[go] evidence code ontology

[Suzanna Lewis]

Chris said it much better than I.

I agree fully with this summary.

-S

On Feb 5, 2008, at 4:01 PM, Chris Mungall wrote:

>
> At the moment, ECO isn't very ontology-like. As Larry pointed out,  
> it's more of a terminology of codes with specific instructions on  
> what fields should be filled in the GAF. The adoption of ECO by  
> phenoscape and the extension to homology-based evidence types is a  
> good thing and should hopefully keep ECO general enough for use  
> outside GO. At the same time, ECO has to be guaranteed to fulfill  
> certain GO requirements.
>
> OBI is a massive and impressive effort - but it is still young. Its  
> emphasis is on representing actual experiments and associated  
> entities - rather than codes - which is a good thing. It is  
> certainly the OBO ontology for representing an experiment. But ECO  
> doesn't represent experiments per se - it represents evidence and/or  
> inference, which presents additional challenges.
>
> I would say the evidence group should be actively engaging OBI, we  
> should be trying to define ECO terms using OBI terms where possible.  
> Likewise the OBI group should treat ECO as a set of requirements.  
> And I think we can use OBI to provide a better structure to ECO. But  
> I think it is too soon to talk of immediately subsuming ECO into OBI  
> - sorry Sue, you don't get out of it that easily!!
>
>
>
> On Feb 5, 2008, at 3:40 PM, Sue Rhee wrote:
>
>> Hi GO and Phenoscape colleagues,
>>
>> Larry Hunter pointed me to the OBI project (http://obi.sourceforge.net 
>> ) recently, which I wasn't aware of. It seems to me that the ECO is  
>> redundant to and much less developed than the OBI and I would like  
>> to suggest that OBI take over merging ECO into their ontology.  
>> Please let me know if you have any views on this.
>>
>> Best,
>> Sue
>>
>> -- 
>> Sue Rhee
>> Staff Scientist
>> Carnegie Institution, Department of Plant Biology
>> 260 Panama Street, Stanford, CA 94305
>> Email: (650) 325-1521 x251
>> Fax: (650) 325-6857
>>
>>
>
>