Hi Team, We set up cTAKES4.0.0 as our NLP engine for our profile recently . We have faced situations where some of the expected tokens are not picked up by cTAKES during clinical text extraction. So our first thought process was to identify where the dictionary is configured and how that can be updated. After some code analysis it was found that the dictionary is configured in the below path under ctakes/resources for sources RxNorm and SNOMEDCT_US [cid:image003.png@01D635F4.428C6D80]
We were able to open the hsqldb using the hsql db gui and found out that some of our required entries are already there . So if I come specifically to our current problem. The Pap Smear and Mamogram are two clinical terms which are not currently recognized by cTAKES in our profile. * If I look into the .script file , Pap Smear and Mammogram/Mammography is already present in the .script file and in the respective tables. PFB a snapshot as below [cid:image006.jpg@01D635F4.428C6D80] [cid:image010.jpg@01D635F4.428C6D80] But still this was not recogonised by cTAKES. I see there are some filters working on top of the available entries in dictionary(ctakes-gui and ctake-gui-res). Will that be because of these filters the tokens are not recognized as expected. Could you pls. share us what exactly these filters do. This will help us in future also when we are trying to add new terms into the dictionary * What are the steps to do if we need to add/edit entries into the existing dictionaries. I see we can add/edit the existing values in .scripts files but our primary doubt is if suppose I have a term 'xyz' to be added to dictionary how can I get the CUI and other values like TUI,RINDEX,TCOUNT and PREFTERM. Is it fine if I can give any random value for the TUI/CUI/RINDEX/TCOUNT. I could also see options to create custom bsv dictionaries but couldn't see much documentation for it. Kindly advise which is the better option from the below 3. o Generate a custom dictionary using METAMORPHOSYS UML installation tool(where we provide sources as ICD10,RxNORM,SNOMEDCT_US) and leverage the full set of .rrf files in the meta folder . Is this approach better if the entries to be populated are maximal? o Add/edit the available dictionary sno_rx_16ab and in that case how to provide valid values for each columns like CUI, TUI,RINDEX,TCOUNT and PREFTERM. If the entries to be populated are minimal is this approach would be better?. o Use a custom bsv , in that case how should we add values to custom bsv. Could you also provide a sample in that case. I found a Metathesaurus browser in the below url , where I can search for the terms and get the CUI and the respective source like ICD/CPT/MDR. But still I was unable to get the other required attributes to be populated like TUI,RINDEX,TCOUNT and PREFTERM. Could you pls. brief what these attributes signifies https://uts.nlm.nih.gov//metathesaurus.html<https://uts.nlm.nih.gov/metathesaurus.html> Kindly advise us on how to proceed on this and correct us if we went wrong somewhere. This would be of great help for us P.S : We comply with UMLS license Thanks & Regards [cid:D3145E69-CD94-48C1-877F-5134EEAFB598] Abad Ayyub Vnet: 406170 | Cell : +91-9447379028 This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored. This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored.
