Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from aridag

arianna dagliati aridag at gmail.com
Tue May 15 01:19:23 PDT 2012


Dear Trish and Paul,
sorry for my late reply, but now everything works, both i2b2-ncbo tool and
the view information editing page :)

Just want to inform you better about what happened with the i2b2-ncbo tool.
First i've modified the tool in order to extract virtual ontology, and it
 worked well with all the other
view (eg neoplasm_hamartoma --> ID 2085)
Before you've parsed the subtree i didn't get a specific error but the file
i get was empty, that never happened with other virtual ontology i used in
the past. As i could understand the problem was due to the SNOMED-CT
version i've used.

Thanks very much for your precious help.
Best
Arianna



2012/5/14 Trish Whetzel <whetzel at stanford.edu>

> 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
>
>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20120515/6f2ca841/attachment-0001.html>


More information about the bioontology-support mailing list