public abstract class UmlsToSnomedConsumerImpl extends BaseLookupConsumerImpl
getSnomedCodes
and implement
looking up the CUI->SNOMED mappingsBaseLookupConsumerImpl.LookupHitKey
Modifier and Type | Field and Description |
---|---|
private java.util.Set<java.lang.String> |
_antSiteTuiSet |
private java.util.Set<java.lang.String> |
_disorderTuiSet |
private java.util.Set<java.lang.String> |
_findingTuiSet |
private java.util.Set<java.lang.String> |
_medicationSet |
private java.util.Set<java.lang.String> |
_procedureTuiSet |
private java.util.Set<java.lang.String> |
_validTuiSet |
private static java.lang.String |
ANT_SITE_TUIS_PRP_KEY |
private static java.lang.String |
CODING_SCHEME_PRP_KEY |
private static java.lang.String |
CUI_MF_PRP_KEY |
private static java.lang.String |
DISORDER_TUIS_PRP_KEY |
private static java.lang.String |
FINDING_TUIS_PRP_KEY |
private static java.lang.String |
MEDICATION_TUIS_PRP_KEY |
private static java.lang.String |
PROCEDURE_TUIS_PRP_KEY |
protected java.util.Properties |
props |
private static java.lang.String |
TUI_MF_PRP_KEY |
Constructor and Description |
---|
UmlsToSnomedConsumerImpl(UimaContext aCtx,
java.util.Properties properties) |
Modifier and Type | Method and Description |
---|---|
void |
consumeHits(JCas jcas,
java.util.Iterator<LookupHit> lhItr)
Consumes the hits produced by the LookupAnnotator.
|
private java.util.Collection<UmlsConcept> |
createConceptCol(JCas jcas,
java.lang.String cui,
java.lang.String tui,
java.util.Collection<java.lang.String> snomedCodesCol)
For each SNOMED code, create a corresponding JCas UmlsConcept object and
store in a Collection.
|
private int |
getNamedEntityType(java.lang.String tui) |
protected abstract java.util.Set<java.lang.String> |
getSnomedCodes(java.lang.String umlsCode)
Searches for the Snomed codes that are synonyms of the UMLS concept with CUI
umlsCode |
private static java.lang.String |
getUniqueKey(java.lang.String cui,
java.lang.String tui) |
private static java.util.Set<java.lang.String> |
loadList(java.lang.String delimitedString)
Load a comma delimited list
|
createLookupHitMap, organizeByOffset
private static final java.lang.String CUI_MF_PRP_KEY
private static final java.lang.String TUI_MF_PRP_KEY
private static final java.lang.String CODING_SCHEME_PRP_KEY
private static final java.lang.String MEDICATION_TUIS_PRP_KEY
private static final java.lang.String ANT_SITE_TUIS_PRP_KEY
private static final java.lang.String PROCEDURE_TUIS_PRP_KEY
private static final java.lang.String DISORDER_TUIS_PRP_KEY
private static final java.lang.String FINDING_TUIS_PRP_KEY
private java.util.Set<java.lang.String> _medicationSet
private java.util.Set<java.lang.String> _antSiteTuiSet
private java.util.Set<java.lang.String> _procedureTuiSet
private java.util.Set<java.lang.String> _disorderTuiSet
private java.util.Set<java.lang.String> _findingTuiSet
private java.util.Set<java.lang.String> _validTuiSet
protected java.util.Properties props
public UmlsToSnomedConsumerImpl(UimaContext aCtx, java.util.Properties properties) throws java.lang.Exception
java.lang.Exception
protected abstract java.util.Set<java.lang.String> getSnomedCodes(java.lang.String umlsCode) throws java.sql.SQLException, DictionaryException
umlsCode
umlsCode
- -SQLException,
- DictionaryExceptionjava.sql.SQLException
DictionaryException
public void consumeHits(JCas jcas, java.util.Iterator<LookupHit> lhItr) throws AnalysisEngineProcessException
jcas
- CAS for storing datalhItr
- Iterator over LookupHit objects. These objects contain data
about the annotation span plus any associated metadata.AnalysisEngineProcessException
private int getNamedEntityType(java.lang.String tui) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
private java.util.Collection<UmlsConcept> createConceptCol(JCas jcas, java.lang.String cui, java.lang.String tui, java.util.Collection<java.lang.String> snomedCodesCol)
jcas
- -snomedCodesCol
- -private static java.lang.String getUniqueKey(java.lang.String cui, java.lang.String tui)
private static java.util.Set<java.lang.String> loadList(java.lang.String delimitedString)
delimitedString
- -