Hi Matthew, Go to the directory that has your dictionary and run "grep -i "type 2 diabetes" <YourDictName>.script"
Do you see the line: INSERT INTO CUI_TERMS VALUES(11860,2,3,'type 2 diabetes','diabetes') ? If not, then it wasn't added when your dictionary was created. The dictionary will only contain terms from selected sources. The synonym "type 2 diabetes" is in the following sources: "Type 2 Diabetes" MEDLINEPLUS MSH NCI NDFRT "type 2 diabetes" CHV CSP ICPC2P MEDCIN Make sure that when you install the umls you select one of those sources. If you only selected snomed as a source then you will not have the synonym that you want. Sean -----Original Message----- From: Matthew Vita [mailto:[email protected]] Sent: Saturday, September 16, 2017 1:50 PM To: [email protected] Subject: Followup Question on ICD10 Dictionary and Concept Matching Quality [EXTERNAL] Hi cTAKES Community, Sean, Tim, As you recall, I recently put together the YouTube video "cTAKES: How to Create an ICD10 Dictionary" (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=0rSQwwsnqghITPXgFr7F3NcE_8eV69HKjbyH_tkNlLg&s=s7WhFcIc-cj3SGUkzmi25-SxiPrf_LiVbu1sK9FhLE0&e= ) to improve the documentation of using the NIH/UMLS and cTAKES tooling to generate custom dictionaries. It is working well and Dr. Tim Miller's cTAKES Docker repository will soon have further documentation/support for using this approach in establishing multiple custom cTAKES dictionaries. However, I am writing to because while everything with ICD10 is working, I'm finding the concept matching to be inadequate as compared to SNOMED/RXNORM (I'm sure I'm just missing something :) ). For example, if I type in "Type 2 Diabetes", there is no concept match. However, when I type "Type 2 Diabetes Mellitus", there is a match. Is there a way I can better "train" or configure the dictionary to have matching at parity with that of the SNOMED/RXNORM dictionaries? For reference, here is the ICD10 configuration I'm using: <dictionary> <name>icd10Terms</name> <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary</implementationName> <properties> <property key="jdbcDriver" value="org.hsqldb.jdbcDriver" /> <property key="jdbcUrl" value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/icd10/icd10" /> <property key="jdbcUser" value="sa" /> <property key="jdbcPass" value="" /> <property key="rareWordTable" value="cui_terms" /> <property key="umlsUrl" value=" https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=0rSQwwsnqghITPXgFr7F3NcE_8eV69HKjbyH_tkNlLg&s=kxXUD2JtkzM0fU7rtE8DGCpCXTjF9ollYienRopcCF8&e= " /> <property key="umlsVendor" value="NLM-6515182895" /> <property key="umlsUser" value="CHANGE_ME" /> <property key="umlsPass" value="CHANGE_ME" /> </properties> </dictionary> <conceptFactory> <name>icd10Concepts</name> <implementationName>org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory</implementationName> <properties> <property key="jdbcDriver" value="org.hsqldb.jdbcDriver" /> <property key="jdbcUrl" value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/icd10/icd10" /> <property key="jdbcUser" value="sa" /> <property key="jdbcPass" value="" /> <property key="umlsUrl" value=" https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=0rSQwwsnqghITPXgFr7F3NcE_8eV69HKjbyH_tkNlLg&s=kxXUD2JtkzM0fU7rtE8DGCpCXTjF9ollYienRopcCF8&e= " /> <property key="umlsVendor" value="NLM-6515182895" /> <property key="umlsUser" value="CHANGE_ME" /> <property key="umlsPass" value="CHANGE_ME" /> <property key="tuiTable" value="tui" /> <property key="prefTermTable" value="prefTerm" /> <property key="icd10cmTable" value="text" /> <property key="icd10amaeTable" value="text" /> <property key="icd10amTable" value="text" /> <property key="srcTable" value="text" /> <property key="icd10Table" value="text" /> <property key="icd10aeTable" value="text" /> <property key="icd10pcsTable" value="text" /> </properties> </conceptFactory> As always, I appreciate the hard work this community has done and, based on the feedback from this thread, I will do my best to improve the documentation for others. Thanks, Matthew Vita www.matthewvita.com
