uk.ac.ebi.microarray.zooma.context
Interface OntologyMappingContext

All Known Implementing Classes:

AggregatedContext, DefaultMappingContext, NewTermContext, OntocatContext, OWLContext

public interface OntologyMappingContext

A representation of the context in which an OntologyMapper may wish to operate. The only critical type, which all contexts must encapsulate, is the source of the mapping. Implementations are free then to add as much or as little extra metadata as they choose. Typically this may include experiment type, the degree to which the term exactly matches the value, or other informative details that may alter the hypothesis on which a mapping is based.

By default, ZOOMA only uses context for inspection of sources (in RankingBasedCalculator) and assessment of equality or equivalence, in formulating hypotheses to aggregate terms mapped in the same context (in ContextSensitiveMappingFormulator). However, you could easily supply new implementations with extra logic to do more intricate mappings, using additional metadata provided by new context types if desired.

Author:

Tony Burdett

See Also:

RankingBasedCalculator, ContextSensitiveMappingFormulator

Field Summary

static java.lang.String	IRRELEVANT_VALUE A value signifying that the parameter is irrelevant for comparison purposes and should be ignored
static java.lang.String	UNKNOWN_VALUE An unknown value that can be used in any parameter
static java.lang.String	USER_SUBMITTED A value to be used whenever a none-standard parameter, supplied by the user, is required

Method Summary

Source

getSource() The "source" in which a mapping is asserted.

Field Detail

UNKNOWN_VALUE

static final java.lang.String UNKNOWN_VALUE

An unknown value that can be used in any parameter

See Also:

Constant Field Values

IRRELEVANT_VALUE

static final java.lang.String IRRELEVANT_VALUE

A value signifying that the parameter is irrelevant for comparison purposes and should be ignored

See Also:

Constant Field Values

USER_SUBMITTED

static final java.lang.String USER_SUBMITTED

A value to be used whenever a none-standard parameter, supplied by the user, is required

See Also:

Constant Field Values

Method Detail

getSource

Source getSource()

The "source" in which a mapping is asserted. This will usually describe the name of the datasource in which a mapping is stated, or possibly the ontology in which a value exactly matches a class name.

Returns:

the source of a mapping assertion