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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 13:04:35 PDT 2013


Dear Ryan,

I have managed to work with the URL
http://rest.bioontology.org/obs/annotator from Java, it is working fine.
However, the problem with MeSH and the Semantic types persist here. I get
T999 as semantic type when annotating with MeSH (virtual id 1351) while
with SNOMED-CT (virtual id 1353) I do get T109 and T124. When will it
solved?

And the XML that I get in Java is different from the one that I get from
the Annotator interface, the last one seems to be incomplete.

Thanks,
Jael


On Tue, Oct 8, 2013 at 8:33 PM, Jael GarcíaCastro <
leyla.jael.garcia at gmail.com> wrote:

> 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/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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