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

Tomasz Adamusiak tomasz at ebi.ac.uk
Wed May 12 01:20:07 PDT 2010


Hi Misha,

Thanks for a prompt reply. This is not much of a problem for me at the 
moment, but I would be grateful if you could let me know when a solution 
becomes available.

Cheers
Tomasz

On 10/05/2010 19:42, Michael Dorf wrote:
> 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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