RefGenome12Feb08 Phone Conference (Archived)
Tuesday February 12, 10 AM CDT (8 AM PDT, 4 PM BST)
Present
Next Reference Genome Meeting
April 20-21, Salt Lake City
This will be followed by a GO Consortium Meeting on April 22 and 23 in Salt Lake City.
Karen Eilbeck: host
Orthology determination
Kara: update
Curation tool update
Chris, Siddhartha, Seth, Mary, Pascale, David, Doug
Updated graphs
Mary
- I have posted new refG graphs (temporarily) at:
http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/ We will move them to the GO site when refG folks have had a chance to review them (some time next week?)
To simplify comparison of organism annotations (and following Chris' lead on detecting outliers) I have modified the comparison matrix to show only high order GO terms, e.g. PEX1 http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/5189.html#Slim or POLA http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/5422.html#Slim
Please review the graphs and let me know if you notice missing orthologs or annotations -- I am still doing a lot of data editing manually :(
Annotation QC
Review action items
- [ACTION ITEM] Suzi, Pascale, Emily, Val [and others]: Go over the issues relating to quality control. Suzi will email the group, and we will set up a meeting with all those who want to participate.
- [ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO
- [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.
[ACTION ITEM]: DONE: Mary will include IC in the graphs
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]: ADDED TO GOC meeting agenda. Discuss at the GOC meeting whether it would be useful to add the 'comprehensively annotated' tag to all genes, somehow? Either in the gene association file or in the database somehow
[ACTION ITEM]: Mike will set up 'annotation' calls?
[ACTION ITEM]: Mike(pascale) merge two email lists (reference genome and annotation) into 'annotation'
- Should we copy them to the SF tracker?
[ACTION ITEM] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken): Write up recommendations for usage of ISS, IEA, IC: Report by next meeting???
- Started, IEA,_ISS,_IC_Usage_Discussion
[ACTION ITEM]: all: look at Stan's error reports: http://www.geneontology.org/internal-reports/gp2protein/
Next conference call
Tuesday March 11, 2008, 1 PM CDT, 11 AM PDT, 7 PM GMT
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