Re: [SO-devel] SOFA

[Karen E. <ei...@fr...>]

Dear Payan,
I think what you are referring to is the the fact that between the  
release 2.0 and 2.1, the ontology became 'is_a complete'.
Previous to this, terms like exon were indeed part of transcripts etc  
but they had no is_a relationship to anything. The OBO ontologies  
such as GO are mandated to be is_a complete as it is good ontological  
practice and essential for reasoning and future interoperability.

What is an exon?
Technically it is a region just like a transcript is a region. All we  
did was fill in these relationships, and add in a couple of terms.
A region can be part of another region. Think of it as a substring.
I don't see how this complicates gff3 at all.
Everything in col 3 is a located_sequence_feature, so either a region  
or a junction.

Hope this helps,
--Karen
On Apr 30, 2007, at 9:53 AM, Canaran, Payan wrote:

> Hi,
>
> I'm looking for any documentation on changes from SOFA release 2.0  
> (revision 1.12) to SOFA release 2.1 (revision 1.14)?
>
> I believe additional terms ("transcript_region", "mRNA_region",  
> etc.) that brigde between top-level terms such as "region" have  
> been in this transition. One effect of this seems to be that now  
> some terms have a recursive "is_a" relationship to region. For  
> example, "exon" is_a "region" through "transcript_region" in  
> release 2.1.
>
> This makes interpretation of part_of relationships somewhat tricky  
> from a GFF3 perspective. For example, in release 2.0, exon is  
> part_of a transcript, which is a member_of gene. In release 2.1,  
> exon can still be a part_of (through recursive is_a and part_of  
> relationships) of a gene. However, both exon and gene are "is_a"  
> region through recursive "is_a" relationships. Since they are of  
> the same type of feature, I'm not sure how they can be part of each  
> other.
>
> I might be misinterpreting the relationships. I would very much  
> appreciate any input or pointer to documentation that would help me  
> understand this. Thank you.
>
> Payan
>
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