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[bioontology-support] [BioPortal] Feedback from aridag

Trish Whetzel whetzel at stanford.edu
Mon May 14 09:51:28 PDT 2012


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>
> 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>
>> Dear Trish,
>> thank you very much for your help!
>> 
>> Best
>> Arianna
>> 
>> 
>> 2012/5/4 Trish Whetzel <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 wrote:
>>> 
>>>> 
>>>> Name: aridag
>>>> 
>>>> Email: 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
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> 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
>>> 
>>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>> 
>>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>>> 
>>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> 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

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

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