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[bioontology-support] [bioontology-info] Mappings

Trish Whetzel whetzel at stanford.edu
Wed Dec 2 17:03:13 PST 2009


Hi Robin,

No worries, I am hear to answer questions :-)

Yes, the Recommender can be accessed via a Perl client similar to the  
Annotator. However, we do not yet have a sample client available for  
download. There is a html client at: http://obs.bioontology.org/recommender/Recommender1.1.html 
, and Clement mentioned the input parameters are the ones in Bold if  
you would like to develop a Perl client. The values are those stated  
in the form and the POST URL is:
http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/recommender1.1/


Trish


On Dec 2, 2009, at 12:05 PM, Smith, Robin wrote:

> Hi Trish,
>
> Sorry to keep on bothering you.  When I use a small block of text,  
> the recommender is able to return a result quickly.
>
> However, with a large set (> a few thousand words), the 20 second  
> time out is exceeded.  Is there any way to get around this with a  
> longer timeout or by automation?  Can the recommender service be  
> accessed via a Perl client like the annotator?
>
> Robin
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, December 01, 2009 5:02 PM
> To: Smith, Robin
> Subject: Re: [bioontology-info] Mappings
>
> Other than any limits set in the form, there should not be a limit  
> on the size of the corpus that can be passed to the Recommender.
>
> Trish
>
>
> On Dec 1, 2009, at 1:44 PM, Smith, Robin wrote:
>
>
> It shouldn't be too big of a problem to have occasional interruptions.
>
> Do you know if there is a limit on how large of a corpus can be  
> passed into the web form?  For the Annotator we just used the web  
> service to sequentially annotate records from a database using  
> Pipeline Pilot.
>
> Robin
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, December 01, 2009 4:40 PM
> To: Smith, Robin
> Subject: Re: [bioontology-info] Mappings
>
> Ok, since this service is currently only deployed to the stage  
> server and not a production server it is likely that there will be  
> interruptions in the service.  Can you indicate the level of  
> severity that interruptions will cause to your overall project?
>
> Trish
>
>
> On Dec 1, 2009, at 12:00 PM, Smith, Robin wrote:
>
>
>
> Yes I was using that URL.
>
> I just tried it again and now it's working just fine - maybe it was  
> just a temporary thing.
>
> Thanks!
>
> Robin
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Tuesday, December 01, 2009 2:57 PM
> To: Smith, Robin
> Subject: Re: [bioontology-info] Mappings
>
> Hi Robin,
>
> Are you accessing the Recommender at: http://stage.bioontology.org/recommender 
>  and can you send which parameters you are using?
>
> Thanks,
> Trish
>
>
>
> On Dec 1, 2009, at 11:44 AM, Smith, Robin wrote:
>
>
>
>
> Hi Trish,
>
> I've been trying to use the Recommender service but it seems to time  
> out regardless of what input or settings I use.  Could this have  
> something to do with the 20s search time?
>
> Thanks,
>
> Robin
>
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Wednesday, November 25, 2009 6:20 AM
> To: Smith, Robin
> Cc: support at bioontology.org
> Subject: Re: [bioontology-info] Mappings
>
> Hi Robin,
>
> There is a prototype tool that we are working on called the Ontology  
> Recommender. Documentation is available at: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service 
>  and this includes links to the service. Let us know if you have any  
> questions.
>
> Best regards,
> Trish
>
>
> On Nov 23, 2009, at 8:58 AM, Smith, Robin wrote:
>
>
>
>
>
> To Whom it May Concern,
>
> My name is Robin Smith and I'm a postdoc at the University of  
> Miami.  We've been using the NCBO Annotator web service recently to  
> annotate a large cheminformatics database and have gotten some great  
> data out of it.
>
> I was wondering whether you could provide us with an XML/tab  
> delimited file,  similar to http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obs/ontologies 
>  , in which the total number of annotations for each ontology is  
> listed.  We've been noticing that some ontologies, such NCI and  
> SNOMED, provide almost too many annotations, and it would be helpful  
> to be able to normalize to see which ontologies describe our data  
> set the best.
>
> Thanks,
>
> Robin
>
> _______________________________________________
> bioontology-info mailing list
> bioontology-info at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-info
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu
> http://www.bioontology.org
>
>
>
>
>
>

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