RefGenome8Apr08 Phone Conference (Archived): Difference between revisions
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== ACTION ITEMS == | == ACTION ITEMS == | ||
# Chris/Emily: figure out secondary IDs problems (many sequences were not loaded because the IDs were secondary). Maybe a script can be generated to map IDs? | # Chris/Emily: figure out secondary IDs problems (many sequences were not loaded because the IDs were secondary). Maybe a script can be generated to map IDs? | ||
# IN PROGRESS. 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. | |||
# (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. | |||
# (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 | |||
== Reference Genome Meeting == | == Reference Genome Meeting == |
Revision as of 12:08, 4 April 2008
Tuesday April 8, 10 AM CDT (8 AM PDT, 4 PM BST)
Present
ACTION ITEMS
- Chris/Emily: figure out secondary IDs problems (many sequences were not loaded because the IDs were secondary). Maybe a script can be generated to map IDs?
- IN PROGRESS. 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.
- (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.
- (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
Reference Genome Meeting
April 20-21, Salt Lake City
- Discuss agenda
SLC_GO_Reference_Genome_Project_Meeting#Draft_Agenda
Orthology determination
- Kara: update:
Curation tool update
- Some requirements are here (David, Doug, Pascale): http://wiki.geneontology.org/index.php/Image:Refgene_Database_V3.ppt
- Chris, Siddhartha, Seth, Mary, Pascale, David, Doug
Annotation Quality Control
- See Annotation_QC