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[bioontology-support] Annotator help request

Trish Whetzel whetzel at
Tue Jun 15 16:40:22 PDT 2010

Hi Beecher,

Comments inline.

On Jun 15, 2010, at 7:04 AM, Beecher Greenman wrote:

> My name is Beecher Greenman. I've been using the Annotator Web  
> service in a wiki to support the Human Salivary Proteome Project,  
> but I have some questions based on what appear to be recent service  
> changes.
> 1) When I query for annotations in certain ontologies -for example,  
> the NCI Thesaurus- I find that the results no longer include  
> accession numbers for the terms found. In some cases, like the  
> aforementioned NCI, I seem to receive URLs for another page instead,  
> while in other cases I essentially get the preferred name of the  
> term. In still other cases, such as the Medical Subject Headings, I  
> continue to get accession numbers as I expected. Is this change  
> intentional, and is there any other way to

Can you send the parameters that you are using with the Annotator and  
examples of the current and past output that resulted from the Web  

> 2) Some time ago, I stopped getting any annotations from the  
> Mammalian Phenotype ontology, even for terms I knew to be part of  
> it, such as "cellular phenotype" and "abnormal muscle weight". More  
> recently, as I was looking through your Flash client at < 
> >, I noticed that Mammalian Phenotype does not seem to be in the  
> list of supported ontologies anymore. Has it been removed?

There was an earlier problem with the list of ontologies available for  
use with the Annotator. The Mammalian phenotype ontology is now  
available. This Web service call displays which ontologies are  


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