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[bioontology-support] Annotator help request

Trish Whetzel whetzel at stanford.edu
Fri Oct 1 09:34:33 PDT 2010


I checked with the developers on this item and as it turns out, the source data contains the term identifier in this form, e.g.  B7... (Full example from source ontology file: C0086692|ENG|S|L0085417|VO|S0599364|Y|A0654833||||RCD|PT|B7...|Benign tumour|3|N|256| ).  The Full Ids, e.g. http://purl.bioontology.org/ontology/RCD/B7...  do resolve, however I see that BioPortal is creating the hyperlink without one of the "." as part of the link.
Trish 

On Sep 28, 2010, at 4:23 PM, Trish Whetzel wrote:

> 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
> 
>  
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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