unsubscribe On Sat, Jun 15, 2019 at 1:40 PM Remy Sanouillet <re...@foreseemed.com> wrote:
> Yes, I agree it would be nice because the tokenization that occurs when > creating the dictionaries from the releases make comparisons a bit tricky > and is not 100% reversible. I would love to hear an answer to your > quandary. > > Remy > > On Sat, Jun 15, 2019 at 1:23 PM Jeffrey Miller <jeff...@gmail.com> wrote: > > > Thanks, I was curious if the cTAKES devs that created the sno_rx_16ab > > dictionary had put the differences applied to the default UMLS output > into > > version control in some form. I imagine the > > additions/synonyms/abbreviations that were added manually must have been > > collected over time somewhere prior to merging them with 2016ab UMLS > > release? I basically want to recreate the default cTAKES 4.0.0 release > with > > an additional ontology and the latest terms. I can likely come up with a > > diff myself but was wondering if this was already maintained as part of > > cTAKES. > > > > On Sat, Jun 15, 2019 at 12:24 PM Remy Sanouillet <re...@foreseemed.com> > > wrote: > > > > > Yes, that's pretty much what we do too. Not only to enhance the > > dictionary, > > > but to put in corrections because, lo and behold, there are some errors > > in > > > there!. As you know, an ontology is a constant curation job and that > > > script, under SCM, allows you to isolate those changes and, if > necessary, > > > re-apply them to new versions. > > > > > > Remy > > > > > > On Sat, Jun 15, 2019 at 8:36 AM gandhi rajan <gandhiraja...@gmail.com> > > > wrote: > > > > > > > Hi Jeff, > > > > > > > > As far as I know, maintaining a separate SQL script to add additional > > > > entries should work seamlessly. > > > > > > > > On Saturday, June 15, 2019, Jeffrey Miller <jeff...@gmail.com> > wrote: > > > > > > > > > Thanks Remy. Does anyone know if these manually curated > > > > > modifications/synonyms are tracked anywhere (aside from the > > dictionary > > > > > itself) so they can be carried forward in future dictionary > updates? > > > > > > > > > > On Fri, Jun 14, 2019 at 4:28 PM Remy Sanouillet < > > re...@foreseemed.com> > > > > > wrote: > > > > > > > > > > > From my experience, it seems pretty obvious that sno_rx_16ab is a > > > > curated > > > > > > dictionary based on the SNOMED 2016AB release. It does not > contain > > > the > > > > > full > > > > > > set but it has additional edits and synonyms that are pretty > useful > > > > > > (including 'dm'). > > > > > > > > > > > > We have had to manage those mods as an adjunct. > > > > > > > > > > > > Remy > > > > > > > > > > > > On Fri, Jun 14, 2019 at 1:03 PM Jeffrey Miller < > jeff...@gmail.com> > > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > I have created a custom dictionary from the latest UMLS release > > > with > > > > > > > SNOMEDCT_US and RxNorm and I've noticed it seems to be > > generating > > > > > > .script > > > > > > > file with unexpected differences as compared to the sno_rx_16ab > > > file > > > > > > > available as part of the cTAKES release. Specifically, for > > > diabetes, > > > > it > > > > > > is > > > > > > > missing these two rows: > > > > > > > INSERT INTO CUI_TERMS VALUES(11849,0,1,'dm','dm') > > > > > > > INSERT INTO CUI_TERMS VALUES(11849,0,1,'diabetes','diabetes') > > > > > > > > > > > > > > and only has this one: > > > > > > > INSERT INTO CUI_TERMS VALUES(11849,1,2,'diabetes > > > > mellitus','mellitus') > > > > > > > > > > > > > > The end result is that "diabetes" is not being picked up in the > > > test > > > > > > text I > > > > > > > am running through- it requires the full 'diabetes mellitus'. > > > > > > > > > > > > > > Is there any setting on the UMLS install side or the ctTAKES > > > > dictionary > > > > > > > creator that could account for missing alternative forms like > > this? > > > > > I've > > > > > > > tried downloading the 2016AB release (which I think is the one > > used > > > > to > > > > > > > create the bundled sno_rx_16ab package?) and I am not getting > the > > > > > > alternate > > > > > > > forms in that dictionary either. > > > > > > > > > > > > > > Thanks, > > > > > > > Jeff > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Regards, > > > > Gandhi > > > > > > > > "The best way to find urself is to lose urself in the service of > others > > > > !!!" > > > > > > > > > >
