I like GFF file format. Plain old ASCII text, human and machine-readable, simple yet full-featured and good BioPerl support.
- The features that I would like to annotate are transmembrane helices (and the loops between them), as predicted using TMHMM. There does not seem to be a “TM helix” feature in the SO, which I think is a rather major omission.
- It’s not clear to me if the SO project is still actively maintained. A lot of their SourceForge pages seem to be slow, broken or not updated for some time. The Term Tracker mechanism for suggesting new terms seems to be non-functional.
If anyone knows the current status of the SO, I’d like to hear about it. I’d also suggest that terms to describe both transmembrane helices and the extramembrane regions connected to them would be rather useful.