uk.ac.ebi.microarray.zooma.formulate
Interface OntologyMappingFormulator

All Known Implementing Classes:

ContextSensitiveMappingFormulator, NoPossibleMappingFormulator

public interface OntologyMappingFormulator

Formulates a plan by which ontology mappings can be asserted. This is essentially a facade over the subsystem that retrieves ontology terms and constructs mapping hypotheses.

Author:

Tony Burdett

Method Summary

java.util.Collection<OntologyMappingHypothesis>

formulateHypotheses(Value value) Formulate a set of hypotheses that describe the possible mappings that might be made about the given value.

Method Detail

formulateHypotheses

java.util.Collection<OntologyMappingHypothesis> formulateHypotheses(Value value)
                                                                    throws HypothesisFormulationException

Formulate a set of hypotheses that describe the possible mappings that might be made about the given value. It is possible to use this method to formulate any hypothesis, whether this is the null or alternative hypothesis.

Implementations may use a specific strategy to fetch mappings that may, for example, spread across multiple sources. Such implementations should not usually be suitable for formulating the null hypothesis - normally the null hypothesis will prefer a mapping from a dedicated source or it will assert that no mapping is possible.

Implementations should retrieve, or construct, context information for each hypothesis formulated. Some implementations may wish to formulate hypotheses from the same source with different levels of sensitivity, for example: in some cases, species information may be required whereas in others it may be irrelevant.

Generally, formulators act as a facade over the OntologyTermRetriever and OntologyMappingHypothesisFactory interfaces to retrieve then generate hypotheses. However, most implementations will also describe some higher logic to consider only those hypotheses from relevant or interesting contexts.

Parameters:

value - the description to hypothesise about

Returns:

the collections of mapping hypotheses that were formulated

Throws:

HypothesisFormulationException - if any hypotheses could not be generated, due to invalid data or a failure of retrieval