RefGenome8Jul08 Phone Conference (Archived): Difference between revisions
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[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs. | [Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs. | ||
[Action item]: Discuss use of binding/regulation terms (GOC meeting) | [Action item]: Discuss use of binding/regulation terms (GOC meeting) | ||
==Electronic jamboree== | |||
==PPOD update== | ==PPOD update== |
Revision as of 14:05, 8 July 2008
Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST
Present
- Pascale dictyBase
- Kimberly wormbase
- Ranjana wormbase
- Kara ppod
- Mike SGD
- Ruth
- Tanya TAIR
- Donghui TAIR
- Emily GOA
- Petra dictybase
- Jim Hu
- Seth
- Victoria RGD
- Susan flybase
Review old/ongoing action items
DONE:
- Seth: send URL sometime to the prototype of the ortholog tool this week (will do!)
- [Action item]: MGI: verify GRIN1 annotation binding/complex
Ongoing:
- All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1]
see also Annotation_QC for some general documentation and previous issues
- All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.
- All (ongoing): Develop annotation SOPs
There are some wiki pages about that on the ref genome main page's annotation section: Reference_Genome_Annotation_Project#Gene_Annotation
[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs. [Action item]: Discuss use of binding/regulation terms (GOC meeting)
Electronic jamboree
PPOD update
Our programmer is back from leave and will be rolling out several new features to the PPOD web interface as soon as tomorrow.
I need to check in with Paul to see where they are, and whether we should start a new OrthoMCL and Jaccard run from the gp2protein/fasta files that he has used for PANTHER analysis.
Software
Source Forge QC discussion
General points
- From TNNT2
- see also RefGenome11Mar08_Phone_Conference#2._TNNT2 March 2008 discussion; not sure of the resolution.
discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading: from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog?
- (Pascale: Note that Kara's ortho MCL analysis puts 'up' with TNNT2)
ACVR1B
Ranjana [[2]]
EIF2B2
Stacia [[3]]
Next conference call
Tuesday August 12, 2008, 10 AM CDT (8 AM PDT, 4 PM BST)
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