uk.ac.ebi.microarray.zooma.retrieval
Interface OntologyTermRetriever

All Known Implementing Classes:

CompositeOntologyTermRetriever, EFOOntocatRetriever, OntocatRetriever, OntologyRetriever

public interface OntologyTermRetriever

A service that fetches ontology terms from some repository. The fetched OntologyTerms are used them to generate a set of new OntologyMappingHypothesis objects

Retrievers should not have state, and should be threadsafe, so that multiple clients can use the same retriever to fetch terms.

Author:

Tony Burdett

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.

Method Detail

fetchTerms

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

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

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

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

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.

Parameters:

value - the original description used to retrieve the supplied term

term - the term that is mapped to this description - usually, retrieved by 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