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[bioontology-support] Open Biomedical Annotator

Trish Whetzel whetzel at stanford.edu
Tue Sep 29 15:21:53 PDT 2009


Hi Omkar,

Service to the Annotator has been restored. Thank you for your  
patience. If you notice any other issues, please let us know.

Best regards,
Trish


On Sep 29, 2009, at 2:01 PM, Omkar Lele wrote:

> Trish,
> I was wondering if the OBA (or NCBO) service is down? I have been  
> trying to use it since today morning, but the operation times out.
> Just for your reference, I’ve been using code that is similar to the  
> one posted at “http://www.bioontology.org/wiki/index.php/Annotator_Client_Examples 
> ”.
>
> Thanks,
> Omkar
>
>
> On 8/5/09 4:27 AM, "Trish Whetzel" <whetzel at stanford.edu> wrote:
>
>> Hi Omkar,
>>
>> The Annotator has many parameters that can be modified, e.g.  
>> ontology selection, levels of the hierarchy to expand, inclusion of  
>> mappings, however it seems in this case with the given parameters  
>> that the amount of text to submit needs to be modified. Can you  
>> submit the text in chunks of ~400 words?
>>
>> Clement, do you have other suggestions?
>>
>> Trish
>>
>>
>> On Aug 4, 2009, at 1:36 PM, Omkar Lele wrote:
>>
>>> Hi Trish,
>>>  I am a knowledge engineering developer at The Ohio State  
>>> University, Center for Clinical and Translational Science. I was  
>>> trying to use OBA to annotate information extracted from FDA  
>>> Packet Inserts ( a sample file attached as doc1.txt)
>>>  The text has about 4500 words and the web service simply stops  
>>> responding (times out). I’m following the example posted at “http://bioontology.org/wiki/index.php/Annotator_Client_Examples 
>>> ”.
>>>  Is there a way around this problem? Following is the list of  
>>> parameters I’m using,
>>>  method.addParameter("longestOnly", "true");
>>>  method.addParameter("scored", "true");
>>>  method.addParameter("mappingTypes", "null");
>>>
>>>  Thanks for your help.
>>>  Omkar Lele
>>>
>>>
>>>
>>>
>>>  ------ Forwarded Message
>>>  From: "Jonquet, Clement Marie" <jonquet at stanford.edu>
>>>  Date: Mon, 3 Aug 2009 16:34:58 -0700
>>>  To: Tara Payne <tara.payne at osumc.edu>, Omkar Lele <omkar.lele at osumc.edu 
>>> >
>>>  Cc: "Whetzel, Patricia L" <whetzel at stanford.edu>
>>>  Subject: RE: Open Biomedical Annotator
>>>
>>>  Dear Tara, dear Omkar,
>>>
>>>  I would be pleased to help you to use the NCBO Annotator  
>>> (formerly OBA).
>>>  I CCed Trish Whetzel. She is supervising NCBO’s user interaction  
>>> and collaboration.
>>>
>>>  I want let you know that since the AMIA summit we have released a  
>>> new version of the NCBO Annotator web service:
>>>  It’s part of NCBO BioPortal: http://bioportal.bioontology.org/annotate
>>>  And you can also learn how to access the web service here:
>>>  http://bioontology.org/wiki/index.php/Annotator_Web_service
>>>
>>>  Best regards,
>>>  Clement
>>>
>>>   
>>> ------------------------------------------------------------------------------------------------------------------------------
>>>  Dr. Clement JONQUET - PhD in Informatics
>>>  Postdoctoral Research Fellow - Stanford University - National  
>>> Center for Biomedical Ontology
>>>
>>>  *email*:       
>>> jonquet at stanford.edu                                       
>>> *web*:      http://www.stanford.edu/~jonquet <http://www.stanford.edu/~jonquet 
>>> >
>>>  *tel/fax*:    (001) 650 724-0388 / (001) 650 725-7944        
>>> *skype*:   clementpro
>>>
>>>  Stanford Center for Biomedical Informatics Research  
>>> (BMIR)           http://bmir.stanford.edu/ <http://bmir.stanford.edu/ 
>>> >
>>>  Medical School Office Building, Room X-215
>>>  251 Campus Drive
>>>  Stanford, CA 94305-5479  USA
>>>   
>>> ------------------------------------------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> From: Tara Payne [mailto:tara.payne at osumc.edu]
>>>  Sent: Monday, August 03, 2009 2:21 PM
>>>  To: Jonquet, Clement Marie
>>>  Cc: Lele, Omkar
>>>  Subject: Open Biomedical Annotator
>>>
>>>  Dr. Jonquet -
>>>
>>>  I’m not sure if you remember me, but we met briefly at your  
>>> presentation at the most recent Translational Bioinformatics  
>>> Summit in San Francisco.  Omkar Lele (cc’ed) and I are working on  
>>> a project that involves the annotation of biomedical free text  
>>> with concepts from standard terminologies/ontologies, and have  
>>> been exploring the use of your Open Biomedical Annotator tool to  
>>> meet our needs.  As we begin evaluating and utilizing this tool,  
>>> would it be ok to contact you if/when any questions or issues  
>>> should arise?
>>>
>>>  Thanks,
>>>  Tara
>>>
>>>  --------------------------------------------
>>>  Tara (Borlawsky) Payne, MA
>>>  Knowledge Engineer, OSU Center for Clinical and Translational  
>>> Science and OSUMC Information Warehouse
>>>  Instructor, OSU Department of Biomedical Informatics
>>>
>>> Phone: (614) 293-9592
>>>  Email: tara.payne at osumc.edu
>>>
>>> ***Help the James lead the charge against cancer
>>>  http://www.pelotonia.org/ride/riders_profile.jsp?MemberID=836&RiderName=Tara%20Payne&SearchStart=0&PAGING
>>>
>>>
>>>  ------ End of Forwarded Message
>>>
>>>   <doc1.txt>
>>
>>
>> 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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