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

Natasha Noy noy at stanford.edu
Tue Sep 29 16:26:06 PDT 2009


And another option is using Protege OWL with a database backend: if  
you edit the ontology in the graphical user interface (either in a  
Protege desktop client or WebProtege), the memory footprint is pretty  
small, since Protege loads only the information necessary to support  
whatever it is you are viewing at the time.

If you give us more details about the way you plan to use an OWL  
editor, we can give you some suggestions on the appropriate  
configuration.

Natasha


On Sep 28, 2009, at 5:41 PM, Trish Whetzel wrote:

> 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 (http://protegewiki.stanford.edu/index.php/WebProtege 
> ) to edit the ontology content or the BioPortal REST web services to  
> access the ontology content  (http://www.bioontology.org/wiki/index.php/BioPortal_REST_services 
> ). Do these options meet your needs?
>
> Trish
>
>
> On Sep 28, 2009, at 3:02 AM, Davis, Neil wrote:
>
>>
>> Dear bio-ontology.org,
>>
>> 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 stanford.edu
> http://www.bioontology.org
>
>
>
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