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[bioontology-support] [BioPortal] Feedback from aridag

Trish Whetzel whetzel at stanford.edu
Mon May 14 10:18:49 PDT 2012


In reviewing further, since neither version has parsed this would prevent the i2b2-ncbo tool from working. I'll try to get the latest version parsed. Do you have a deadline for converting this file into the i2b2 format?

Trish 


On May 14, 2012, at 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>
>> 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
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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