[Phenoscape] Re: [go] evidence code ontology

[Chris Mungall]

On Feb 6, 2008, at 11:05 AM, Larry Hunter wrote:

>
> On Feb 6, 2008, at 10:23 AM, Peter E. Midford wrote:
>
>> The similarity and homology codes recently added to the ECO on  
>> behalf of Phenoscape raise serious issues of contradiction and how  
>> to evaluate multiple types of evidence:  evidence from phylogeny  
>> (IP) might support or contradict an assertion of homology based on  
>> an observable similarity (e.g., IMS).  ...
>>
>> I didn't raise this issue in the Phenoscape discussion of these  
>> terms (directly) because it isn't a reason not to annotate with  
>> these codes, but it will affect how we reason with them.
>
> Peter,
>
> You have hit precisely on why I think it is so important that we  
> come up with a set of relations to describe the situation.  Even in  
> the most basic of assertions regarding biology (e.g. your homology  
> example), it is possible that there be conflicting evidence.  It  
> should surely be possible for our ontological infrastructure to  
> support the formal representation of such situations.

Let's be clear about what you're asking for.

If we have two assertions:

[1] R(X,Y)
[2] R(X,not-Y)

Where assertion [1] is supported by e1, and assertion [2] is  
supported by e2.

e1 and e2, on the surface, contradict one another (this situation is  
actually a bit more subtle than this, it depends on how we treat [1]  
and [2]).

You would like relations such as has_evidence, between the assertion  
and the evidence, and a contradicts relation between evidences that  
is entailed by the assertions?

I agree we should have such relations in RO

> One interesting question, raised indirectly by Matthias Samwald  
> when he said:
>
>> http://www.mail-archive.com/public-semweb-lifesci@w3.org/ 
>> msg02549.html ->
>> scroll down to section "2) What is evidence?", then continue  
>> reading the
>> replies titled 'Evidence'.
>
> And then in that thread's reference to the work of David Schum  
> (e.g. http://www.evidencescience.org/content/Science.doc) which, if  
> nothing else, clearly demonstrates the complexity of the  
> relationship between observations (of various types) and the  
> propositions that they are taken to support or contradict.    
> Although Figure 1 (p. 24) is supposed to be a taxonomy of types of  
> evidence, I find it informative for thinking about what sorts of  
> relationships their might be between observations (of various  
> kinds) and hypotheses.   Schum calls it types of "evidence  
> classified on inferential grounds."  It is the columns in that  
> figure (the "relevance dimension") rather than the rows (the  
> "credibility dimension") that is probably more important to the RO  
> (the latter is really more about legal evidence than scientific, as  
> all scientific evidence is either of the tangible or accepted facts  
> type).  Three distinction are made: directly relevant evidence,  
> which can be linked to the hypothesis by a "defensible chain of  
> reasoning"; circumstantial evidence, which provides "one  
> inferential step... but is always inconclusive;" and indirect  
> evidence, which is "meta-evidence" that "bears upon the strength or  
> weakness of other evidence."
>
> Do you folks think that it is possible to reliably make a  
> distinction between directly relevant evidence and circumstantial  
> evidence based on the content scientific publications?  Is it  
> important to do so?

Interesting. Will have to read this document

> Larry
>
>
>