Hi Pratik, You can create a custom dictionary as per your requirement using the dictionary-gui tool. This tool is a standalone Java project and you can install and run it separately from cTAKES. The following mail from the archives will help:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201601.mbox/%3CCA+jqmuyBcv-h67bxg=gummpVkE_khOXpSfRvSqx=jk3pzz7...@mail.gmail.com%3E Once you have the tool in your workspace, run CreatorGui.java, this will bring up a gui from where you can select the required vocabularies. After the build is complete, the tool will create new script and xml files that you can plug into your cTAKES installation. Also, before you can run the dictionary-gui tool, you need to have a local installation of the UMLS. thanks Nishant On Mon, Dec 5, 2016 at 6:20 AM, pratik agarwal <[email protected]> wrote: > 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/[email protected]/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 > >
