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

Jael GarcíaCastro leyla.jael.garcia at
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, now, I saw in the documentation ( that it
should be, 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

Using the apikey used by the annotator interface when XML format is
required (,
with the URL I get a "Method Not
Allowed", while with 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?

Thanks so much in advance,

On Wed, Sep 25, 2013 at 3:19 AM, Ray Fergerson
<ray.fergerson at>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 [mailto:
> bioontology-support-bounces at] *On Behalf Of *Jael
> GarcíaCastro
> *Sent:* Tuesday, September 24, 2013 12:09 PM
> *To:* support at
> *Subject:* [bioontology-support] UMLS semantic types in NCBO Annotator
> and SPARQL endpoint****
> ** **
> Hi all, ****
> I tried DESCRIBE <> at
> The description includes the UMLS semantic
> type as ****
> <> <>****
> ** **
> I noticed that the URL
> does not
> resolve. Do you plan these UMLS semantic type URLs to be resolvable?****
> I also tried the NCBO Annotator 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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