RE: BagOfCuisGenerator.java, same idea for getConceptText()
Hi Maite, I just checked the log and it looks like you'll need to use a copy of cTakes built after 12/08/2014 to get Snomed codes. Sean -Original Message- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Monday, February 16, 2015 12:19 PM To: dev@ctakes.apache.org Subject: Re: BagOfCuisGenerator.java, same idea for getConceptText() Sean, I have a question, is it because I am using fast dictionary I don't get snomed-oid or snomed-code? Instead, it's snomed_oid: null#CTAKES. Thank you. Maite On Fri, Feb 13, 2015 at 1:32 PM, Maite Meseure Hugues meseure.ma...@gmail.com wrote: Thank you for your replies, It's helpful. I was working on 3.2.0 version, so it looks like 3.2.1 allows to get the UMLS preferred text. Maite On Thu, Feb 12, 2015 at 2:25 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Oh yeah - use the -fast dictionary to get preferred text. The fastest way to get cuis only is with CuisOnlyPlaintextUMLSProcessor. If you want polarity make sure you uncomment the section with PolarityCleartkAnalysisEngine. Sean -Original Message- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Thursday, February 12, 2015 2:46 PM To: dev@ctakes.apache.org Subject: BagOfCuisGenerator.java, same idea for getConceptText() Hi everyone, I am currently working on BagOfCuisGenerator, and I would like to add the concept text to the output. I 've seen some discussions about getting the original text and UMLS preferred text in addition to the cui. Can someone give me pointers to do that? Thanks in advance for your time. Maite -- -- Maïté Meseure Hugues -- -- Maïté Meseure Hugues -- -- Maïté Meseure Hugues
Re: BagOfCuisGenerator.java, same idea for getConceptText()
Sean, I have a question, is it because I am using fast dictionary I don't get snomed-oid or snomed-code? Instead, it's snomed_oid: null#CTAKES. Thank you. Maite On Fri, Feb 13, 2015 at 1:32 PM, Maite Meseure Hugues meseure.ma...@gmail.com wrote: Thank you for your replies, It's helpful. I was working on 3.2.0 version, so it looks like 3.2.1 allows to get the UMLS preferred text. Maite On Thu, Feb 12, 2015 at 2:25 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Oh yeah - use the -fast dictionary to get preferred text. The fastest way to get cuis only is with CuisOnlyPlaintextUMLSProcessor. If you want polarity make sure you uncomment the section with PolarityCleartkAnalysisEngine. Sean -Original Message- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Thursday, February 12, 2015 2:46 PM To: dev@ctakes.apache.org Subject: BagOfCuisGenerator.java, same idea for getConceptText() Hi everyone, I am currently working on BagOfCuisGenerator, and I would like to add the concept text to the output. I 've seen some discussions about getting the original text and UMLS preferred text in addition to the cui. Can someone give me pointers to do that? Thanks in advance for your time. Maite -- -- Maïté Meseure Hugues -- -- Maïté Meseure Hugues -- -- Maïté Meseure Hugues
Re: BagOfCuisGenerator.java, same idea for getConceptText()
Thank you for your replies, It's helpful. I was working on 3.2.0 version, so it looks like 3.2.1 allows to get the UMLS preferred text. Maite On Thu, Feb 12, 2015 at 2:25 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Oh yeah - use the -fast dictionary to get preferred text. The fastest way to get cuis only is with CuisOnlyPlaintextUMLSProcessor. If you want polarity make sure you uncomment the section with PolarityCleartkAnalysisEngine. Sean -Original Message- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Thursday, February 12, 2015 2:46 PM To: dev@ctakes.apache.org Subject: BagOfCuisGenerator.java, same idea for getConceptText() Hi everyone, I am currently working on BagOfCuisGenerator, and I would like to add the concept text to the output. I 've seen some discussions about getting the original text and UMLS preferred text in addition to the cui. Can someone give me pointers to do that? Thanks in advance for your time. Maite -- -- Maïté Meseure Hugues -- -- Maïté Meseure Hugues
RE: BagOfCuisGenerator.java, same idea for getConceptText()
Try something like the following for output:
private int extractFeatures( final IdentifiedAnnotation annotation ) {
// Extract the IdentifiedAnnotation itself
final CollectionString umlsInfos = getUmlsInfos( annotation,
_printSnomed );
if ( umlsInfos == null ) {
return 0;
}
final int begin = annotation.getBegin();
final int end = annotation.getEnd();
final String annotationText = annotation.getCoveredText();
final int polarity = annotation.getPolarity();
int count = 0;
for ( String umlsInfo : umlsInfos ) {
saveAnnotation( annotationText, umlsInfo, polarity, begin, end );
count++;
}
return count;
}
static private CollectionString getUmlsInfos( final IdentifiedAnnotation
identifiedAnnotation ) {
final FSArray fsArray = identifiedAnnotation.getOntologyConceptArr();
if ( fsArray == null ) {
return Collections.emptySet();
}
final FeatureStructure[] featureStructures = fsArray.toArray();
final SetString umlsInfos = new HashSetString(
featureStructures.length );
for ( FeatureStructure featureStructure : featureStructures ) {
final OntologyConcept ontologyConcept = (OntologyConcept)
featureStructure;
String info = null;
if ( ontologyConcept instanceof UmlsConcept ) {
final UmlsConcept umlsConcept = (UmlsConcept) ontologyConcept;
info = umlsConcept.getCui();
final String tui = umlsConcept.getTui();
if ( tui != null !tui.isEmpty() ) {
info += _ + tui;
}
final String preferredText = umlsConcept.getPreferredText();
if ( preferredText != null !preferredText.isEmpty() ) {
info += = \ + preferredText + \;
}
umlsInfos.add( info );
}
}
return umlsInfos;
}
public void saveAnnotation( final String spannedText, final String umlsInfo,
final int polarity,
final int begin, final int end ) {
final String text = begin + , + end + + (polarity 0 ? - : )
+ umlsInfo + + spannedText;
if ( _writer == null ) {
System.out.println( text );
return;
}
try {
_writer.write( text );
_writer.newLine();
} catch ( IOException ioE ) {
logger.error( ioE.getMessage() );
}
}
-Original Message-
From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com]
Sent: Thursday, February 12, 2015 2:46 PM
To: dev@ctakes.apache.org
Subject: BagOfCuisGenerator.java, same idea for getConceptText()
Hi everyone,
I am currently working on BagOfCuisGenerator, and I would like to add the
concept text to the output.
I 've seen some discussions about getting the original text and UMLS preferred
text in addition to the cui. Can someone give me pointers to do that?
Thanks in advance for your time.
Maite
--
--
Maïté Meseure Hugues
RE: BagOfCuisGenerator.java, same idea for getConceptText()
Oh yeah - use the -fast dictionary to get preferred text. The fastest way to get cuis only is with CuisOnlyPlaintextUMLSProcessor. If you want polarity make sure you uncomment the section with PolarityCleartkAnalysisEngine. Sean -Original Message- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Thursday, February 12, 2015 2:46 PM To: dev@ctakes.apache.org Subject: BagOfCuisGenerator.java, same idea for getConceptText() Hi everyone, I am currently working on BagOfCuisGenerator, and I would like to add the concept text to the output. I 've seen some discussions about getting the original text and UMLS preferred text in addition to the cui. Can someone give me pointers to do that? Thanks in advance for your time. Maite -- -- Maïté Meseure Hugues
