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] NCBO annotator

Trish Whetzel whetzel at stanford.edu
Sun Oct 30 12:38:09 PDT 2011


That might have caused an issue with the Annotator population process. It looks like about half of the terms for AERO have the identifier rather than term label populated in the Annotator database. I've put in a bug report to have AERO re-populated. The values for <label> from the "Get root terms" and "Get all terms" web services now looks correct.  

Trish  


On Oct 29, 2011, at 12:25 PM, Melanie Courtot wrote:

> Hi Trish,
> I was wondering if it may be linked to the fact that I don't have the protege language declaration in the file (you may remember the subsequent issue with labels display). Though it doesn't seem like it should matter.
> Thanks for looking into it!
> Melanie
> 
> 
> 
> 
> On 2011-10-29, at 12:21 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> 
>> Hi Melanie, 
>> 
>> I'm running some tests to identify the source of the error. 
>> 
>> Trish 
>> 
>> 
>> On Oct 28, 2011, at 8:58 AM, Melanie Courtot wrote:
>> 
>>> Hi,
>>> 
>>> I am trying out the annotator; just starting, so fairly basic test.
>>> 
>>> Right now, I just want to get an idea of how the annotation is done and what I could get back, and generally check it works out as expected.
>>> 
>>> My test is selecting the AERO ontology, and entering a text such as "a vaccine adverse event was reported. a seizure happened, including motor manifestations"
>>> 
>>> I expected it to tag "seizure", AERO_0000017, as well as "adverse event", AERO_0000009 - both terms being in the version loaded on BioPortal. I didn't get anything. Adding AEO into the list of sources, I detect "adverse event" from the AEO (see attached screenshot), which seems to indicate that the text is properly parsed and that the issue is with AERO. Do you know if it is because AERO is not loaded properly for some reason, or something else?
>>> 
>>> Thanks,
>>> Melanie
>>> 
>>> <Screen shot 2011-10-27 at 2.16.27 PM.png>
>>> 
>>> ---
>>> Mélanie Courtot
>>> MSFHR/PCIRN trainee, TFL- BCCRC
>>> 675 West 10th Avenue
>>> Vancouver, BC
>>> V5Z 1L3, Canada
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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

Now on Twitter: http://twitter.com/#!/bioontology
and "Like" us on Facebook: http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20111030/ea90fc65/attachment.html>


More information about the bioontology-support mailing list