12 JAN 2010 RefGen Phone Conference (Archived)
- 1 Present
- 2 Jan/Feb curation targets
- 3 Incorporating new protein family annotations via GAF files
- 4 Next electronic annotation jamboree: Monday the 22nd of February.
- 5 GO nuts
- 6 Reference Genome Annotation Camp
- 7 Lung development curation targets
- 8 PAINT update
- 9 PPOD update
- 10 GO mirror
- 11 Advertising ref genome
- GOA: Emily
- BHF-UCL: Varsha, Ruth
- MGI: Li, Mary, Judy, David
- RGD: Stan
- dictyBase: Pascale, Petra
- TAIR: Tanya, Donghui
- SGD: Julie
- Ecoli: Jim (arrived late)
- PPOD: Mike, Kara
Jan/Feb curation targets
The January curation targets will be available by the end of the week. Because of the delay, and because we have an annotation jamboree in February, there wont be any targets next months (other than the two jamboree targets, SLIT2 and NIPBL).
Incorporating new protein family annotations via GAF files
Survey_Handling_PAINT-generated_GAF results are available.
Next electronic annotation jamboree: Monday the 22nd of February.
- The curation call will, as usual, take place at 11am EST, 10 AM CST, 8am PST, 4pm GMT and last a maximum of 2 hours
- Curation targets are SLIT2 and NIPBL
There has been several improvements : search columns, etc
Reference Genome Annotation Camp
There will be a Reference Genome Annotation Camp in Geneva from June 14-18. Emily, Serenella and I are working on the agenda.
Lung development curation targets
- Judy says they now have enough targets; we should starting doing the inferences soon.
- wiki Curation tracking: Reference_Genome_Annotation_Project#Lung_Development_related_Gene_Annotation_Progress
- To do:
- First pass curation (all MODs)
[ACTION ITEM]: Li : check curation status of December genes to make a plan as to when we can do all those steps.
- Inferences (Kara, Mike, Pascale, Paul)
- Verification: MGI curators, outside experts + MODs
- We'll add notes field that will become the reference for each family annotation.
- We'll add a 'grid' view of the annotations versus the proteins, to give an overview of the annotations
This should be ready to demo by next meeting (Feb 9th)
We did a new run on the 12 Reference Genome protein sets using a new version of OrthoMCL. These results are viewable on the web. In addition, we ran OrthoMCL on all 48 PANTHER species for incorporation into PAINT; currently, these data are only available for bulk download because we have not yet scaled our web interface to handle the much larger families.
Note that the PPOD IDs have changed from previous versions. Kara is working on having all the information re-mapped in the google spreadsheets by the next Ref Genome call.
- Princeton has set up a GO mirror
Advertising ref genome
[ACTION ITEM?]* Ruth suggests creating a logo from which the MODs could link to the GO ref genome page.
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