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[bioontology-support] [BioPortal] Feedback from aridag

Paul R Alexander palexander at stanford.edu
Mon May 14 11:35:06 PDT 2012


Editing the view information should now work properly. Sorry for the 
inconvenience.

Paul R Alexander
Senior Software Engineer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 5/14/12 9:51 AM, Trish Whetzel wrote:
> Hi Arianna,
>
> You are listed as the admin for the new version so I'm not sure why 
> selecting the Admin tab option "Edit View Information" is re-directing 
> you to the "Home" page. Paul, do you know why this is happening?
>
> What error message is the i2b2-ncbo extraction tool returning? Are you 
> using the ontology version id "48004" with the tool? The latest 
> version, 48006, did not complete parsing and we will look into this.
>
> Trish
>
>
> On May 14, 2012, at 8:15 AM, arianna dagliati wrote:
>
>> Dear Trish,
>> you can find the screenshot attached.
>> I'm using the NCBO Extraction tool package that you find at this link 
>> https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools
>>
>> Arianna
>>
>> 2012/5/14 Trish Whetzel <whetzel at stanford.edu 
>> <mailto:whetzel at stanford.edu>>
>>
>>     BioPortal is designed to support multiple versions of ontologies,
>>     therefore I'm not sure that is the issue. Can you send a
>>     screenshot of the page with the Administer link, is it the page:
>>     http://bioportal.bioontology.org/ontologies/2105?p=terms ?
>>
>>     Also, is this the link for the i2b2 ncbo tool you refer to:
>>     http://i2b2.bioontology.org/
>>
>>     Trish
>>
>>
>>     On May 14, 2012, at 3:21 AM, arianna dagliati wrote:
>>
>>>     Dear Trish,
>>>     i'm sorry to disturb you again, but i still can't use the i2b2
>>>     ncbo tool through ncbo rest service, i think it's due to the
>>>     duplication of the view (mine, wrong, in owl/xml and the one
>>>     you've uploaded in the correct rdf/owl format).
>>>     is it possible for you to delete the wrong one?
>>>     i think there could be a bug because when i click on administer
>>>     --> edit version i'm redirected to the bioportal homepage.
>>>
>>>     Thanks!
>>>
>>>     Best
>>>     Arianna
>>>
>>>     2012/5/7 arianna dagliati <aridag at gmail.com
>>>     <mailto:aridag at gmail.com>>
>>>
>>>         Dear Trish,
>>>         thank you very much for your help!
>>>
>>>         Best
>>>         Arianna
>>>
>>>
>>>         2012/5/4 Trish Whetzel <whetzel at stanford.edu
>>>         <mailto:whetzel at stanford.edu>>
>>>
>>>             Hi Arianna,
>>>
>>>             The file was saved as OWL/XML, but needs to be saved as
>>>             RDF/XML for loading into BioPortal. I've re-loaded the
>>>             the RDF/XML formatted file.
>>>
>>>             Trish
>>>
>>>
>>>             On May 3, 2012, at 11:23 AM, Trish Whetzel wrote:
>>>
>>>>             We'll take a look at this.
>>>>
>>>>             Trish
>>>>
>>>>
>>>>             On May 3, 2012, at 2:45 AM, support at bioontology.org
>>>>             <mailto:support at bioontology.org> wrote:
>>>>
>>>>>
>>>>>             Name: aridag
>>>>>
>>>>>             Email: aridag at gmail.com <mailto:aridag at gmail.com>
>>>>>
>>>>>             Location: http://bioportal.bioontology.org/
>>>>>
>>>>>             Comment:
>>>>>             Dear NCBO support,
>>>>>             i've submitted a SNOMED view ontology last week.
>>>>>             =======================
>>>>>             Description: The Body Structure subtree in SNOMED-CT
>>>>>             Ontology ID: 2105
>>>>>             =======================
>>>>>             but i got an error back accessing it
>>>>>             (http://bioportal.bioontology.org/ontologies/2105?p=terms)
>>>>>             and i can't use the extraction rest service (for i2b2
>>>>>             NCBO tool).
>>>>>
>>>>>             Could you please advice me if there's anything wrong
>>>>>             with the owl file i've uploaded? or it's just a matter
>>>>>             of time you need to process the view?
>>>>>
>>>>>             Thank you.
>>>>>             Best
>>>>>             Arianna - aridag at gmail.com <mailto:aridag at gmail.com>
>>>>>             _______________________________________________
>>>>>             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
>>>>
>>>>             Trish Whetzel, PhD
>>>>             Outreach Coordinator
>>>>             The National Center for Biomedical Ontology
>>>>             Ph: 650-721-2378
>>>>             http://www.bioontology.org <http://www.bioontology.org/>
>>>>
>>>>             "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>>>
>>>>             Follow NCBO on Twitter:
>>>>             http://twitter.com/#!/bioontology
>>>>             <http://twitter.com/#%21/bioontology>
>>>>
>>>>             Join in Discussions on LinkedIn: http://linkd.in/ncbo-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
>>>
>>>
>>>
>>>
>>
>>
>>
>> <Schermata 2012-05-14 a 17.08.24.png>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> http://www.bioontology.org
>
> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>
> Follow NCBO on Twitter: http://twitter.com/#!/bioontology 
> <http://twitter.com/#%21/bioontology>
>
> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>


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