Hi Matthew, That is great! I am trying to be on vacation but can't wait to check out the video!
Sean ________________________________________ From: Matthew Vita <[email protected]> Sent: Friday, September 1, 2017 11:24 PM To: [email protected] Subject: Re: ICD10 Dictionary Issue [EXTERNAL] Sean, I am pleased to inform you that I created a YouTube video for creating ICD10 dictionaries for cTAKES: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yytpXZalgLQI4oY7ELBurCxIbP-GKkjS3AeHNoehsxQ&s=eCy04Y5cdHQPEPFN4J2CTVmZXIVpk06JYPvd9czyh7o&e= . Thank you again for the tips! I haven't actually hooked up my cTAKES to use it ( https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tmills_ctakes-2Ddocker_blob_master_ctakes-2Das-2Dpipeline_Dockerfile&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yytpXZalgLQI4oY7ELBurCxIbP-GKkjS3AeHNoehsxQ&s=j1_OFYmNeIpUdo0jZkbUEjBMd6vEKYQ5nnUEnaGqYrU&e= is what I will be using to pull it in), but I'm pretty sure I am on the right track! Please let me know if I've missed anything. Thanks, Matthew Vita www.matthewvita.com On Mon, Aug 28, 2017 at 8:48 AM Finan, Sean < [email protected]> wrote: > 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 > > >
