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[bioontology-support] UMLS semantic types in NCBO Annotator and SPARQL endpoint

Ray Fergerson ray.fergerson at stanford.edu
Tue Sep 24 19:19:52 PDT 2013


Jael,



We may make the UMLS property URI’s that we generate resolvable but this
is not a high priority at the moment.



There does seem to be something wrong with the sematic types and MeSH.
They work fine for other ontologies (e.g. SNOMED). By the way, Serotonin
has types T109 and T124 (not T016 has stated below). These types are
returned in the XML for “working” ontologies.



Whatever the problem with MeSH, we are about to replace this entire
backend system in a couple of days. Thus we are not going to look into
this problem. The new system should work correctly. If it doesn’t then we
will fix it. Stay tuned.



Ray



From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Jael
GarcíaCastro
Sent: Tuesday, September 24, 2013 12:09 PM
To: support at bioontology.org
Subject: [bioontology-support] UMLS semantic types in NCBO Annotator and
SPARQL endpoint



Hi all,

I tried DESCRIBE <http://purl.bioontology.org/ontology/MDDB/07224> at
http://sparql.bioontology.org. The description includes the UMLS semantic
type as

<http://bioportal.bioontology.org/ontologies/umls/hasSTY>
<http://bioportal.bioontology.org/ontologies/umls/sty/T121>



I noticed that the URL
http://bioportal.bioontology.org/ontologies/umls/sty/T121 does not
resolve. Do you plan these UMLS semantic type URLs to be resolvable?

I also tried the NCBO Annotator http://bioportal.bioontology.org/annotator
with the term "serotonin" and the ontology MeSH. This term is associated
to the UMLS semantic type T016. However, if I retrieve the annotation in
the XML format using the  option "Format Result As", the semantic type
retrieved is T999 "NCBO BioPortal concept". I was expecting T016, is not
the semantic type reported by the annotator the UMLS one?

Thanks,

Jael

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