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

Ray Fergerson ray.fergerson at stanford.edu
Tue Oct 8 13:51:24 PDT 2013


The documentation for the new API is at:



http://data.bioontology.org/documentation



Ray



From: Jael GarcíaCastro [mailto:leyla.jael.garcia at gmail.com]
Sent: Tuesday, October 08, 2013 1:25 PM
To: Paul R Alexander
Cc: Ray Fergerson; support at bioontology.org
Subject: Re: [bioontology-support] UMLS semantic types in NCBO Annotator
and SPARQL endpoint



Thanks Paul,

Could you please point me to the documentation about the API
data.bioontology.org? In rest.bioontology.org, the parameter for the text
to be annotated used to be "textToAnnotate" but I saw it is now "text" in
data.bioontology.org. I would like to check the rest of parameters to make
sure I am using it in the proper way.

Thanks again,

Jael



On Tue, Oct 8, 2013 at 9:11 PM, Paul R Alexander <palexander at stanford.edu>
wrote:

Jael,



The new API code is released at data.bioontology.org, so you should point
there and not stagedata.bioontology.org (this is our testing platform).



rest.bioontology.org is essentially deprecated as of now, so new fixes
won't end up there.



There is indeed a bug on the xml output at data.bioontology.org that is
causing the class information to not appear. This will be fixed later
today. If you need to see the output now, you can try the json
serialization. The xml will look different than the xml provided at
rest.bioontology.org, primarily because of the transition to our new API,
which is now more uniform across individual NCBO APIs.



Please let me know if you have further questions.



Paul





On Oct 8, 2013, at 1:04 PM, Jael GarcíaCastro
<leyla.jael.garcia at gmail.com> wrote:



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
<http://data.bioontology.org/annotator?text=serotonin&max_level=0&ontologi
es=MESH&format=xml&apikey=xxx>
&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><m
appingsCollection/></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 <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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