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From Harish Kulkarni <harish.m.kulka...@gmail.com>
Subject Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge
Date Sat, 15 Jun 2019 21:16:48 GMT
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On Sat, Jun 15, 2019 at 1:40 PM Remy Sanouillet <remys@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 <jeffmax@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 <remys@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 <gandhirajan.n@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 <jeffmax@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 <
> > remys@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 <
> jeffmax@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
> > > > !!!"
> > > >
> > >
> >
>

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