
* <p>
* A isA relationship in BEL.
* </p>
*/
public static final Resource IsA =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#IsA");
/**
* <p>
* A KAM.
* </p>
*/
public static final Resource KAM =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#KAM");
/**
* <p>
* An edge in the KAM.
* </p>
*/
public static final Resource KAMEdge =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#KAMEdge");
/**
* <p>
* A node in the KAM.
* </p>
*/
public static final Resource KAMNode =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#KAMNode");
/**
* <p>
* A kinase activity in BEL.
* </p>
*/
public static final Resource KinaseActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#KinaseActivity");
/**
* <p>
* A list in BEL.
* </p>
*/
//public static final Resource List = m_model
// .createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#List");
/**
* <p>
* A micro RNA abundance in BEL.
* </p>
*/
public static final Resource MicroRNAAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#MicroRNAAbundance");
/**
* <p>
* A molecular activity in BEL.
* </p>
*/
public static final Resource MolecularActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#MolecularActivity");
/**
* <p>
* An namespace.
* </p>
*/
public static final Resource Namespace =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Namespace");
/**
* <p>
* A negativeCorrelation relationship in BEL.
* </p>
*/
public static final Resource NegativeCorrelation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#NegativeCorrelation");
/**
* <p>
* A orthologous relationship in BEL.
* </p>
*/
public static final Resource Orthologous =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Orthologous");
/**
* <p>
* A paremeter in the KAM.
* </p>
*/
public static final Resource Parameter =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Parameter");
/**
* <p>
* A pathology in BEL.
* </p>
*/
public static final Resource Pathology =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Pathology");
/**
* <p>
* A peptidase activity in BEL.
* </p>
*/
public static final Resource PeptidaseActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#PeptidaseActivity");
/**
* <p>
* A phosphatase activity in BEL.
* </p>
*/
public static final Resource PhosphataseActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#PhosphataseActivity");
/**
* <p>
* A positiveCorrelation relationship in BEL.
* </p>
*/
public static final Resource PositiveCorrelation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#PositiveCorrelation");
/**
* <p>
* A products in BEL.
* </p>
*/
public static final Resource Products =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Products");
/**
* <p>
* A prognosticBiomarkerFor relationship in BEL.
* </p>
*/
public static final Resource PrognosticBiomarkerFor =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#PrognosticBiomarkerFor");
/**
* <p>
* A protein abundance in BEL.
* </p>
*/
public static final Resource ProteinAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ProteinAbundance");
/**
* <p>
* A protein modification in BEL.
* </p>
*/
public static final Resource ProteinModification =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ProteinModification");
/**
* <p>
* A rateLimitingStepOf relationship in BEL.
* </p>
*/
public static final Resource RateLimitingStepOf =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#RateLimitingStepOf");
/**
* <p>
* A reactantIn relationship in BEL.
* </p>
*/
public static final Resource ReactantIn =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#ReactantIn");
/**
* <p>
* A reactants in BEL.
* </p>
*/
public static final Resource Reactants =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Reactants");
/**
* <p>
* A reaction in BEL.
* </p>
*/
public static final Resource Reaction =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Reaction");
/**
* <p>
* A relationship in the KAM.
* </p>
*/
public static final Resource Relationship =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Relationship");
/**
* <p>
* A ribosylation activity in BEL.
* </p>
*/
public static final Resource RibosylationActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#RibosylationActivity");
/**
* <p>
* An RNA abundance in BEL.
* </p>
*/
public static final Resource RnaAbundance =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#RnaAbundance");
/**
* <p>
* An edge in the KAM.
* </p>
*/
public static final Resource Statement =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Statement");
/**
* <p>
* A subProcessOf relationship in BEL.
* </p>
*/
public static final Resource SubProcessOf =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#SubProcessOf");
/**
* <p>
* A substitution in BEL.
* </p>
*/
public static final Resource Substitution =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Substitution");
/**
* <p>
* A term in the KAM.
* </p>
*/
public static final Resource Term =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Term");
/**
* <p>
* A transcribedTo relationship in BEL.
* </p>
*/
public static final Resource TranscribedTo =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#TranscribedTo");
/**
* <p>
* A transcriptional activity in BEL.
* </p>
*/
public static final Resource TranscriptionalActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#TranscriptionalActivity");
/**
* <p>
* A translatedTo relationship in BEL.
* </p>
*/
public static final Resource TranslatedTo =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#TranslatedTo");
/**
* <p>
* A translocates relationship in BEL.
* </p>
*/
public static final Resource Translocates =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Translocates");
/**
* <p>
* A translocation in BEL.
* </p>
*/
public static final Resource Translocation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Translocation");
/**
* <p>
* A transport activity in BEL.
* </p>
*/
public static final Resource TransportActivity =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#TransportActivity");
/**
* <p>
* A truncation in BEL.
* </p>
*/
public static final Resource Truncation =
m_model
.createResource("http://resource.belframework.org/belframework/1.0/schema/1.0/kam#Truncation");
/**
* Retrieves the RDF {@link Resource} for the BEL {@link FunctionEnum}.
*
* @param function
* {@link FunctionEnum}, the BEL function
* @return {@link Resource} the rdf resource for the Function type
*/
public static final Resource resourceForFunction(FunctionEnum function) {
return F_TO_R.get(function);
}
/**
* Retrieves the RDF {@link Resource} for the BEL {@link RelationshipType}.
*
* @param rtype
* {@link RelationshipType}, the BEL relationship
* @return {@link Resource} the rdf resource for the Relationship type
*/
public static final Resource
resourceForRelationship(RelationshipType rtype) {
return R_TO_R.get(rtype);
}
// statically-initialize F_TO_R and R_TO_R
static {
FunctionEnum[] funcs = FunctionEnum.values();
F_TO_R = constrainedHashMap(funcs.length);
for (FunctionEnum func : funcs) {
switch (func) {
case ABUNDANCE:
F_TO_R.put(func, Abundance);
break;
case BIOLOGICAL_PROCESS:
F_TO_R.put(func, BiologicalProcess);
break;
case CATALYTIC_ACTIVITY:
F_TO_R.put(func, CatalyticActivity);
break;
case CELL_SECRETION:
F_TO_R.put(func, CellSecretion);
break;
case CELL_SURFACE_EXPRESSION:
F_TO_R.put(func, CellSurfaceExpression);
break;
case CHAPERONE_ACTIVITY:
F_TO_R.put(func, ChaperoneActivity);
break;
case COMPLEX_ABUNDANCE:
F_TO_R.put(func, ComplexAbundance);
break;
case COMPOSITE_ABUNDANCE:
F_TO_R.put(func, CompositeAbundance);
break;
case DEGRADATION:
F_TO_R.put(func, Degradation);
break;
case FUSION:
F_TO_R.put(func, Fusion);
break;
case GENE_ABUNDANCE:
F_TO_R.put(func, GeneAbundance);
break;
case GTP_BOUND_ACTIVITY:
F_TO_R.put(func, GtpBoundActivity);
break;
case KINASE_ACTIVITY:
F_TO_R.put(func, KinaseActivity);
break;
case MICRORNA_ABUNDANCE:
F_TO_R.put(func, MicroRNAAbundance);
break;
case MOLECULAR_ACTIVITY:
F_TO_R.put(func, MolecularActivity);
break;
case PATHOLOGY:
F_TO_R.put(func, Pathology);
break;
case PEPTIDASE_ACTIVITY:
F_TO_R.put(func, PeptidaseActivity);
break;
case PHOSPHATASE_ACTIVITY:
F_TO_R.put(func, PhosphataseActivity);
break;
case PRODUCTS:
F_TO_R.put(func, Products);
break;
case PROTEIN_ABUNDANCE:
F_TO_R.put(func, ProteinAbundance);
break;
case PROTEIN_MODIFICATION:
F_TO_R.put(func, ProteinModification);
break;
case REACTANTS:
F_TO_R.put(func, Reactants);
break;
case REACTION:
F_TO_R.put(func, Reaction);
break;
case RIBOSYLATION_ACTIVITY:
F_TO_R.put(func, RibosylationActivity);
break;
case RNA_ABUNDANCE:
F_TO_R.put(func, RnaAbundance);
break;
case SUBSTITUTION:
F_TO_R.put(func, Substitution);
break;
case LIST:
// List is not a KAM function as these are always expanded
// F_TO_R.put(func, List);
break;
case TRANSCRIPTIONAL_ACTIVITY:
F_TO_R.put(func, TranscriptionalActivity);
break;
case TRANSLOCATION:
F_TO_R.put(func, Translocation);
break;
case TRANSPORT_ACTIVITY:
F_TO_R.put(func, TransportActivity);
break;
case TRUNCATION:
F_TO_R.put(func, Truncation);
break;
default:
throw new UnsupportedOperationException(func.name()
+ " is not yet supported.");
}
}
RelationshipType[] rtypes = RelationshipType.values();
R_TO_R = constrainedHashMap(rtypes.length);
for (RelationshipType rtype : rtypes) {
switch (rtype) {
case ACTS_IN:
R_TO_R.put(rtype, ActsIn);
break;
case ANALOGOUS:
R_TO_R.put(rtype, Analogous);
break;
case ASSOCIATION:
R_TO_R.put(rtype, Association);
break;
case BIOMARKER_FOR:
R_TO_R.put(rtype, BiomarkerFor);
break;
case CAUSES_NO_CHANGE:
R_TO_R.put(rtype, CausesNoChange);
break;
case DECREASES:
R_TO_R.put(rtype, Decreases);
break;
case DIRECTLY_DECREASES:
R_TO_R.put(rtype, DirectlyDecreases);
break;
case DIRECTLY_INCREASES:
R_TO_R.put(rtype, DirectlyIncreases);
break;
case HAS_COMPONENT:
R_TO_R.put(rtype, HasComponent);
break;
case HAS_COMPONENTS:
R_TO_R.put(rtype, HasComponents);
break;
case HAS_MEMBER:
R_TO_R.put(rtype, HasMember);
break;
case HAS_MEMBERS:
// Not a KAM relationship as these are always expanded to HAS_MEMBER relationships
// R_TO_R.put(rtype, HasMembers);
break;
case HAS_MODIFICATION:
R_TO_R.put(rtype, HasModification);
break;
case HAS_PRODUCT:
R_TO_R.put(rtype, HasProduct);
break;
case HAS_VARIANT:
R_TO_R.put(rtype, HasVariant);
break;
case INCLUDES:
R_TO_R.put(rtype, Includes);
break;
case INCREASES:
R_TO_R.put(rtype, Increases);
break;
case IS_A:
R_TO_R.put(rtype, IsA);
break;
case NEGATIVE_CORRELATION:
R_TO_R.put(rtype, NegativeCorrelation);
break;
case ORTHOLOGOUS:
R_TO_R.put(rtype, Orthologous);
break;
case POSITIVE_CORRELATION:
R_TO_R.put(rtype, PositiveCorrelation);
break;
case PROGNOSTIC_BIOMARKER_FOR:
R_TO_R.put(rtype, PrognosticBiomarkerFor);
break;
case RATE_LIMITING_STEP_OF:
R_TO_R.put(rtype, RateLimitingStepOf);
break;
case REACTANT_IN:
R_TO_R.put(rtype, ReactantIn);
break;
case SUB_PROCESS_OF:
R_TO_R.put(rtype, SubProcessOf);
break;
case TRANSCRIBED_TO:
R_TO_R.put(rtype, TranscribedTo);
break;
case TRANSLATED_TO:
R_TO_R.put(rtype, TranslatedTo);
break;
case TRANSLOCATES:
R_TO_R.put(rtype, Translocates);
break;
default:
throw new UnsupportedOperationException(rtype.name()
+ " is not yet supported.");
}
}
}
}