Re: [SO-devel] SOFA

[Payan C. <ca...@cs...>]

Hi Karen,

Thanks for the info. Yes, this clarifies it. My question was in relation
to column 9 (ID and Parent relationships) rather than column 3. For each
term I walk up the tree towards the top using is_a, part_of and
member_of relationships, identify parents (for ID-Parent relationships)
and also determine features that have a "is_a" relationship with the
parents. 

Since, the only change is addition of "is_a" relationships from each
node to the top-level node, I can simply disregard is_a relationships
from top-level nodes when calculating parent-child pairs for use in
column 9.

Regards,

Payan

On Mon, 2007-04-30 at 11:11 -0600, Karen Eilbeck wrote:
> 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
> >
> > ---------------------------------------------------------------------- 
> > ---
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > SOng-devel mailing list
> > SOn...@li...
> > https://lists.sourceforge.net/lists/listinfo/song-devel
> >
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> SOng-devel mailing list
> SOn...@li...
> https://lists.sourceforge.net/lists/listinfo/song-devel