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[bioontology-support] Annotator help request

Trish Whetzel whetzel at stanford.edu
Tue Sep 28 16:23:57 PDT 2010


Dear Marco,

Thanks for pointing this out. I was able to reproduce this error directly using the Annotator web service and will investigate further. 

Trish 


On Sep 28, 2010, at 3:12 PM, Marco Ocana wrote:

> Hi,
> 
> My name is Marco Ocana and I am a software consultant. I work with Tim Clark from Harvard University/MGH.
> We are working on integrating your Annotator Web Service with a tool that we are developing.
> 
> We encountered a problem with the results returned from the service.
> Some of the URIs for the found concepts are invalid.
> Below is an extract of the results. Note the ... at the end of the fullId element value. Same for localConceptId.
> 
> We got this result from the Java/Groovy client we are creating and from your HTML web form at:
> http://rest.bioontology.org/test_oba.html
> 
> To reproduce, I just entered (without quotes):
> "This is a test to see if we can find breast cancer or alzheimers disease"
> The only option on the web form I changed or set was XML output.
> 
> Thanks
> 
> Marco Ocana
> Balboa Systems, Inc.
> 
> <annotationBean>
> 
>           <score>7</score>
> 
>           <concept>
> 
>             <id>7576609</id>
> 
>             <localConceptId>42295/B7...</localConceptId>
> 
>             <localOntologyId>42295</localOntologyId>
> 
>             <isTopLevel>0</isTopLevel>
> 
>             <fullId>http://purl.bioontology.org/ontology/RCD/B7...</fullId>
> 
>             <preferredName>Benign tumour</preferredName>
> 
>             <synonyms>
> 
>               <string>Benign neoplasm</string>
> 
>             </synonyms>
> 
>             <definitions/>
> 
>             <semanticTypes>
> 
>               <semanticTypeBean>
> 
>                 <id>10256193</id>
> 
>                 <semanticType>T191</semanticType>
> 
>                 <description>Neoplastic Process</description>
> 
>               </semanticTypeBean>
> 
>             </semanticTypes>
> 
>           </concept>
> 
> _______________________________________________
> 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
whetzel at stanford.edu
http://www.bioontology.org

 

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