RefGenome11Mar08 Phone Conference (Archived)
Tuesday March 11, 1 PM CDT, 11 AM PDT, 7 PM GMT
Present
Orthology determination
- Kara: update:
Curation tool update
Annotation Quality Control
Action items
[ACTION ITEM]: All: please check and comment new version of the graphs http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/
[ACTION ITEM]: All: Annotation Quality control: Please pick an ortholog set from the Curation Targets table http://spreadsheets.google.com/ccc?key=pwOksMOra5uq4vIYjPgefPw
Enter your name in Column K, and open a new item in the SF tracker http://sourceforge.net/tracker/?group_id=36855&atid=1040173
Contact Suzi if you need to be added to this tracker.
More instructions will follow by email.
Review action items
[ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO [in progress]
- The new loading cycle will incorporate IEAs from everything except GOA/Uniprot. Human is loaded separately.
[ACTION ITEM]: (Amelia): Fix web page where the number of annotations are to give an estimated number of protein-coding genes; problems: unmapped genes; splice variants; etc. Maybe this should also be on the ref genome page. USE count from gp2protein file-- then it's all consistent.
in progress. Amelia had some questions: what should be taken as the correct number, the number of unique IDs in the first column [the db that produced the file], or the number in the second column [the UniProt or NCBI ID]? I just checked with Dan and he says that the mapping may not necessarily be one to one.
- Chris/Judy: that may not be a reliable number anyway. At least for human, the proteome is not well documented.
- best would be total number of gene predictions.
- Judy: look at Sue Rhee's recent paper
Ongoing action items
[ACTION ITEM]: can Mary show the date completed on the index page? Possibly - she will try
[ACTION ITEM]: Chris: generate new report that would show errors that need fixing for the Orthology determination project
[ACTION ITEM]: Chris will provide date on the ISS outliers query so that we dont always review the same annotations.
[ACTION ITEM] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken): Write up recommendations for usage of ISS, IEA, IC
- Started, IEA,_ISS,_IC_Usage_Discussion
- This depends on whether the IEAs can be shown in AmiGO, at least for ref genomes.
[ACTION ITEM]: Mike will set up 'annotation' calls?
[ACTION ITEM]: all: look at Stan's error reports: http://www.geneontology.org/internal-reports/gp2protein/
- not updated since october
Next conference call
Tuesday April 8, 2008, 10 PM CDT, 8 AM PDT, 4 PM GMT
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