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[bioontology-support] REST term services if concept id is a uri

Michael Dorf mdorf at stanford.edu
Mon May 10 11:42:29 PDT 2010


Hi Tomasz,

I'm sorry to say, but what you are reporting is an unfortunate way in
which these services currently operate. The hierarchy services are
implemented as "wrappers" around a different system, called OBS, that
provides data for Annotator. At this point, these services don't provide
support for passing full concept IDs as parameters.  I will discuss this
issue with my developers to see if we can come up with a short term
"workaround" before we implement a broader solution.

I am sorry for the inconvenience this causes in your work and I hope we
can resolve it quickly.

Misha


-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Tomasz Adamusiak
Sent: Monday, May 10, 2010 3:26 AM
To: Paul R Alexander
Cc: tomasz.adamusiak at ebi.ac.uk; support at bioontology.org
Subject: Re: [bioontology-support] REST term services if concept id is a
uri

Hi Paul,

To follow up on this. This does not seem to be working for hierarchy 
services (examples below). Is there some other way?

http://rest.bioontology.org/bioportal/virtual/parents/1084/?conceptid=http
%3a%2f%2fontology.neuinfo.org%2fNIF%2fBiomaterialEntities%2fNIF-Molecule.o
wl%23nifext_5168 


http://rest.bioontology.org/bioportal/virtual/rootpath/1084/?conceptid=htt
p%3a%2f%2fontology.neuinfo.org%2fNIF%2fBiomaterialEntities%2fNIF-Molecule.
owl%23nifext_5168 


Thanks
Tomasz

On 07/05/2010 17:30, Paul R Alexander wrote:
> Tomasz,
>
> Concept IDs that are URLs need to be passed via a query string parameter
> and be URL-encoded, so the proper format would be:
>
http://rest.bioontology.org/bioportal/virtual/ontology/1084/?conceptid=htt
p%3a%2f%2fontology.neuinfo.org%2fNIF%2fBiomaterialEntities%2fNIF-Molecule.
owl%23nifext_5168
>
>
> Thanks,
> Paul Alexander
> Web / UI Developer
> NCBO BioPortal
>
> On 5/7/10 7:52 AM, Tomasz Adamusiak wrote:
>> Hi,
>>
>> I can't figure a way to use term services for terms that have uri as
>> concepts IDs, e.g. NIFSTD lipoxin A4 which is visible on the web GUI:
>>
>>
http://bioportal.bioontology.org/visualize/42622/?conceptid=http://ontolog
y.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl%23nifext_5168
>>
>>
>> But not accessible through REST API:
>>
http://rest.bioontology.org/bioportal/virtual/ontology/1084/http://ontolog
y.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#nifext_5168
>>
>>
>> URL encoded doesn't work either:
>>
http://rest.bioontology.org/bioportal/virtual/ontology/1084/http%3a%2f%2fo
ntology.neuinfo.org%2fNIF%2fBiomaterialEntities%2fNIF-Molecule.owl%23nifex
t_5168
>>
>>
>> Thanks for looking into it.
>>
>> Cheers
>> Tomasz
>>
>>
>>
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