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[bioontology-support] [icat-users] Re: SNOMED CT concept search and representation problems

Trish Whetzel whetzel at stanford.edu
Fri Mar 19 10:01:45 PDT 2010


The search web service supports search from partial words, difference  
in parameter between contains and exact match. However if the search  
string contains two partial words "cand vul" that does not work.

Misha, is this something that Lucene can accommodate, returning  
results from input of "cand vul"?  Also, there seems to be a problemin  
that using the input term "candidias of vul" does not return results  
even though only the last term is not complete. A search using  
"candidias of" will return "Candidiasis of vulva" as one of the results.

Perhaps it would be worthwhile to talk in person with Misha about how  
the Lucene index is set-up?

Trish


On Mar 19, 2010, at 8:43 AM, Tania Tudorache wrote:

> I don't know if BioPortal plans to support partial word queries, or  
> if you have suggestions how we can simulate them... Please see below  
> what WHO needs.
>
> Unfortunately, Alan Rector has already concluded that we cannot use  
> BioPortal for the Snomed search because of this missing feature,  
> which is not good for any of the teams..
>
> Thanks!
> Tania
>
>
>
> -------- Original Message --------
> Subject:	[icat-users] Re: SNOMED CT concept search and  
> representation problems
> Date:	Fri, 19 Mar 2010 03:25:22 -0700 (PDT)
> From:	Robert Chalmers <r.chalmers at man.ac.uk>
> Reply-To:	icat-users at googlegroups.com
> To:	iCat Users Group <icat-users at googlegroups.com>
>
> Dear Tania
>
> Thank you for this.   I should just like to emphasize a suggestion
> made in my comments above.  Most of the SNOMED lookups I was
> discussing were in the SNOMED references tab.
>
> As I previously wrote:
>
> CliniClue very rapidly finds terms by allowing partial word searches
> in any order.   Thus the search string "ep bu ac" rapidly identifies
> the correct term by interpreting the query as "string [includes word
> "ep*"]
> AND [includes word "bu*"] AND [includes word "ac*"].  I wonder how
> easy it would
> be to incorporate that into the iCAT SNOMED CT search. Otherwise I
> think a lot of cross-mappings will be missed.
>
> Alternatively one will have to wade through hundreds of irrelevant
> terms.
>
> I should like to give another example of where my suggestion would
> have been helpful.
>
> B37.3 Candidiasis of vulva and vagina
>
> Searching for "Candidiasis of vulva and vagina" brings up a blank
> Searching for "Candidiasis" brings up 64 results including
> "Candidiasis of Vulva" and "Candidiasis of Vagina"
>
> IN CliniClue a search string "cand vul" and "cand vag" would have
> immediately identified the two relevant entries.
>
> I think it would be immensely helpful to have this implemented in
> iCAT.
>
> One other small point here relates to the display of tabs in the
> content area. If you open iCAT in a normal (not maximised) window then
> drag the right edge of the window to enlarge the window, the tab box
> does not enlarge with it.  There is up to 8 cm of blank screen between
> the tabs and the right arrow.   I imagine that there is a property
> that could be changed easily to rectify this.   I unfortunately can't
> do a screen dump here to illustrate this.
>
> Best wishes
>
> Robert
>
>
>
>
> On Mar 18, 2:49 am, Tania Tudorache <tudora... at stanford.edu> wrote:
> > Search on synonyms should work now.
> >
> > Tania
> >
> > On 03/16/2010 09:16 PM, Tania Tudorache wrote:
> >
> >
> >
> > > Hi Robert,
> >
> > > Thank you for the comments on the search functionality. It seems  
> that
> > > the search on synonyms does not work in the specific values sets  
> (e.g.
> > > SNOMED Anatomy that is linked from Body Part), and it should. We  
> are
> > > working with the BioPortal people to see why it doesn't.
> >
> > > The search is already made in the preferred term, and that seems  
> to work.
> >
> > > We could have the search by SNOMED ID working. Several fields in  
> iCAT
> > > are linked to specific value sets in SNOMED (e.g. body part ->  
> Snomed
> > > Anatomy branch, Investigations -> Snomed Test Findings, etc.). So,
> > > when you search for a body part, the search is restricted to a
> > > specific value set in Snomed. It seems that there is a problem  
> with
> > > searching by Snomed ID and synonym in the specific values sets.
> >
> > > There are some fields for which the search is not restricted, e.g.
> > > Severity. If you use the "Find term" link from Severity, it will
> > > search in the entire Snomed, and in that field, the search by id  
> and
> > > synonym work fine.
> >
> > > So a very quick work around until we figure out the search in  
> value
> > > sets problem, is to remove the search in value sets for body part,
> > > investigations, etc. and instead search in the entire Snomed.
> >
> > > Tania
> >
> > > On 03/13/2010 03:08 AM, Robert Chalmers wrote:
> > >> I have been doing some cross-mapping to SNOMED CT (mainly in  
> section
> > >> LB of Chapter 12).  I realise that it is very easy to miss  
> SNOMED CT
> > >> concepts in the way that the search is set up and have had to  
> resort
> > >> to searching in CliniClue.
> >
> > >> Take the example of epidermolysis bullosa acquisita (LB44) or  
> EBA.
> > >> This is present "as is" in SNOMED CT as a synonym to "acquired
> > >> epidermolysis bullosa" of which it is essentially a lexical  
> variant.
> > >> A search of "epidermolysis bullosa acquisita"  does produce a  
> range of
> > >> entries in SNOMED CT, all of which are children of EBA, but  
> does not
> > >> find not the parent term.
> >
> > >> Drug-induced epidermolysis bullosa acquisita
> > >> Epidermolysis bullosa acquisita, Brunsting-Perry type
> > >> Epidermolysis bullosa acquisita, bullous pemphigoid-like
> > >> Epidermolysis bullosa acquisita, cicatricial pemphigoid-like
> > >> Epidermolysis bullosa acquisita, classical acral type
> > >> Epidermolysis bullosa acquisita, oral mucosal involvement
> >
> > >> In order to find EBA you need to know that SNOMED CT's preferred
> > >> descriptor is "acquired epidermolysis bullosa"
> >
> > >> If I had just put in "epidermolysis" then I would have found the
> > >> correct term amongst 47 others.   With other elements which are  
> more
> > >> commonly used, such as "erythema" or "dermatitis", I should  
> have had
> > >> to wade through 246 and 328 terms respectively to see if the  
> specific
> > >> term I was looking for was present.
> >
> > >> CliniClue very rapidly finds terms by allowing partial word  
> searches
> > >> in any order.   Thus the search string "ep bu ac" rapidly  
> identifies
> > >> the correct term by interpreting the query as "string [includes  
> "ep*"]
> > >> AND [includes"bu*"] AND [includes "ac*"].  I wonder how easy it  
> would
> > >> be to incorporate that into the iCAT SNOMED CT search.  
> Otherwise I
> > >> think a lot of cross-mappings will be missed.
> >
> > >> The same will obviously apply to all other elements of the  
> content
> > >> model where SNOMED CT is it will be even more important to  
> ensure that
> > >> the most appropriate term is found.  In these cases it is not  
> just a
> > >> matter of finding the same disease descriptor as is being used  
> for
> > >> ICD.   The editor will not be likely to know exactly how the  
> concept
> > >> he or she is looking for is represented in SNOMED CT.  Thus  
> under Body
> > >> Part a search for "toe web" would bring a blank but "toe" alone  
> would
> > >> bring up 563 entries from SNOMED ANATOMY including "toe of hoof".
> > >> "Toe web" is in SNOMED CT as a synonym to "structure of  
> interdigital
> > >> space of foot", a further synonym of which is "web space of  
> toe".  Had
> > >> I searched for "web", I should have found 32 concepts but again  
> not
> > >> the one I was looking for.   The CliniClue search of "toe web"  
> would
> > >> have identified both "toe web" and "web space of toe".   I  
> would then
> > >> have decided that the latter was a preferable descriptor and  
> opted for
> > >> that.
> >
> > >> I think that my experience so far brings up a number of issues.
> >
> > >> 1.  A search of SNOMED CT synonyms as well as preferred terms is
> > >> essential.
> > >> 2.  Ideally a search query should replicate that provided in  
> CliniClue
> > >> 3.  Should iCAT permit synonym descriptors to be displayed  
> (e.g. "web
> > >> space of toe") rather automatically select the SNOMED CT  
> preferred
> > >> term (in this instance "structure of interdigital space of  
> foot")?
> > >> For clarity I think it should be possible to override use of the
> > >> preferred descriptor if necessary.
> > >> 4.  If none of these is going to be possible then should it be
> > >> possible to search by SNOMED CT Concept ID or Description ID  
> copied
> > >> and pasted from CliniClue or other SNOMED browser.  (It would  
> perhaps
> > >> be possible for an integer to be recognised in the search box as
> > >> either a concept ID or a description ID rather than be treated  
> as a
> > >> text string).
> > >> 5.  As 80% of concepts from our principal source terminology are
> > >> already cross-mapped to SNOMED CT and as the majority of concepts
> > >> which will be entered into the ICD-11 foundation layer will  
> also be
> > >> represented in that source terminology, it would be very useful  
> to
> > >> have feature 4 available.
> >
> > >> Thanks to all who have persevered and read to the end of this  
> message.
> >
> > >> Robert
>
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