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[bioontology-support] [BioPortal] Feedback from Mark Williams

Mark Williams mwilliam at ebi.ac.uk
Thu Aug 25 01:31:09 PDT 2016


Hi John and Alejandra,

Ken Haug (MetaboLights project manager) has the desk next to mine :-)

He is currently, compiling the new version of IsaCreator 1.7.9, we 
currently have a version of 1.7.8 running.  Let's see if this solves the 
problem (fingers crossed).

And ............. It works.

Problem solved.

Thank you very much both of you for your help.

Much appreciated.

Mark


On 24/08/2016 21:43, Alejandra Gonzalez-Beltran wrote:
> Hi John, Mark
>
> I am part of the ISAtools team and can investigate the issue further. 
> Thanks John for bringing this report to our attention.
>
> It is not clear from the email below what tool is being used, but I 
> assume ISAcreator?
>
> I have tested ISAcreator development version and the query for "group" 
> retrieves multiple results. A new release will be provided soon and we 
> are also working with the BioPortal team to solve other issues.
>
> Mark, please contact the ISAtools team at <isatools at googlegroups.com 
> <mailto:isatools at googlegroups.com>> for any issues and it would be 
> great if you could provide more details about what tool/version/your 
> system details.
>
> Many thanks,
>
> Alejandra
>
>
> On 24 August 2016 at 18:25, John Graybeal <jgraybeal at stanford.edu 
> <mailto:jgraybeal at stanford.edu>> wrote:
>
>     Thank you Mark for the followup.
>
>     While it might have been a BioPortal issue, as I mentioned, it is
>     working fine for me now, so the problem is I can't duplicate the
>     issue to troubleshoot it. Hence my question about whether you
>     could confirm it is still failing for you.
>
>     We actually work with the ISATools team in other contexts, so we
>     can follow up with them directly. Can you just confirm the
>     behavior is still occurring, ideally with a screen grab from the
>     tool?  Then we can pursue it on our end with them.
>
>     Thanks, sorry for all this go-around!
>
>     john
>
>
>>     On Aug 24, 2016, at 1:25 AM, Mark Williams <mwilliam at ebi.ac.uk
>>     <mailto:mwilliam at ebi.ac.uk>> wrote:
>>
>>     Hi John,
>>
>>     We are using ISATools which queries your API to fetch various
>>     ontology terms from BioPortal.  The problem has only surfaced
>>     recently and the ISATools code has not been changed/updated for
>>     many many months so it's probably a change that has happened at
>>     your end.
>>
>>     It's a third-party tool so it might take a bit of time to work
>>     out what the exact call to the API.  If there is anything obvious
>>     at your end that has recently been changed that might help us
>>     narrow down where the problem may be occurring then please let us
>>     know.
>>
>>     Sorry to be so vague :-)
>>
>>     Cheers,
>>
>>     Mark
>>
>>     On 24/08/2016 00:36, John Graybeal wrote:
>>>     Hi Mark,
>>>
>>>     Thanks for this email. When I just tried entering 'group' at the
>>>     http://bioportal.bioontology.org/search
>>>     <http://bioportal.bioontology.org/search> page, it returned the
>>>     expected number of hits. Can you try again?  Possibly some
>>>     service was briefly not working, I'm not sure what else would
>>>     explain it.
>>>
>>>     If your problem was with the API, please send us the call you
>>>     used (without the key) so that we can have a look. Thanks.
>>>
>>>     John
>>>
>>>>     On Aug 23, 2016, at 8:52 AM, support at bioontology.org
>>>>     <mailto:support at bioontology.org> wrote:
>>>>
>>>>     Name: Mark Williams
>>>>
>>>>     Email: mwilliam at ebi.ac.uk <mailto:mwilliam at ebi.ac.uk>
>>>>
>>>>     Location: http://bioportal.bioontology.org/search
>>>>     <http://bioportal.bioontology.org/search>
>>>>
>>>>
>>>>     *Feedback:*
>>>>
>>>>     Hi,
>>>>
>>>>     Your web service does not appear to be returning hits for the
>>>>     search term 'group'.
>>>>
>>>>
>>>>     _______________________________________________
>>>>     bioontology-support mailing list
>>>>     bioontology-support at lists.stanford.edu
>>>>     <mailto:bioontology-support at lists.stanford.edu>
>>>>     https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>     <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
>>>
>>>     ========================
>>>     John Graybeal
>>>     Technical Program Manager
>>>     Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>>     Stanford Center for Biomedical Informatics Research
>>>
>>>
>>
>>     _______________________________________________
>>     bioontology-support mailing list
>>     bioontology-support at lists.stanford.edu
>>     <mailto:bioontology-support at lists.stanford.edu>
>>     https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>     <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
>
>     ========================
>     John Graybeal
>     Technical Program Manager
>     Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>     Stanford Center for Biomedical Informatics Research
>     650-736-1632
>     skype: graybealski
>
>
>
>     _______________________________________________
>     bioontology-support mailing list
>     bioontology-support at lists.stanford.edu
>     <mailto:bioontology-support at lists.stanford.edu>
>     https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>     <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
>
>

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