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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 16:24:00 GMT
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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