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[bioontology-support] Semantic Types for MeSH Mapping

Paul R Alexander palexander at stanford.edu
Thu Jul 19 17:53:19 PDT 2012


Sam,

Unfortunately, there was a bug in a recent data population that we did 
and the semantic types are currently unavailable in the Annotator. We're 
working on re-populating the data and it should be available in 3-4 
weeks time.

As a workaround, you can call use our web services to look up the 
semantic type for the concepts that are returned by the annotator, 
removing those that don't match your preferred list. Documentation on 
using the term service is available here:
http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses

Please let me know if you have any other questions.

Paul R Alexander
Senior Software Engineer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 7/19/12 3:43 PM, Sam Stewart wrote:
> Hello list,
>
> I'm new to the Annotator list, so forgive me if this has been asked
> before.  I sent this question yesterday, but I didn't get a response,
> and I didn't see it in the digest, so it might just not have worked.
>
> I'm exploring using the Annotator to map to just MeSH terms, and I'm
> having trouble with the semantic types.  When I restrict my mapping to
> just the terms from MeSH (ontologiesToKeepInResult=1351) then all of
> the semantic types for my mappings are "T999 - NCBO BioPortal
> concept". If I remove the restriction then I get the right concepts.
>
> I'd like to be able to restrict my mapping to just MeSH, but I'd also
> like to eliminate a number of semantic types that aren't pertinent to
> my subject.  Is there something I'm doing wrong?
>
> The best example I can come up with is using the web portal:
> http://rest.bioontology.org/test_oba.html
>
> set ontologiesToKeepInResult to 1351
> set isVirtualOntologyID to true
> enter the following text: Melanoma is a malignant tumor of melanocytes
> which are found predominantly in but also in the bowel and the eye
>
> Check the xml output, and then process.  The resulting mappings all
> have T999 as their semantic type.  If you remove the 1351 ontology
> restriction and let it map to all the ontologies then it gets the
> semantic types right.
>
> The odd thing is that, when you navigate to the actual entry for a
> MeSH term, like the one below for Pain, the semantic type is there and
> correct.
>
> http://bioportal.bioontology.org/ontologies/46836?p=terms&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMSH%2FD010146
>
> Any help would be appreciated.
>
> --
> Sam Stewart, MMath, A.Stat
> IDPhD Candidate (Health Informatics)
> Faculty of Computer Science, Dalhousie University
> 6050 University Ave.
> Halifax, NS, Canada, B3H 1W5
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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