Johnsd11 opened a new issue, #64: URL: https://github.com/apache/ctakes/issues/64
### What’s your question? Hello, I’ve run into a problem and a question when running cTAKES. If I have a document and process it through cTAKES, then the XMI output will contain numerous XML tags. The tags our lab is interested in are the CUIs, for example, the XMI tag <refsem:UmlsConcept xmi:id="16626" codingScheme="SNOMEDCT_US" code="7092007" score="0.0" disambiguated="false" cui="C0025859" tui="T109" preferredText="Metoprolol-containing product"/> Would indicate the CUI C0025859 for Metoprolol-containing product is found in a given document. If I look at the input document text, then I can locate three instances of the drug Metoprolol in the document text. When I look at the cTAKES XMI output in the cTAKES XMI CVD viewer, each of the results for Metoprolol is part of ontologyConceptArr, with 4 members each, looking like this: // found at org.apache.ctakes.typesystem.type.textsem.EventMention // org.apache.ctakes.typesystem.type.textsem.MedicationMention // ontologyConceptArr = uima.cas.FSArray[4] <refsem:UmlsConcept xmi:id="16626" codingScheme="SNOMEDCT_US" code="7092007" score="0.0" disambiguated="false" cui="C0025859" tui="T109" preferredText="Metoprolol-containing product"/> <refsem:UmlsConcept xmi:id="16646" codingScheme="SNOMEDCT_US" code="7092007" score="0.0" disambiguated="false" cui="C0025859" tui="T121" preferredText="Metoprolol-containing product"/> <refsem:UmlsConcept xmi:id="16616" codingScheme="SNOMEDCT_US" code="372826007" score="0.0" disambiguated="false" cui="C0025859" tui="T109" preferredText="Metoprolol-containing product"/> <refsem:UmlsConcept xmi:id="16636" codingScheme="SNOMEDCT_US" code="372826007" score="0.0" disambiguated="false" cui="C0025859" tui="T121" preferredText="Metoprolol-containing product"/> Although not shown here, it is possible for there to be different CUIs within a single uima.cas.FSArray, with this array mapping to a single string of text in the document. If I walk the XMI file and retrieve all CUIs, then the result will be the CUI C0025859 being found 12 times, however, if I extend the JCasAnnotator_ImplBase java class to extract the CUIs from the jCas annotations, then it only finds this CUI 3 times. If part of the output needs to include a count of all CUIs found by cTAKES within a given document, which method is correct? Thanks! ### Context _No response_ ### What category does this question fall under? None ### Contact Details _No response_ -- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. To unsubscribe, e-mail: [email protected] For queries about this service, please contact Infrastructure at: [email protected]
