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
Mon Jan 14 11:02:07 PST 2013


Hi Melanie,

The version of AERO that is processed for use with the Annotator is from 5/31/2012 and this version does not contain the term "wheezing".  

Trish 


On Jan 14, 2013, at 10:15 AM, Melanie Courtot wrote:

> Dear Ray and Trish,
> 
> Sarbjit (cc) was trying to use the annotator to fetch AERO terms. He has an issue similar to the one I had below; specifically when looking for "wheezing" the annotator only retrieves the SNOMED term and not the AERO one.
> 
> Do you know if there is an indexing issue again?
> 
> Thanks,
> Melanie
> 
> 
> On 2011-11-09, at 2:59 PM, Melanie Courtot wrote:
> 
>> Thanks Ray, 
>> There is no rush, I just somehow understood from Trish's email that it would be done fairly quickly if not immediatly, so thought there was something else going wrong when I didn't fetch any result.
>> 
>> Cheers,
>> Melanie
>> 
>> 
>> On 2011-11-09, at 2:55 PM, Ray Fergerson wrote:
>> 
>>> Melanie,
>>> 
>>> We temporarily halted the processing of new ontologies for annotation while we were checking into a known bug. We have now restarted the processing of ontologies but it will realistically be a couple weeks before we are caught up again. Thus a reasonable target date is around Thanksgiving.
>>> 
>>> Ray
>>> 
>>> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Trish Whetzel
>>> Sent: Wednesday, November 09, 2011 11:47 AM
>>> To: Melanie Courtot
>>> Cc: support at bioontology.org Support
>>> Subject: Re: [bioontology-support] NCBO annotator
>>> 
>>> Hi Melanie, 
>>> 
>>> AERO has not been re-populated yet for use with the Annotator. Ray can provide more details on when AERO will be ready. 
>>> 
>>> Trish 
>>> 
>>> 
>>> On Nov 9, 2011, at 11:43 AM, Melanie Courtot wrote:
>>> 
>>> 
>>> Hi Trish,
>>> 
>>> I just tried again unsuccessfully. Do you have any more news on the status?
>>> 
>>> Thanks,
>>> Melanie
>>> 
>>> 
>>> On 2011-10-30, at 12:38 PM, Trish Whetzel wrote:
>>> 
>>> 
>>> 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
>>> 
>>> 
>>> 
>>> 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
>>> 
>> 
> 



More information about the bioontology-support mailing list