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[bioontology-support] Semantic Types for MeSH Mapping

Sam Stewart samstewart11 at
Thu Jul 19 15:43:31 PDT 2012

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:

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

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

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