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[bioontology-support] [bioontology-info] OBO-In-OWL pragmatics

Trish Whetzel whetzel at
Mon Sep 28 17:41:45 PDT 2009

Hi Neil,

Can you expand on how you would work with the ontology? For example,  
would your work involve adding new terms specific for your needs or is  
the work related to accessing and using the term to annotate data? Two  
ideas that come to mind are using Web Protege ( 
) to edit the ontology content or the BioPortal REST web services to  
access the ontology content  ( 
). Do these options meet your needs?


On Sep 28, 2009, at 3:02 AM, Davis, Neil wrote:

> Dear,
> I’m currently working on a project using OBO based biomedical  
> ontologies. This pretty much limits us to using the OBO-Edit tool  
> which has been problematic in some cases. The idea of moving to OWL  
> has some appeal in terms of greater scope of tools and using a web  
> standard rather than a non-standard-standard. However I have come  
> across the big problem that on a 32-bit machine the OWL version of  
> the disease ontology - one of the smaller ontologies we work with -  
> won’t open in a JAVA based editor because of the memory limitations  
> (1.86GB if memory serves). As it appears that pretty much every OWL  
> editor out there is JAVA based this somewhat limits the utility of  
> the OWL translation. Do you, or anyone you know of, plan on  
> addressing this and bringing out a non JAVA based editor so that the  
> large biomedical ontologies can actually be opened and worked with.
> Thanks in advance
> Neil
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at

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