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From Remy Sanouillet <re...@foreseemed.com>
Subject Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge
Date Sat, 15 Jun 2019 20:39:41 GMT
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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