Thanks, Timothy. I fixed the permissions issue and was able to progress further. I am now stuck at the very last step (it would seem), the Dictionary Creator GUI page says this: --- Once a new dictionary has been built, point to it in one of 2 ways: Set the fast dictionary parameter LookupXml to org/apache/ctakes/dictionary/lookup/fast/DictionaryName.xml ---
Where is this LookupXml parameter to be found/added? On Wed, Aug 22, 2018 at 4:50 PM, Miller, Timothy < [email protected]> wrote: > Looks like maybe you don't have permissions to write to that directory > (/usr/local/). Can you write it somewhere else? > > > ------------------------------ > *From:* Ory Henn <[email protected]> > *Sent:* Wednesday, August 22, 2018 9:15 AM > *To:* [email protected] > *Subject:* Re: How do I add a dictionary (like NCI) to cTakes lookup? > [EXTERNAL] > > Thanks a lot Ghandi, Michael, for quick and helpful replies. > The video especially was very useful, but I'm encountering an error at the > last part (building the actual dictionary). > It looks like it has a problem with an HsqlDB table (log output below). > Can anyone help with this? Do I need to install HsqlDB, or does it come as > part of UMLS/Metamorphosys? > Thanks, > Ory > > > 22 Aug 2018 16:06:40 INFO MrConsoParser - File Lines: 14089874 Concepts: > 450236 Texts: 1380174 > 22 Aug 2018 16:06:40 INFO DictionaryBuilder - Performing Poor man's WSD > ... > 22 Aug 2018 16:06:42 INFO DictionaryBuilder - Concepts: 446510 Texts: > 1162474 > 22 Aug 2018 16:06:42 INFO DictionaryBuilder - Done Parsing Concepts > 22 Aug 2018 16:06:42 INFO JdbcUtil - Connecting to > jdbc:hsqldb:file:/usr/local/apache-ctakes-4.0.0/resources/ > org/apache/ctakes/dictionary/lookup/fast/umls_test_nci/umls_test_nci as SA > 22 Aug 2018 16:06:42 INFO ENGINE - Checkpoint start > 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose start > 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose synched > 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose script done > 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose end > 22 Aug 2018 16:06:42 INFO ENGINE - Checkpoint end - txts: 1 > 22 Aug 2018 16:06:43 ERROR RareWordDbWriter - user lacks privilege or > object not found: NCI_NCI in statement [insert into nci_nci_hl7 > (CUI,NCI_NCI-HL7) values (?,?)] > 22 Aug 2018 16:06:43 ERROR MainPanel - Dictionary umls_test_nci could not > be built in /usr/local/apache-ctakes-4.0.0 > > > On Mon, Aug 20, 2018 at 10:13 PM, Michael Trepanier <[email protected]> > wrote: > >> Ory, >> >> In response to Gandhi's comments, the video below outlines custom >> dictionary creation in detail: >> >> https://www.youtube.com/watch?v=4aOnafv-NQs >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=A8Md_8ifzCAHha2tRJ_d-kGLk26gNMdOgfpXd3_qKHI&e=> >> >> Best, >> >> Mike >> >> >> >> On Mon, Aug 20, 2018 at 2:09 AM, Gandhi Rajan Natarajan < >> [email protected]> wrote: >> >>> Hi Ory, >>> >>> I guess RxNORM and SNOMED_CT dictionaries are loaded by default. If you >>> want to lookup from other dictionaries like MEDDRA etc. , you may have to >>> create your custom dictionary using cTAKES dictionary generator GUI. That’s >>> what I did to include MEDDRA dictionary terms. >>> >>> -----Original Message----- >>> From: Ory Henn <[email protected]> >>> Sent: Monday, August 20, 2018 1:52 PM >>> To: [email protected] >>> Cc: Guy Gildor <[email protected]> >>> Subject: How do I add a dictionary (like NCI) to cTakes lookup? >>> >>> Hello, >>> New user here (-; >>> I've downloaded and installed cTakes (+UMLS + all resources), and am >>> trying to parse a single document. >>> I see that cTakes (CVD/CPE) identifies CUIs only from RxNORM and >>> SNOMED_CT. >>> >>> 1. What is the way to make cTakes look in more UMLS dictionaries? I >>> specifically need NCI as well. >>> 2. Is there an easy way to make cTakes look in all UMLS dictionaries? >>> Thanks, >>> Ory >>> >>> -- >>> >>> <https://trialmatch.me >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__trialmatch.me&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=lQh_YM3Iht4AIa0E39KpnFIY7XbD4TaYkEkMESEQoEA&e=> >>> >www.trialjectory.com >>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.trialjectory.com&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=ooC-oaVMc9CCPBbbTUyU23H7BlBi1TB3foqR0TCnHr8&e=> >>> <https://trialjectory.com >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__trialjectory.com&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=GUqLl8XdNiDmvZStF8lT2GP9uRvxuncPAyxBrSk-uvU&e=> >>> > >>> This email and any files transmitted with it are confidential and >>> intended solely for the use of the individual or entity to whom they are >>> addressed. If you are not the named addressee you should not disseminate, >>> distribute or copy this e-mail. Please notify the sender or system manager >>> by email immediately if you have received this e-mail by mistake and delete >>> this e-mail from your system. If you are not the intended recipient you are >>> notified that disclosing, copying, distributing or taking any action in >>> reliance on the contents of this information is strictly prohibited and >>> against the law. >>> >> >> >> >> -- >> [image: MetiStream Logo - 500] >> Mike Trepanier| Big Data Engineer | MetiStream, Inc. | >> [email protected] | 845 - 270 - 3129 (m) | www.metistream.com >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.metistream.com_&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=_-eXxPXJ9Ltpd4KTdRwj-pDyQ42Xbpt0_9ydetCzIR0&e=> >> > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__trialmatch.me&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=lQh_YM3Iht4AIa0E39KpnFIY7XbD4TaYkEkMESEQoEA&e=> > www.trialjectory.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__trialjectory.com&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=GUqLl8XdNiDmvZStF8lT2GP9uRvxuncPAyxBrSk-uvU&e=> > -- <https://trialmatch.me>www.trialjectory.com <https://trialjectory.com>
