Package psidev.psi.mi.jami.bridges.obo

Class OntologyOboLoader

java.lang.Object

uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

psidev.psi.mi.jami.bridges.obo.AbstractOboLoader<OntologyTerm>

psidev.psi.mi.jami.bridges.obo.OntologyOboLoader

All Implemented Interfaces:

uk.ac.ebi.ols.loader.interfaces.Loader

public class OntologyOboLoader
extends AbstractOboLoader<OntologyTerm>

The ontologyOboLoader is a loader of OntologyTerm with parents and children

Since:

17/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COMMENT_KEY	Constant COMMENT_KEY="comment"
protected static String	EXACT_KEY	Constant EXACT_KEY="exact"
protected static String	LINE_BREAK	Constant LINE_BREAK="\n"
protected static String	META_XREF_SEPARATOR	Constant META_XREF_SEPARATOR=":"
protected static String	METHOD_REFERENCE	Constant METHOD_REFERENCE="method reference"
protected static String	METHOD_REFERENCE_MI_REF	Constant METHOD_REFERENCE_MI_REF="MI:0357"
protected static String	PMID	Constant PMID="PMID"
protected static String	RESID	Constant RESID="resid"
protected static String	RESID_MI_REF	Constant RESID_MI_REF="MI:0248"
protected static int	XREF_TYPE	Constant XREF_TYPE=3

Fields inherited from class psidev.psi.mi.jami.bridges.obo.AbstractOboLoader

log

Fields inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

ALT_ID, BATCH_MODE, BROAD, DEV_FROM_SET, DEVELOPS_FROM, EXACT, FULL_NAME, IS_A, IS_A_SET, logger, NARROW, ontBean, ONTOLOGY_DEFINITION, ontologyTerms, parser, PART_OF, PART_OF_SET, QUERY_URL, RELATED, SHORT_NAME, SOURCE_URL, SYNONYM, useGreedy

Fields inherited from interface uk.ac.ebi.ols.loader.interfaces.Loader

RELATION_TYPE, SYNONYM_TYPE

Constructor Summary

Constructors

Constructor	Description
OntologyOboLoader(String databaseName)	Constructor for OntologyOboLoader.
OntologyOboLoader(CvTerm database)	Constructor for OntologyOboLoader.

Method Summary

Modifier and Type	Method	Description
protected void	addLinkToTerm(String parentId, String childId, Map<String,OntologyTerm> id2Terms)	addLinkToTerm.
void	buildOntology(Map<String,OntologyTerm> id2Terms, Map<String,OntologyTerm> name2Terms)	buildOntology.
protected void	buildTermRelationships(Map<String,OntologyTerm> id2Terms)	buildTermRelationships.
protected void	createDefinitionFor(String def, OntologyTerm term)	createDefinitionFor.
protected OntologyTerm	instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.
protected void	processAnnotations(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	Process the annotations of a term
protected void	processDefinition(String definition, OntologyTerm ontologyTerm)	Process the definition String
protected void	processDefinition(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	Process the definition of a term
protected void	processInfoInDescription(String definition, String otherInfoString, OntologyTerm ontologyTerm)	Process the other information in the description
protected void	processShortLabel(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processShortLabel.
protected void	processSynonyms(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processSynonyms.
protected void	processXref(String db, String accession, OntologyTerm ontologyTerm)	processXref.
protected String	processXrefDefinition(String xref, String database, String accession, String pubmedPrimary, OntologyTerm ontologyTerm)	processXrefDefinition.
protected void	processXrefs(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processXrefs.

Methods inherited from class psidev.psi.mi.jami.bridges.obo.AbstractOboLoader

configure, createNewTerm, getOntologyDatabase, parseOboFile

Methods inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

dumpOntology, dumpOntologyStats, dumpTerm, getOntology, getRootTerms, getUnknownRelationTermBean, initializeCommonObjects, initializeTermBean, load, process, processTerm, safeTrim, safeTrim, setParser, setUseGreedy, unload

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EXACT_KEY

protected static final String EXACT_KEY

Constant EXACT_KEY="exact"

See Also:

Constant Field Values

XREF_TYPE

protected static final int XREF_TYPE

Constant XREF_TYPE=3

See Also:

Constant Field Values

META_XREF_SEPARATOR

protected static final String META_XREF_SEPARATOR

Constant META_XREF_SEPARATOR=":"

See Also:

Constant Field Values

LINE_BREAK

protected static final String LINE_BREAK

Constant LINE_BREAK="\n"

See Also:

Constant Field Values

COMMENT_KEY

protected static final String COMMENT_KEY

Constant COMMENT_KEY="comment"

See Also:

Constant Field Values

PMID

protected static final String PMID

Constant PMID="PMID"

See Also:

Constant Field Values

METHOD_REFERENCE

protected static final String METHOD_REFERENCE

Constant METHOD_REFERENCE="method reference"

See Also:

Constant Field Values

METHOD_REFERENCE_MI_REF

protected static final String METHOD_REFERENCE_MI_REF

Constant METHOD_REFERENCE_MI_REF="MI:0357"

See Also:

Constant Field Values

RESID

protected static final String RESID

Constant RESID="resid"

See Also:

Constant Field Values

RESID_MI_REF

protected static final String RESID_MI_REF

Constant RESID_MI_REF="MI:0248"

See Also:

Constant Field Values

Constructor Detail

OntologyOboLoader

public OntologyOboLoader(CvTerm database)

Constructor for OntologyOboLoader.

Parameters:

database - a CvTerm object.

OntologyOboLoader

public OntologyOboLoader(String databaseName)

Constructor for OntologyOboLoader.

Parameters:

databaseName - a String object.

Method Detail

buildOntology

public void buildOntology(Map<String,OntologyTerm> id2Terms,
                          Map<String,OntologyTerm> name2Terms)

buildOntology.

Overrides:

buildOntology in class AbstractOboLoader<OntologyTerm>

Parameters:

id2Terms - a Map object.

name2Terms - a Map object.

instantiateNewTerm

protected OntologyTerm instantiateNewTerm(String name,
                                          Xref identity)

instantiateNewTerm.

Specified by:

instantiateNewTerm in class AbstractOboLoader<OntologyTerm>

Parameters:

name - a String object.

identity - a Xref object.

Returns:

a T object.

createDefinitionFor

protected void createDefinitionFor(String def,
                                   OntologyTerm term)

createDefinitionFor.

Specified by:

createDefinitionFor in class AbstractOboLoader<OntologyTerm>

Parameters:

def - a String object.

term - a T object.

processAnnotations

protected void processAnnotations(uk.ac.ebi.ols.model.interfaces.Term term,
                                  OntologyTerm ontologyTerm)

Process the annotations of a term

Overrides:

processAnnotations in class AbstractOboLoader<OntologyTerm>

Parameters:

term - a Term object.

ontologyTerm - a OntologyTerm object.

processXrefs

protected void processXrefs(uk.ac.ebi.ols.model.interfaces.Term term,
                            OntologyTerm ontologyTerm)

processXrefs.

Overrides:

processXrefs in class AbstractOboLoader<OntologyTerm>

Parameters:

term - a Term object.

ontologyTerm - a OntologyTerm object.

processXrefDefinition

protected String processXrefDefinition(String xref,
                                       String database,
                                       String accession,
                                       String pubmedPrimary,
                                       OntologyTerm ontologyTerm)

processXrefDefinition.

Overrides:

processXrefDefinition in class AbstractOboLoader<OntologyTerm>

Parameters:

xref - a String object.

database - a String object.

accession - a String object.

pubmedPrimary - a String object.

ontologyTerm - a OntologyTerm object.

Returns:

a String object.

processXref

protected void processXref(String db,
                           String accession,
                           OntologyTerm ontologyTerm)

processXref.

Overrides:

processXref in class AbstractOboLoader<OntologyTerm>

Parameters:

db - a String object.

accession - a String object.

ontologyTerm - a OntologyTerm object.

processDefinition

protected void processDefinition(uk.ac.ebi.ols.model.interfaces.Term term,
                                 OntologyTerm ontologyTerm)

Process the definition of a term

Overrides:

processDefinition in class AbstractOboLoader<OntologyTerm>

Parameters:

term - a Term object.

ontologyTerm - a OntologyTerm object.

processDefinition

protected void processDefinition(String definition,
                                 OntologyTerm ontologyTerm)

Process the definition String

Overrides:

processDefinition in class AbstractOboLoader<OntologyTerm>

Parameters:

definition - a String object.

ontologyTerm - a OntologyTerm object.

processInfoInDescription

protected void processInfoInDescription(String definition,
                                        String otherInfoString,
                                        OntologyTerm ontologyTerm)

Process the other information in the description

Overrides:

processInfoInDescription in class AbstractOboLoader<OntologyTerm>

Parameters:

definition - a String object.

otherInfoString - a String object.

ontologyTerm - a OntologyTerm object.

processSynonyms

protected void processSynonyms(uk.ac.ebi.ols.model.interfaces.Term term,
                               OntologyTerm ontologyTerm)

processSynonyms.

Overrides:

processSynonyms in class AbstractOboLoader<OntologyTerm>

Parameters:

term - a Term object.

ontologyTerm - a OntologyTerm object.

processShortLabel

protected void processShortLabel(uk.ac.ebi.ols.model.interfaces.Term term,
                                 OntologyTerm ontologyTerm)

processShortLabel.

Overrides:

processShortLabel in class AbstractOboLoader<OntologyTerm>

Parameters:

term - a Term object.

ontologyTerm - a OntologyTerm object.

buildTermRelationships

protected void buildTermRelationships(Map<String,OntologyTerm> id2Terms)

buildTermRelationships.

Parameters:

id2Terms - a Map object.

addLinkToTerm

protected void addLinkToTerm(String parentId,
                             String childId,
                             Map<String,OntologyTerm> id2Terms)

addLinkToTerm.

Parameters:

parentId - a String object.

childId - a String object.

id2Terms - a Map object.