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[bioontology-support] Exposure Ontology question

Trish Whetzel whetzel at stanford.edu
Thu Jan 12 08:45:36 PST 2012


Hi Carolyn, 

I reviewed the file in OBO-Edit and the tree hierarchy appears the same as in BioPortal, therefore I suspect a newer version has not been uploaded. New versions can be submitted by manually uploading the new ontology file or by providing a URL where the latest version of the ontology is posted when new versions are generated. If a URL is provided, new versions will automatically be uploaded into BioPortal when new ontology versions are available at the specified URL.  

As administrator of the ontology, when you are logged into BioPortal and navigate to the page: http://bioportal.bioontology.org/ontologies/1575 you will see a drop-down menu titled "Administer" with selections to "Submit New Version" and "Edit Ontology Metadata". It looks like your email address may have changed since you first requested your account and if so we can update your account information. 

BioPortal does provide a few mechanisms to collect user feedback on ontologies. There is the Notes feature that can be used to provide general comments on terms and collect term proposals and their discussions. When viewing the ontology hierarchy, there are additional tabs in the right-hand panel, one of which is for Notes (screenshot). Information added as a Note can be accessed through the BioPortal web interface, Notes Web services[1,2] and users can subscribe via email to receive alerts about new Notes.

There is also a feature to collect overall reviews of ontologies. Users can be directed to the ontology summary page [3] and the Reviews section to submit reviews. 

Trish 

[1] http://www.bioontology.org/wiki/index.php/Ontology_Notes 
[2] http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
[3] http://bioportal.bioontology.org/ontologies/1575 





On Jan 12, 2012, at 7:41 AM, Carolyn Mattingly wrote:

> Hi there - you have posted our ontology, ExO. We are currently trying to get a manuscript describing this project published. We have 4 major concept areas (receptor, stressor, exposure and outcome). Although I can download the obo file here: http://bioportal.bioontology.org/ontologies/1575 and find all of the terms - when I click to view the 81 terms on this page:
> http://bioportal.bioontology.org/ontologies
> onlly the stressor an receptor concepts are shown. I'm thinking you may have an older version of the file posted - can I submit a replacement and view it?
> Also - do you have suggestions about how to use your site to invite feedback from the community so that we can make modifications in a version-controlled manner?
> Thanks.
> Carolyn
> 
> 
> __________________________
> Carolyn Mattingly, PhD
> Associate Professor
> North Carolina State University
> Department of Biology
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

Now on Twitter: http://twitter.com/#!/bioontology
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