Re: BioRDF Brainstorming

On Feb 12, 2008, at 8:59 AM, Colin Batchelor wrote:

> How do you propose we cope with hedging, that is "It is not impossible
> that bananas are green", "Taken together, these results would indicate
> that bananas are blue" and so forth?  This is much more common that  
> the
> unwary reader might suspect.

When you say cope with, can I assume that you mean at the  
representation level? (as opposed to the text mining aspect, which is  
harder, I think).

At the representational level, I think there are several choices.

For starters, one could use some scheme like the GO evidence codes,  
and use them in the way we did for the HCLS demo representation of  
gene ontology annotations. The idea is to define a class, then mark  
the class as to whether the claim is that it exists or not, and  
associate with that class an evidence code, which in turn cites a paper.

In this case we could either state that there exist blue bananas, or  
that there doesn't exist bananas that are not blue.

e.g.

"There are no green bananas"
Class(claim1 Complete intersectionOf(banana restriction(has_color  
someValuesFrom(green))))
Class(claim1 Annotation(sc:has_denying_evidence Individual(evidence1)))
Individual(evidence1 type(<some ECO class>) value 
(sc:cites_evidence_source pmid:<this paper's pmid>))

"There are only blue bananas"
Class(claim2 Complete intersectionOf(banana restriction(has_color  
someValuesFrom(complementOf(blue)))))
Class(claim2 Annotation(sc:has_denying_evidence Individual(evidence2)))
Individual(evidence2 type(<some ECO class>) value 
(sc:cites_evidence_source pmid:<this paper's pmid>))

Some further discussion of this at
http://sourceforge.net/tracker/index.php? 
func=detail&aid=1887478&group_id=177891&atid=886178

Evidence code ontology: http://purl.org/obo/owl/ECO
http://purl.org/science/owl/sciencecommons
(note that we currently have sc:has_supporting_evidence, but not  
sc:has_denying_evidence - easy enough to add)

-Alan