Possible paper (Kara)
I was asked to do a write-up on PPOD in for a chapter on inferring evolutionary relationships in Current Protocols in Bioinformatics (www.currentprotocols.com), due November 15.
However, it occurred to me that we could instead use this as a forum for the phylogenetic-based annotation, specifically the Annotation Tracker that we have been working on, which can end up as a really handy portal to this project for the general community (in addition to us using this as an internal tool). To do this, we'd need to:
1) be comfortable rolling this out in production to the general public. This would just require a little clean-up (eg hiding the "Not in DB" fields), and adding some additional info to make it more useful to general users.
2) provide a way for users to query the phylotree pages in a useful way. One idea: from the Gene Product Search Results, we just add a link under the Ref Genome line that links to the correct phylotree page.
Note that, at least at this point, we don't expect this to be the main face of the project, rather it would be at least one hook in for people to explicitly see the phylogenetic-based annotations in one place, can see our progress, etc.