[go] evidence code ontology

[Chris Mungall]

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
>
>