Thanks Brandon, Jessica for response. I will look at dictionary tools as mentioned and will try to figure out how it can be used for my purpose. I will certainly get back on mailing list with more queries if any.
As of now with limited understanding, I understand that current UMLS2015 database will be converted to hsql format which I can use in the pipeline by changing configurations in required XMLs. One more query, cTakes also provides "DictionaryLookupAnnotatorDB" which is supposed to be used if we want to connect to required tables in umls database. Please correct my understanding but do we have similar tool/script to be execute on umls database to generate the required format table "umls2015ab" which can be directly included in dictionary lookup. Thanks for the help! Regards Stuti Awasthi From: Glover, Jessica [mailto:[email protected]] Sent: Tuesday, March 29, 2016 5:17 PM To: '[email protected]' Subject: RE: Integrate cTakes with latest UMLS DB Hi Stuti, One thing to note about the dictionary tool is that it is still in sandbox mode, so there is no official documentation or step-by-step guide for it. However, it contains a readme, and it has been discussed on the mailing list, so you can search the archive for that "documentation." Searchable cTakes mailing list archive: http://ctakes.markmail.org/search/ Regards, Jessica From: Stuti Awasthi [mailto:[email protected]] Sent: Tuesday, March 29, 2016 7:10 AM To: '[email protected]' Subject: RE: Integrate cTakes with latest UMLS DB Hi All, Any help will be good. Im still waiting for some response. Thanks &Regards Stuti Awasthi From: Stuti Awasthi Sent: Monday, March 28, 2016 2:46 PM To: [email protected]<mailto:[email protected]> Subject: Integrate cTakes with latest UMLS DB Hi All, I have been exploring cTakes and wanted to use latest UMLS 2015ab with it. To achieve the same, I have installed UMLS in mysql database. Database Name: umls Numbers of Tables created : 53 Eg : mysql> show tables; +--------------------------+ | Tables_in_umls | +--------------------------+ | AMBIGLUI | | AMBIGSUI | | DELETEDCUI | | DELETEDLUI | | DELETEDSUI ...... | SRSTRE1 | | SRSTRE2 | Now im not able to find any step by step guide to integrate cTakes with umls database. Here is what I have done : 1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my database along with username and password. Now I believe I also need to modify LookupDesc_DB.xml with some umls tablename which can get cui, tui and text info. I need some help , which table should I be pointing to lookup ? Also after is there any other step or I should be good in executing clinical pipeline with umls database. Also please point some steps guide/document of available for cTakes integration with UMLS. Thanks &Regards Stuti Awasthi ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------
