Good information to know. Thanks Kean. Peter
On Mon, Feb 15, 2021 at 4:47 PM Kean Kaufmann <k...@recordsone.com> wrote: > Yes, but that way you can't get the SNOMED code if you need it - the code >> becomes a custom vocabulary item. > > > Not if you hang it off an existing UMLS CUI and integrate the > BsvRareWordDictionary and the UmlsJdbcRareWordDictionary using > <dictionaryConceptPairs> . Don't recall exactly where this is in the Fast > Dictionary Lookup > <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Fast+Dictionary+Lookup> > docs/examples, > but it's there somewhere... > > [image: image.png] > > I do use the BSV for concepts that are not in the script file at all. > > > I use BSV files for adding both synonyms and concepts. The concept BSV > has its own <conceptFactory>; the synonym BSV doesn't. > > > On Mon, Feb 15, 2021 at 10:21 AM Peter Abramowitsch < > pabramowit...@gmail.com> wrote: > >> HI Kean >> >> Yes, but that way you can't get the SNOMED code if you need it - the code >> becomes a custom vocabulary item. Adding a synonym gets you the real >> linkage. I do use the BSV for concepts that are not in the script file at >> all. >> >> I don't "edit" the HSQL file per se. I have a parallel SED script which >> does the editing (add, change, delete) of many items. I maintain the sed >> script and use it to massage the dictionary I created using the creator. >> >> Peter >> >> >> >> On Mon, Feb 15, 2021 at 4:16 PM Kean Kaufmann <k...@recordsone.com> >> wrote: >> >> > FWIW, rather than editing the HSQLDB script, we use Sean's >> > BsvRareWordDictionary to add phrases with a BSV file: >> > >> > cTakesHsql.xml: >> > >> > <lookupSpecification> >> > <dictionaries> >> > <!-- phrases not in dictionary --> >> > <dictionary> >> > <name>AddPhrases</name> >> > >> > >> > >> <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary</implementationName> >> > <properties> >> > <property key="bsvPath" >> > >> > >> value="org/apache/ctakes/dictionary/lookup/fast/custom2020ab/AddPhrases.bsv"/> >> > </properties> >> > </dictionary> >> > >> > AddPhrases.bsv: >> > >> > C1276061|nstemi >> > C1276061|non st elevation mi >> > C1276061|non-st elevation mi >> > C1536222|non-stemi >> > C1276061|non st elevation myocardial infarction >> > C1276061|non st elevated myocardial infarction >> > C1276061|non-st elevated myocardial infarction >> > C1276061|non st elevated mi >> > C1276061|non-st elevated mi >> > >> > On Mon, Feb 15, 2021 at 10:09 AM Peter Abramowitsch < >> > pabramowit...@gmail.com> >> > wrote: >> > >> > > Hi Eugenia >> > > There may be better ways to do this, but I would insert these as >> Synonyms >> > > in the CUI_TERMS table. The concept is already there: >> > > >> > > insert this: >> > > INSERT INTO CUI_TERMS VALUES(1303258,0,1,'stemi','stemi') >> > > >> > > the concept is already declared here >> > > INSERT INTO PREFTERM VALUES(1303258,'Acute ST segment elevation >> > myocardial >> > > infarction (disorder)') >> > > >> > > >> > > >> > > >> > > >> > > >> > > On Mon, Feb 15, 2021 at 3:46 PM Monogyiou, Eugenia < >> > > eugenia.monogy...@nttdata.com> wrote: >> > > >> > > > Hello, >> > > > >> > > > Peter we had a discussion quite some time ago about additions and >> > > removals >> > > > that would result into a good dictionary. I have a specific example >> I >> > > would >> > > > ask for your help please (or anyone else that has an idea :) ) >> > > > >> > > > So STEMI and NSTEMI are correctly annotated but "Code" and "Coding >> > > Scheme" >> > > > are null... when that happens in my tests it is usually because of a >> > > badly >> > > > formed term interpretation which is to be discarded anyway. I have >> > found >> > > > similar cases mentioned as "ghost" terms in the UMLS documentation; >> in >> > > this >> > > > case, however, they are valid interpretations and quite important >> to my >> > > > tests because I am working on heart attack and cardiac disease >> cohorts. >> > > > >> > > > I tried associating with the appropriate code by adding the >> following >> > > > inserts but it did not work ... >> > > > >> > > > INSERT INTO UPPER VALUES(1276061,'','NSTEMI','',31,1) >> > > > INSERT INTO UPPER VALUES(1303258,'','STEMI','',31,1) >> > > > >> > > > Any ideas please? >> > > > >> > > > Many thanks in advance, >> > > > >> > > > Kind Regards, >> > > > >> > > > Eugenia Monogyiou | NTT Data UK >> > > > Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG >> > > > >> > > > Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com<mailto: >> > > > eugenia.monogy...@nttdata.com> >> > > > >> > > > Disclaimer: This email and any attachments are sent in strictest >> > > > confidence for the sole use of the addressee and may contain legally >> > > > privileged, confidential, and proprietary data. If you are not the >> > > intended >> > > > recipient, please advise the sender by replying promptly to this >> email >> > > and >> > > > then delete and destroy this email and any attachments without any >> > > further >> > > > use, copying or forwarding. >> > > > >> > > >> > >> >
