Hi Jeff
You are absolutely right: when I use sno_rx with the term WBC in a simple
context it is not showing up as a T059. I was surprised about that
I was wrong about the term I was looking at. Here's the scenario that did
change
Text context
afebrile, but has elevated WBC count;
*Using sno_rx*
canonical text: White blood cell count increased (lab result)
CUI: C0750426,
location: Leukocytes,
location_snomed: 52501007
range_text: elevated WBC count,
vocab_term: 414478003,
vocab_type: SNOMEDCT_US
...other params.
*Using new dict based on 2020AA*
Missing:
Reason:
*grep elevated newdict_750426*
INSERT INTO CUI_TERMS VALUES(750426,0,4,'elevated white blood
count','elevated')
INSERT INTO CUI_TERMS VALUES(750426,0,5,'elevated white blood cell
count','elevated')
*grep elevated olddict_750426*
INSERT INTO CUI_TERMS VALUES(750426,0,4,'elevated white blood
count','elevated')
INSERT INTO CUI_TERMS VALUES(750426,1,3,'elevated wbc count','wbc')
<---------------------- missing
INSERT INTO CUI_TERMS VALUES(750426,0,5,'elevated white blood cell
count','elevated')
So back to your recommendation on using MMSYS
You chose the ACTIVE_SUBSETS option - right?
And on the Sources to Exclude/Include page, do you deselect all sources to
exclude?
Have you tweaked the precedence of subsets or do you leave the default
order alone?
Many thanks,
Peter
On Thu, Aug 6, 2020 at 8:11 AM Jeffrey Miller <jeff...@gmail.com> wrote:
> Peter,
>
> I have experienced similar issues with how text spans translate to
> different CUIs depending on the included vocabularies as well. I had a
> similar conversation with Sean on the dev forum last year I believe.
>
> I do not believe the behavior of 'wbc' has changed- if I run the clinical
> pipeline with sno_rx_16ab dictionary, it is tagged as an
> AnatomicalSiteMention. Are you seeing something different?
>
> Jeff
>
> On Wed, Aug 5, 2020 at 11:24 PM Peter Abramowitsch <
> pabramowit...@gmail.com>
> wrote:
>
> > Hi Jeff
> >
> > I thought I did load them all, but I'll go back and check.
> >
> > When looking at my gene issue the result is that the lookup arbitrarily
> > (seemingly anyway) flips between one and another when there are overlaps
> > between vocabularies. Ie. I see that both Vocab A & B both contain
> geneX
> > and geneY. Neither of these are in SNOMED. So in my output, I get one
> of
> > the genes associated with Vocab A and another with Vocab B. When I
> remove
> > Vocab B then obviously both are associated with Vocab A - which is what I
> > wanted.
> >
> > If, for you, WBC is showing up as an anatomical location, rather than a
> > T059 then probably it's not getting the correct SNOMED code though.
> > Wouldn't that be a problem for your researchers?
> >
> > Peter
> >
> > On Wed, Aug 5, 2020 at 5:37 PM Jeffrey Miller <jeff...@gmail.com> wrote:
> >
> > > Hi Peter,
> > >
> > > If I create a dictionary using UMLS 2020aa with just snomed and rxnorm
> my
> > > cTAKES dictionary still seems to have a CUI associated with the string
> > > 'wbc' that links to the snomed term for Leukocyte (Cell). It is not
> > mapping
> > > to a lab result TUI, but rather an anatomical site, but it seems to be
> > the
> > > same CUI that 'wbc' resolves to in sno_rx_16ab. Maybe HGNC is
> conflicting
> > > with that too?
> > >
> > > Just to double check, when you installed UMLS through Metamorphosys,
> did
> > > you install all of the available vocabularies?
> > >
> > > Jeff
> > >
> > > On Wed, Aug 5, 2020 at 6:52 PM Peter Abramowitsch <
> > pabramowit...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Hi All
> > > >
> > > > I've been setting up a custom dictionary using UMLS with the goal of
> > > simply
> > > > adding a comprehensive genetic vocabulary HGNC to the latest UMLS
> > SNOMED
> > > > and RXNORM vocabularies in the hope of getting somewhere close to the
> > > > cTakes default dictionary again.
> > > >
> > > > However, there are changes to concept vocabularies in UMLS2020AA that
> > > > affect the ability of cTakes to work well with older notes and
> possibly
> > > the
> > > > note-writing practices of older physicians and labs. Some of the
> > tried
> > > > and true acronyms such as WBC for leukocytes, RBC, and EOS
> (eosinophil
> > > > count) are no longer part of SNOMED. Probably this is because the
> > > > components of these parameters are now broken out into more granular
> > > > types. The other reason this may be is that a few of these acronyms
> > now
> > > > overlap the names of Genes. EOS is one of them. This is just
> > > speculation.
> > > >
> > > > In order to have these common parameters re-included via their common
> > lab
> > > > acronyms, it is necessary to add another common US vocabulary such as
> > > > HL7-V3.0 or NCI_CDISC. Of course one can remap back into SNOMED by
> > > adding
> > > > insert statements into the dictionary script, but it might be a
> > > > non-scalable exercise.
> > > >
> > > > So my point here is that if, one day, we plan to create a new cTakes
> > > > release, and with it, a new UMLS lookup, we may need to consider
> > adding a
> > > > third basic vocabulary into our current set of two.
> > > >
> > > > Thoughts?
> > > > Peter
> > > >
> > >
> >
>
