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

Jael GarcíaCastro leyla.jael.garcia at gmail.com
Tue Oct 8 12:33:42 PDT 2013


Dear Ray,

I have seen that Bioportal has been migrated now to the RDF platform. Now
"serotonin" in MeSH indeed has types T109 and T124 as you mentioned in your
previous mail, great!

However, I am not getting the information I used to with NCBO Annotator.
Before the migration, I used this URL for the annotator
http://rest.bioontology.org/obs/annotator, now, I saw in the documentation (
http://stagedata.bioontology.org/documentation#nav_annotator) that it
should be http://stagedata.bioontology.org/annotator, is that right? In
both cases I am getting an error saying that my API Key is not valid. I
already re-registered myself in case it has expired or kind of, but still I
get the same error with the new API Key. What am I doing wrong? Any
suggestions?

Using the apikey used by the annotator interface when XML format is
required (
http://data.bioontology.org/annotator?text=serotonin&max_level=0&ontologies=MESH&format=xml&apikey=xxx),
with the URL http://rest.bioontology.org/obs/annotator I get a "Method Not
Allowed", while with http://stagedata.bioontology.org/annotator I get an
"Internal Server Error". What could be the problem?

I tried to get the XML from the Annotator interface and the XML now is
different from before, it has less information, is this a new response?
<annotationCollection><annotation><annotatedClass/><hierarchyCollection/><annotationsCollection><annotations><from>1</from><to>9</to><matchType>PREF</matchType><text>SEROTONIN</text></annotations></annotationsCollection><mappingsCollection/></annotation></annotationCollection>


Thanks so much in advance,
Jael


On Wed, Sep 25, 2013 at 3:19 AM, Ray Fergerson
<ray.fergerson at stanford.edu>wrote:

> 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/annotatorwith 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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