uk.ac.ebi.microarray.zooma.retrieval
Class OntocatRetriever

java.lang.Object
  uk.ac.ebi.microarray.zooma.retrieval.OntocatRetriever

All Implemented Interfaces:

OntologyTermRetriever

public class OntocatRetriever
extends java.lang.Object
implements OntologyTermRetriever

An ontology term retriever that utilises ontocat to dispatch queries to OLS, Bioportal and EFO (using a dedicated URL). Exact text matches for the value specified in the description are fetched.

Author:

Tony Burdett

Constructor Summary

OntocatRetriever()

Method Summary

java.util.Collection<OntologyMappingContext>	fetchMappingContexts(Value value, uk.ac.ebi.ontocat.OntologyTerm term) Fetch the contexts in which the given description is mapped to the given term, if any.
java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm>	fetchTerms(Value value) Fetch a collection of terms using the given description as a search parameter.
protected org.slf4j.Logger	getLog()

Methods inherited from class java.lang.Object

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

Constructor Detail

OntocatRetriever

public OntocatRetriever()

Method Detail

getLog

protected org.slf4j.Logger getLog()

fetchTerms

public java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> fetchTerms(Value value)
                                                                throws java.io.IOException

Description copied from interface: OntologyTermRetriever

Fetch a collection of terms using the given description as a search parameter.

Specified by:

fetchTerms in interface OntologyTermRetriever

Parameters:

value - the text description to search for

Returns:

a collection of OntologyTerms retrieved from the repository

Throws:

java.io.IOException - if terms could not be fetched from the underlying source.

fetchMappingContexts

public java.util.Collection<OntologyMappingContext> fetchMappingContexts(Value value,
                                                                         uk.ac.ebi.ontocat.OntologyTerm term)
                                                                  throws java.io.IOException

Description copied from interface: OntologyTermRetriever

Fetch the contexts in which the given description is mapped to the given term, if any. This returns a collection because there are no guarantees that a mapping has been supplied to the given description in exactly one way - there could be several possible context-dependent mappings in a single datasource, for example.

If there is no connection known between the supplied description and the supplied term in the datasource that backs this retriever, this method will return an empty list.

Specified by:

fetchMappingContexts in interface OntologyTermRetriever

Parameters:

value - the original description used to retrieve the supplied term

term - the term that is mapped to this description - usually, retrieved by OntologyTermRetriever.fetchTerms(uk.ac.ebi.microarray.zooma.lang.Value) first

Returns:

the contexts in which this mapping is described in the backing

Throws:

java.io.IOException - if context could not be fetched from the underlying source