Hi everyone I came across cTAKES fairly recently and I'm facing some difficulties with understanding the working of it. I am required to map clinical text notes with the ICD-10-CM and CPT/HCPCS codes. From what I read, or tried, the default dictionaries used with the fast pipeline are SNOMEDCT, RXNORM and ICD9CM.
I am currently trying to work with the user version of cTAKES in Intellij IDEA with Java Oracle JDK 8. It would be great if someone could help me out. I am really sorry if this is too easy a problem, but I've been trying to solve it for a while and I'm stuck. I was able to extract ICD9CM codes from cTAKES with the default resources i.e. ctakesnorx.properties and ctakesnorx.script I wanted to get ICD10CM and ICD10PCS codes, so I downloaded .script and .properties file from this source: https://sourceforge.net/p/ctakesresources/code/HEAD/ tree/trunk/ctakes-resources-snomed-rword-hsqldb-2011ab/ src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakesicd2015/ and made corresponding changes to the cTakesHsql.xml file as mentioned by Sean in: https://www.mail-archive.com/dev@ctakes.apache.org/msg02597.html But this doesn't seem to work. I played around a bit with the parameters in the following lines: <property key="snomedct_usTable" value="long"/> <property key="rxnormTable" value="text"/> <property key="icd9cmTable" value="text"/> <property key="icd10pcsTable" value="text"/> Basically when I was getting blank outputs after making the change. I am using OntologyConceptUtil.getSchemeCodes(JCas) for getting the outputs. I was getting an error with rxnormTable. So I commented that line out. and after that I was getting blank output. So I tried replacing value="text" with value = "icd9cm" for key = "icd9cmTable" and it started returning ICD9CM codes. But I couldn't get anything when I did the same with ICD10PCS. I again got a blank output. Note: I did all this after commenting: <property key="snomedTable" value="snomedct"/> <property key="rxnormTable" value="rxnorm"/> <property key="icd9Table" value="icd9cm"/> <property key="icd10Table" value="icd10pcs"/> It would be great if someone could help me understand how the dictionary mechanism is working. Also, how to get ICD10CM codes and ICD10PCS codes from this. (i) What are the keys and values mentioned above and where can I find these in the script or properties file? Is there a way I can access these? Please help me understand how this is working. (ii) I have a csv file containing the ICD codes with the code in Column 1 and description in Column 2 and similarly for CPT/HCPCS codes. What are the steps I need to take to make it work with OntologyConceptUtil.getSchemeCodes(JCas). I saw from different forums that we can use dictionary-gui tool from sandbox. But I am not really understanding which files do I need to run in that folder. Also, where in the project tree should I place this folder to make it run. Also, what are the parameters required and where do I change them, if any. Thanks a lot. Regards, Pratik Agarwal
