AmiGO Phylotrees

Project lead: Seth, Sven

Purpose

Phylogenetic data informs functional inference and provides useful context for viewing GO annotations. PAINT allows annotation in a phylogenetic context, but is currently targeted at curators.

We want to make the PANTHER phylogenetic context visible to a wider community of users. This includes advanced phylogenetic displays as well as traversals across genes in the same family

Background

• PAINT

Deliverables

PAINT Scraper

(Sven)

• pull in pseudo-newick from Panther
• use phylosoft to convert to multiple other formats
• cached in http-accessible directories for now
  • dir stucture: http://SERVER/phylo/TREEID.{phylo-xml,nhx,phylo-json}
  • Seth to spec out optimal JSON structure, Sven to implement
• stored in database later (Schema_Overhaul)

Basic JS Phylo Viewer

"Bad" version up on beta, but will be removed. "Good" version in progress.

Work is in progress on dev machine (nothing public yet, rapidly changing alpha versions). A parser/JSON emitter will be needed before public beta.

Advanced JS Phylo Viewer

More PAINT-like interface.

TODO

The best working TODO list currently resides in the source file [1].

• Links from gene pages: TODO
• Grid view integrated with js phylo view: TODO