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From Jeffrey Miller <jeff...@gmail.com>
Subject Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge
Date Sat, 15 Jun 2019 20:22:54 GMT
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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