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

Tania Tudorache tudorache at stanford.edu
Fri Mar 19 10:32:47 PDT 2010


OK, thank you for the suggestion. I will talk to Misha. Natasha 
suggested that I should use the Autocomplete widget from BP, and that 
will give a partial solution. So, I will look into that.

Tania

On 03/19/2010 10:01 AM, Trish Whetzel wrote:
> 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
>>
>> To unsubscribe from this group, send email to icat-users+unsubscribegooglegroups.com or reply to this email with the words "REMOVE ME" as the subject.
>>      
>

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