RefGenome8Apr08 Phone Conference (Archived): Difference between revisions

Revision as of 12:09, 4 April 2008

Tuesday April 8, 10 AM CDT (8 AM PDT, 4 PM BST)

Present

ACTION ITEMS

1. 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?

2. 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.

3. (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.

4. (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

@@ Line 5: / Line 5: @@
 == 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
+. IN PROGRESS. All: Annotation Quality control: Please pick an ortholog set from the Curation Targets table
 http://spreadsheets.google.com/ccc?key=pwOksMOra5uq4vIYjPgefPw
@@ Line 15: / Line 15: @@
 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]
+. (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.
+.  (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.