Reference Genome November 2009 (Archived)
PAINT update: Vbeta15
1. You can now enter and save your comments/evidence for the annotations. This is the feature Pascale, Paul and I discussed. It is nothing more than a simple text box, but cutting and pasting works so you can enter URLs and the things you used as background information.
2. In order to make this work you need to be able to save the evidence separate from the GAF and so while I was at it I simply added the ability to save a complete session (tree, gene data, msa, gaf, and evidence). These are stored as a suite of files with an additional xml file as an index to the individual files. This means that you can completely restore a session, although you'll still need a connection for getting the GO term file and the most current GO annotations. But it does round trip
The file menu now works as follows: "Open from database ..." just as it did before, loads the family from the panther db and the go annotations too "Open from files ... " restores tree, gene data, msa, gaf, and evidence from the local file system "Save annotations ... " records tree, gene data, msa, gaf, and evidence to the local file system "Restore annotations ... " this is to be used in conjunction with the open from db option. it lets you first retrieve the tree from the panther db and then overlay your existing locally saved gaf+evidence onto that tree. "Export ..." saves a stripped down version of the GAF to the local file system. these are the files that can be delivered to the mods.
3. Appearance, The color scheme was getting far too overloaded so I tried to simplify it. Here is how it now works: Shapes are used to indicate the state/type of node speciation nodes: circles (as before) duplication nodes: squares rerooted: triangle (as before) collapsed: vertical rectangle subfamily: diamond (as before)
selection is now "pink", no stars, just lines.
Colors are strictly reserved for "painting", as you add more annotation the nodes become more colored (it starts out just black&white with a sprinkling of deep red) Deep red: experimental annotations for the node/gene yellow-orange: direct annotation added by one of you Dark blue: inferred annotation
I'd like to add a color picker (Ed?) so that for each of the above you can pick a color to suit yourself. (same for selection). Your own paintbox as it were. One thing this doesn't really deal with is "completeness", but I think that will come out of the next feature the paint-by-numbers table (where you "color" in the squares).
This survey was done to assess how every participating database was handling GAF files and to see how the PAINT annotations would be integrated. (November 2009)
Meeting in Berkeley: Pascale spent the week of Nov 16-20 in Berkeley; Paul spent a day Thursday 19th
We discussed feature requests for PAINT (some of which are implemented, see above).
Lung Development Genes: December Targets
- Targets are here: http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en