Hi Matthew, The dictionary creator uses a 'full' umls installation to create the custom dictionary. After that any installations of ctakes that contain your custom dictionary do not need the umls data.
Sean -----Original Message----- From: Matthew Vita [mailto:[email protected]] Sent: Sunday, August 27, 2017 9:20 PM To: [email protected] Subject: Re: ICD10 Dictionary Issue [EXTERNAL] Sean, Nice to meet you. Thank you for your high-quality work on cTAKES. I will create the dictionary with the latest ICD10 data and contribute back my documentation + artifacts. My only question is with step 3: *"Select a UMLS installation directory. This is the directory containing the META/ subdirectory (which contains RRF files). After selecting the UMLS installation directory, the available vocabularies are gathered."* - basically, I have been providing my UMLS user/pass to the cTAKES Docker solution and letting it take care of the rest. I suppose I'm going to have to download and configure a custom UMLS dataset installation. This is correct? Thanks, Matthew Vita www.matthewvita.com On Sun, Aug 27, 2017 at 9:05 PM Finan, Sean < [email protected]> wrote: > Hi Matthew, > > One of the updates that happened with ctakes 4.0 was the long-awaited > update to use the current version of hypersql (hsqldb) used by > components such as the dictionary lookup modules. That update made > all of the older dictionary databases obsolete as their format does > not match that used by the current hsqldb. > > Your best option is probably to create an updated '17 icd dictionary > of your own. Have a look at the wiki introduction to the dictionary > creator > gui: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_ > confluence_display_CTAKES_Dictionary-2BCreator-2BGUI&d=DwIFaQ&c=qS4goW > BT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=rn9A67xy_cGUI60xNsFsR3RpAKFa3Sqcq7CFhFkHdaQ&s=QnFljs_2 > PkWy6ow43XdWzMHG9KW_4czYGAwy3gR3Oh0&e= > > Sean > > -----Original Message----- > From: Matthew Vita [mailto:[email protected]] > Sent: Sunday, August 27, 2017 3:29 PM > To: [email protected] > Subject: ICD10 Dictionary Issue [EXTERNAL] > > Hi cTAKES Maintainers, > > My name is Matthew Vita, a healthcare software developer and one of > the OpenEMR project administrators (this is a popular open source EHR > mainly used outside of the US). > > I am interested in integrating cTAKES with the EMR using Docker and a > friendly web frontend. Fortunately, Dr. Timothy Miller has provided an > excellent Docker pipeline solution that I have been using and enhancing. > However, I'm having an issue with ICD10 dictionary support. > Introducing > ctakesicd2015 simply has no effect. > > When observing the SNOMED/RXNORM dictionary, the structure is as follows: > > - sno_rx_16ab.xml > - sno_rx_16ab > - sno_rx_16ab.properties > - sno_rx_16ab.script > > However, when one pulls down the > > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p > _ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2Drw > ord-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictionary_ > lookup_fast_ctakesicd2015&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bmYyxtv1U77 > r3grgB76TXATo01ayCe_Gu1kOvL5VvD8&s=XWhnGpcbuQvkPzwgSYg9uuRlzBBm_K_GwEp > rLsJ0QJk&e= > , the structure is: > > - ctakesicd2015.script > - ctakesicd2015.properties > > cTAKES does not pick up these files. I wonder if it's because the > ctakesicd2015.xml manifest is missing. Can anyone point me to a proper > download of this file? > > I very much appreciate the hard work behind this project and look > forward to hearing back. > > Thanks, > > Matthew Vita > www.matthewvita.com >
