[Ontology-editors] The True Path Rule

[Midori Harris]

Hi,

On Mon, 15 Jun 2009, Amelia Ireland wrote:

> Hello all,
>
> According to the docs,
>
> the true path rule states that "the pathway from a child term all the way up 
> to its top-level parent(s) must always be true"
>
> (from http://www.geneontology.org/GO.usage.shtml#truePathRule)
>
> To accommodate the new GO relations, this would have to be changed to "the 
> pathway from a child term all the way up to its top-level parent(s) must 
> always be true where the pathway is composed of transitive relations", or 
> something like that. The whole of the TPR documentation is rather out of 
> date, and it's really aimed at people editing the ontology, not curators. I 
> would like to pension it off or put it on the wiki somewhere. Do people have 
> any thoughts?

I think we ought to provide some documentation for users about paths in 
GO, but I'm quite happy not to use the existing True Path Rule page for 
the purpose! Users don't need the "true path" jargon*, nor the historical 
chitin example or the stuff about restructuring. The fact that ontology 
developers try to ensure that all the paths are biologically accurate is 
all I'd retain for users from the true path docs.

What would be valuable to users is something that covers:
- subsumption/is_a completeness
- multiple paths, especially when all relationship types are included
- reasoning over paths, implications of following paths over transitive 
vs. non-transitive relations, that sort of thing
- implying annotations by transitivity

* except possibly in a footnote of the "if you hear a GO person mention 
the 'true path rule', this is what they mean" ilk)

cheers,
m