Package ubic.gemma.core.ontology

Interface OntologyService

All Known Implementing Classes:

OntologyServiceImpl

public interface OntologyService

Author:

Paul

Method Summary

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Deprecated.
Map<OntologyTerm,Long>	findObsoleteTermUsage(long timeout, TimeUnit timeUnit)	Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations.
Collection<OntologySearchResult<OntologyTerm>>	findTerms(String query, int maxResults, long timeout, TimeUnit timeUnit)	Given a search string will look through the loaded ontologies for terms that match the search term.
Collection<CharacteristicValueObject>	findTermsInexact(String givenQueryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)	Given a search string will first look through the characteristic database for any entries that have a match.
Map<String,OntologyTerm>	fixOntologyTermLabels(boolean dryRun, long timeout, TimeUnit timeUnit)	Check all system uses of ontology terms for the correct label and fix any mismatches based on the ontology OWL files.
Set<OntologyTerm>	getCategoryTerms()	Obtain terms which are allowed for use in the category of a Characteristic.
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> matchingTerms, boolean direct, boolean includeAdditionalProperties, long timeout, TimeUnit timeUnit)	Obtain the children of a collection of terms.
String	getDefinition(String uri, long timeout, TimeUnit timeUnit)	Obtain a definition for the given URI.
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, long timeout, TimeUnit timeUnit)	Obtain the parents of a collection of terms.
Set<OntologyProperty>	getRelationTerms()	Obtain terms allowed for the predicate (relationship) in a Statement.
OntologyTerm	getTerm(String uri, long timeout, TimeUnit timeUnit)	Obtain a term for the given URI.
Set<OntologyTerm>	getTerms(Collection<String> uris, long timeout, TimeUnit timeUnit)	Return all the terms matching the given URIs.
void	reindexAllOntologies()	Recreate the search indices, for ontologies that are loaded.
void	reinitializeAndReindexAllOntologies()	Reinitialize (and reindex) all the ontologies "from scratch".

Method Details

findObsoleteTermUsage

Map<OntologyTerm,Long> findObsoleteTermUsage(long timeout,
 TimeUnit timeUnit)
                                      throws TimeoutException

Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations. Requires the ontologies are loaded into memory.

Will also find terms that are no longer in an ontology we use.

Returns:

map of value URI to a representative characteristic using the term. The latter will contain a count of how many occurrences there were.

Throws:

TimeoutException

findExperimentsCharacteristicTags

@Deprecated
Collection<CharacteristicValueObject> findExperimentsCharacteristicTags(String searchQuery,
 int maxResults,
 boolean useNeuroCartaOntology,
 long timeout,
 TimeUnit timeUnit)
                                                                 throws SearchException

Deprecated.

Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices

Parameters:

searchQuery - search query

useNeuroCartaOntology - use neurocarta ontology

Returns:

characteristic vos

Throws:

SearchTimeoutException - if the search times out

SearchException

findTerms

Collection<OntologySearchResult<OntologyTerm>> findTerms(String query,
 int maxResults,
 long timeout,
 TimeUnit timeUnit)
                                                  throws SearchException

Given a search string will look through the loaded ontologies for terms that match the search term. If the query looks like a URI, it just retrieves the term. For other queries, this a lucene backed search, is inexact and for general terms can return a lot of results.

Parameters:

query - search query

Returns:

returns a collection of ontologyTerm's

Throws:

SearchTimeoutException - if the search times out

SearchException

findTermsInexact

Collection<CharacteristicValueObject> findTermsInexact(String givenQueryString,
 int maxResults,
 @Nullable
 Taxon taxon,
 long timeout,
 TimeUnit timeUnit)
                                                throws SearchException

Given a search string will first look through the characteristic database for any entries that have a match. If a ontologyTermURI is given it will add all the individuals from that URI that match the search term criteria to the returned list also.

Parameters:

givenQueryString - query string

taxon - Only used if we're going to search for genes or taxon is otherwise relevant; if null, restriction is not used.

Returns:

characteristic vos

Throws:

SearchTimeoutException - if the search times out

SearchException

getCategoryTerms

Set<OntologyTerm> getCategoryTerms()

Obtain terms which are allowed for use in the category of a Characteristic.

getRelationTerms

Set<OntologyProperty> getRelationTerms()

Obtain terms allowed for the predicate (relationship) in a Statement.

getParents

Set<OntologyTerm> getParents(Collection<OntologyTerm> terms,
 boolean direct,
 boolean includeAdditionalProperties,
 long timeout,
 TimeUnit timeUnit)
                      throws TimeoutException

Obtain the parents of a collection of terms.

Throws:

TimeoutException - if the timeout is exceeded

See Also:

• OntologyTerm.getParents(boolean, boolean)

getChildren

Set<OntologyTerm> getChildren(Collection<OntologyTerm> matchingTerms,
 boolean direct,
 boolean includeAdditionalProperties,
 long timeout,
 TimeUnit timeUnit)
                       throws TimeoutException

Obtain the children of a collection of terms.

Throws:

TimeoutException - if the timeout is exceeded

See Also:

• OntologyTerm.getChildren(boolean, boolean)

getDefinition

@Nullable
String getDefinition(String uri,
 long timeout,
 TimeUnit timeUnit)
              throws TimeoutException

Obtain a definition for the given URI.

Throws:

TimeoutException

getTerm

@Nullable
OntologyTerm getTerm(String uri,
 long timeout,
 TimeUnit timeUnit)
              throws TimeoutException

Obtain a term for the given URI.

Throws:

TimeoutException

getTerms

Set<OntologyTerm> getTerms(Collection<String> uris,
 long timeout,
 TimeUnit timeUnit)
                    throws TimeoutException

Return all the terms matching the given URIs.

Throws:

TimeoutException - if the timeout is exceeded

reindexAllOntologies

void reindexAllOntologies()

Recreate the search indices, for ontologies that are loaded.

reinitializeAndReindexAllOntologies

void reinitializeAndReindexAllOntologies()

Reinitialize (and reindex) all the ontologies "from scratch". This is necessary if indices are old etc. This should be admin-only.

fixOntologyTermLabels

Map<String,OntologyTerm> fixOntologyTermLabels(boolean dryRun,
 long timeout,
 TimeUnit timeUnit)
                                        throws TimeoutException

Check all system uses of ontology terms for the correct label and fix any mismatches based on the ontology OWL files. This should be run periodically along with findObsoleteTerms.

Parameters:

dryRun - if true, no changes will be made in the database and just print them out instead.

Returns:

Throws:

TimeoutException