[Ontology-editors] The True Path Rule

[Jennifer Deegan (nee Clark)]

Hi Amelia,

I would quite like the true path rule to stay there for users but I 
would really like to see it better explained. Saying that the 'path must 
always be true' doesn't actually mean anything. I think it is much 
better for users if we expand on this by saying something like:

=========================

"If a gene product is annotated to a given process term then that 
annotation states that the gene product is involved in that process. 
Terms in the ontology inherit the qualities of the parent terms through 
relationships. Looking at our annotation of a gene product to a given 
process term, we can infer that the gene product is also involved in all 
of the processes described by the ancestor terms of the process term to 
which the direct annotation was made. For example:

In the graph below, if we make an annotation to say that a gene product 
is in involved in neuron differentiation, then we can infer from the 
graph that the gene product is also involved in the more general process 
of cell differentation. We can also infer that this gene product is 
involved in some unknown developmental process.

[i]Developmental process
---[i]cell differentiation
------[i]neuron differentiation

The consequence if this heritability is that when annotating gene 
products, or creating a new graph structure, we must check the path all 
the way to the root to be sure that the rules of inheritance hold. 
However, this rigorous checking of inheritance also allows users to make 
useful inferences about the activities of gene products. See [slim 
documentation]"

==================================

I think that could be explained better in simpler language, but do you 
see what I'm getting at? I think "true path" is technical jargon that is 
not currently well explained.

Right now I am involved in a long thread with a user who does not 
understand the true path and so having good documentation would be very 
helpful.

Thanks,

Jen







"

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?
> 
> Cheers,
> Amelia.
> 
> -- 
> Amelia Ireland
> GO Editorial Office
> http://www.berkeleybop.org || http://www.ebi.ac.uk
> BBOP Plant Project: http://bbopgarden.blogspot.com
> 
> 
> 
> 
> 
> 
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