RefGenome8Apr08 Phone Conference (Archived): Difference between revisions

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Victoria RGD<br>
Victoria RGD<br>
Ranjana wormbase<br>
Ranjana wormbase<br>
Kimberly WormBase<br>


==Webex==
==Webex==

Revision as of 11:13, 8 April 2008

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

Present

Pascale dictyBase
Emily EBI
Rachael EBI
Chris NCBO
Val pombe
Stacia SGD
Doug zfin
Seth BBOP
Victoria RGD
Ranjana wormbase
Kimberly WormBase

Webex

Try WebEx "raise hand" feature for next conf call.

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. Fix problems in annotations and graphs pointed out in the SF "ref genome completion set" tracker.

4. (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.

5. (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

6. Annotation summary Graphs:

a. Show the date completed on the index page of the graphs

b. Distinguish 'not yet annotated' from 'no ortholog' in the graphs

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

Annotation Pipeline document

Please have a look: Annotation_pipeline


Annotation Quality Control

  1. HPRT1 (Emily)
  2. GRIN1 (Donghui)