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[bioontology-support] [BioPortal] Feedback from aridag

Trish Whetzel whetzel at stanford.edu
Mon May 14 12:31:37 PDT 2012


Also, the latest version of the Body Structure subtree from SNOMED-CT [1] is now parsed and I have confirmed it can be accessed via the NCBO Web services. I believe it should also be ready for use with the i2b2-ncbo extraction tool.

Trish 

[1] http://bioportal.bioontology.org/ontologies/48006?p=terms


On May 14, 2012, at 11:35 AM, Paul R Alexander wrote:

> 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>
>>> 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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