owltools.gaf.eco
Interface EcoMapper

All Known Subinterfaces:
TraversingEcoMapper
All Known Implementing Classes:
EcoMapperImpl, TraversingEcoMapperImpl

public interface EcoMapper


Field Summary
static String ECO_MAPPING_PURL
          Permanent URL for the mapping of GO evidence codes to ECO classes
static String ECO_PURL
          Permanent URL for the evidence code ontology (ECO) owl file.
static org.semanticweb.owlapi.model.IRI ECO_PURL_IRI
          IRI for the evidence code ontology (ECO) owl file.
 
Method Summary
 Set<org.semanticweb.owlapi.model.OWLClass> getAllEcoClassesForCode(String code)
          Retrieve the ECO classes for the given GO evidence code.
 Map<org.semanticweb.owlapi.model.OWLClass,String> getCodesForEcoClasses()
          Retrieve the mapping from ECO classes to GO evidence codes.
 org.semanticweb.owlapi.model.OWLClass getEcoClassForCode(String code)
          Retrieve the equivalent ECO class for the given GO evidence code.
 org.semanticweb.owlapi.model.OWLClass getEcoClassForCode(String code, String refCode)
          Retrieve the ECO class for the given GO evidence code and reference.
 boolean isGoEvidenceCode(String code)
          Check that the given GO code is a valid code with an existing mapping to ECO
 

Field Detail

ECO_PURL

static final String ECO_PURL
Permanent URL for the evidence code ontology (ECO) owl file.

See Also:
Constant Field Values

ECO_PURL_IRI

static final org.semanticweb.owlapi.model.IRI ECO_PURL_IRI
IRI for the evidence code ontology (ECO) owl file.


ECO_MAPPING_PURL

static final String ECO_MAPPING_PURL
Permanent URL for the mapping of GO evidence codes to ECO classes

See Also:
Constant Field Values
Method Detail

getEcoClassForCode

org.semanticweb.owlapi.model.OWLClass getEcoClassForCode(String code)
Retrieve the equivalent ECO class for the given GO evidence code. Assume, that the reference is 'default'.

Parameters:
code -
Returns:
OWLClass or null

getAllEcoClassesForCode

Set<org.semanticweb.owlapi.model.OWLClass> getAllEcoClassesForCode(String code)
Retrieve the ECO classes for the given GO evidence code. Include the classes to be used with more specific references.

Parameters:
code -
Returns:
set of classes, never null

getEcoClassForCode

org.semanticweb.owlapi.model.OWLClass getEcoClassForCode(String code,
                                                         String refCode)
Retrieve the ECO class for the given GO evidence code and reference. If reference is null, assume default.

Parameters:
code -
refCode -
Returns:
OWLClass or null

isGoEvidenceCode

boolean isGoEvidenceCode(String code)
Check that the given GO code is a valid code with an existing mapping to ECO

Parameters:
code -
Returns:
true if the code is a valid

getCodesForEcoClasses

Map<org.semanticweb.owlapi.model.OWLClass,String> getCodesForEcoClasses()
Retrieve the mapping from ECO classes to GO evidence codes.

Returns:
mapping


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