[SO-devel] SOFA

[Canaran, P. <ca...@cs...>]

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)?=20

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.=20

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.=20

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