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[bioontology-support] SNOMED Ontology

Robert Hausam rrhausam at gmail.com
Fri Jun 6 19:01:11 PDT 2014


The SNOMED CT attribute relationship is "Has active ingredient" (or
represented in BioPortal as has_active_ingredient) - which presumably is
what you found.

As far as obtaining the CUIs goes, though, they are from UMLS and I believe
are probably only available if you actually obtain SNOMED CT from the UMLS
distribution itself (or from BioPortal, which obviously also contains
them).  I'm not aware of any available subsets (RF1) or refsets (RF2) that
provide the CUI mappings (but I possibly could have missed something, as I
haven't been looking for it).  The CUIs certainly could be added to the OWL
representation, possibly by importing them as a separate ontology derived
from one of those sources, but the CUIs won't be available directly from
the SNOMED CT RF2 distribution and its associated Perl script - as you have
discovered.  So, if you really need them, you'll have to obtain them
separately.  But, on the other hand, if the CUI references aren't critical
to your desired application(s), then you don't need to be concerned that
they are "missing."

Rob


On Fri, Jun 6, 2014 at 7:36 PM, ROBERT FRANKLIN LARIO <Robert.Lario at utah.edu
> wrote:

>  Hi Robert,
>
>  I figured out active_ingredient. Still not sure how CUI is ties in.
>
> Robert
>
> On Jun 6, 2014, at 6:26 PM, "ROBERT FRANKLIN LARIO" <Robert.Lario at utah.edu>
> wrote:
>
>   Thanks Robert.
>
>  I have downloaded SNOMED CT and run the PERL scripted as you suggested.
>  The resulting owl file does not appear to be as rich as what is available
> via http://bioportal.bioontology.org/ontologies/SNOMEDCT. For example, I
> can locate the concept active_ingredient_of or CUI.
>
>  Is there an addition set of transformations I need to run?
>
>  Thanks for your help.
>
>  Robert
>
>
>
> On Jun 5, 2014, at 4:26 PM, "Robert Hausam" <rrhausam at gmail.com> wrote:
>
>   There is a PERL script that is distributed with the SNOMED CT
> International and US (and likely other) editions which will transform the
> SNOMED CT Release Format 2 (RF2) distribution files into an OWL
> representation.  The transform is included in the SNOMED CT distributions
> from the NLM for use in the US.  I use it frequently, and I think it's
> likely the best way to get what you're looking for.
>
>  Rob
>
> On Thu, Jun 5, 2014 at 2:59 PM, Ray Fergerson <ray.fergerson at stanford.edu>
> wrote:
>
>>  SNOMED has a more restrictive license than most of the ontologies in
>> BioPortal and we cannot make it available for download. We are only
>> licensed to provide a browser. You should try the contact information on
>> the BioPortal SNOMED summary page to get a copy. I know that some effort
>> has gone into making SNOMED available in OWL but I am not sure if this is
>> even publically available yet.
>>
>>
>>
>> Ray
>>
>>
>>
>> *From:* bioontology-support [mailto:
>> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *ROBERT
>> FRANKLIN LARIO
>> *Sent:* Thursday, June 5, 2014 12:43 PM
>> *To:* support at bioontology.org
>> *Subject:* [bioontology-support] SNOMED Ontology
>>
>>
>>
>> Is it possible to download the Systematized Nomenclature of Medicine -
>> Clinical Terms ontology found here :
>> http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes ?  I
>> would like to work with the ontology locally.
>>
>>
>>
>> I would like to get the information in OWL format if possible.
>>
>>
>>
>> Thanks for your help.
>>
>>
>>
>> Robert
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>
>
> --
>  Robert Hausam, M.D.
> Hausam Consulting
> +1 (801) 949-1556
> rrhausam at gmail.com
>
>


-- 
Robert Hausam, M.D.
Hausam Consulting
+1 (801) 949-1556
rrhausam at gmail.com
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