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[bioontology-support] bioportal annotator ontologies status

Trish Whetzel whetzel at stanford.edu
Mon Jul 19 13:21:02 PDT 2010


Hi Emily,

Apologies for the delay, I was out of the office last week. We are  
currently re-processing ontologies and therefore SNOMED is not  
accessible for use with the Annotator.

To see which ontologies are available for use with the Annotator, you  
can call this service: http://rest.bioontology.org/obs/ontologies and  
check for ontologies with a value of 28 for <status>. This information  
is documented in the User guide: http://www.bioontology.org/wiki/index.php/Annotator_User_Guide 
.

We can talk more at the meeting today.

Trish


On Jul 13, 2010, at 1:39 PM, Emily Howe wrote:

> Hi Trish,
>
> In the Mooney lab we are working on an enrichment analysis project  
> based on automatic annotations.  As I am sure you are aware we are  
> using BioPortal annotator to get our annotations.  We are currently  
> at the point we would like to download all annotations for our data.  
> I plan on starting this one evening this week.   Before I do this I  
> wanted to see if you know the status of the annotator returning all  
> of the ontologies.   A few weeks ago we ran into the issue of the  
> annotator not returning any SnoMed Ontology data.  And also the cell  
> cycle ontology issue.   Do you know of are any outstanding issue  
> like this.  I just want to make sure we get as much data as possible  
> in the annotation phase.
>
> Thanks
> Emily




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