Package ubic.basecode.ontology.ncbo

Class AnnotatorClient

java.lang.Object

ubic.basecode.ontology.ncbo.AnnotatorClient

public class AnnotatorClient
extends Object

Use the NCBO annotator to find ontology terms matching strings.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DOID_ONTOLOGY
static final String	HP_ONTOLOGY

Constructor Summary

Constructors

Constructor	Description
AnnotatorClient()

Method Summary

Modifier and Type	Method	Description
static String	findLabelForIdentifier(String ontologyId, String identifier)	return the label associated with an conceptid.
static Collection<AnnotatorResponse>	findTerm(String term)
static String	removeSpecialCharacters(String txt)

Methods inherited from class java.lang.Object

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

Field Details

HP_ONTOLOGY

public static final String HP_ONTOLOGY

See Also:

• Constant Field Values

DOID_ONTOLOGY

public static final String DOID_ONTOLOGY

See Also:

• Constant Field Values

Constructor Details

AnnotatorClient

public AnnotatorClient()

Method Details

findTerm

public static Collection<AnnotatorResponse> findTerm(String term)
                                              throws IOException,
ParserConfigurationException,
IllegalStateException,
SAXException

Parameters:

term -

Returns:

Throws:

ParserConfigurationException

SAXException

IllegalStateException

Exception

IOException

findLabelForIdentifier

public static String findLabelForIdentifier(String ontologyId,
 String identifier)

return the label associated with an conceptid. FIXME why are we doing things this way, it must be terribly slow

Parameters:

ontologyId - what virtual ontology to use

identifier - the identifier, knows about: OMIM, DOID, MESH

Returns:

the label for that term, example : ABCD syndrome

removeSpecialCharacters

public static String removeSpecialCharacters(String txt)