[go] evidence code ontology

[Helen Parkinson]

On behalf of OBI we'd be very happy to have an interaction with ECO when 
you decide what is the appropriate time and format. OBI developers are 
still working towards a 1.0 release, and after that might be a good 
point in our development process to have this discussion. This is likely 
to be some time in the summer, though a pre 1.0 release will be 
available in March,

thanks

Helen

Sue Rhee wrote:
> 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
>>>>
>>>>
>>>
>>>
>

-- 
Helen Parkinson, PhD
ArrayExpress Production Coordinator,
Microarray Informatics Team, 
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi