[go] evidence code ontology

[Larry Hunter]

Given Sue's comment that

> 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.

it seems clear that the relation(s) between such evidence sources and  
the propositions (hypotheses? assertions?) that they inform still need  
to be defined, and that these epistemic relations could be used by the  
GO, phenoscape and others to make more explicit the relationship of  
evidence to their annotations.

Currently, the GO makes instance level assertions about genes having a  
particular molecular function, participating in a particular  
biological process, or being located in a particular cellular  
component, and links each such assertion to an evidence code  
(sometimes specifying the PMID of a publication that contains the  
evidence).  The instance-level relationship ("has function"  
"participates in" "is located in") is implicit, as is the  
(meta-)relationship between the particular instance level relationship  
and the PMID or other source of evidence.

There may well be value in making these implicit relationships more  
explicit, both for automated reasoning, and for making assertions  
about universals.   There are already RO terms (or proposed terms)  
that will make possible explicit instance level statements (e.g.,  
<gene> "participates in" <process>) -- what I am trying to get to is  
the set of relations necessary to make the relationship between such  
statements and the evidence for them explicit.  Since all of the GO  
evidence codes (and apparently the ones used by Karp's xCyc systems)  
are related to literature assertions, I am inclined to make the  
definitions in terms of OBI DENRIEs), but more on that in another email.

Larry



>
> 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
>