[go] evidence code ontology

[Sue Rhee]

Actually I don't agree with the ECO representing evidence types, 
contrary to the name of the ontology and the term names. Perhaps the 
'inferred from' should probably be omitted from term names and the 
ontology renamed as Evidence Source Ontology. In my view, it represents 
types of methods that are used to generate results that are used as 
evidences for an assertion. So eventually I see the leaf nodes of this 
ontology being individual assay types. In this view, the ECO could be 
considered as some sort of meta ontology for the OBI.

Sue

Suzanna Lewis wrote:
> 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
>>>
>>>
>>
>>

-- 
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