RefGenome11Mar08 Phone Conference (Archived): Difference between revisions

Revision as of 20:01, 10 March 2008

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 March 11, 2008, 1 PM CDT, 11 AM PDT, 7 PM GMT

Return to Reference_Genome_Annotation_Project

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 ==Review action items==
-[ACTION ITEM] Suzi, Pascale, Emily, Val [and others]: [in progress] Go over the issues relating to quality control. We have set up a SF tracker where each curator will examine an ortholog set and comment on whether it's completely curates, and what problems they might find in the annotations.
 [ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO [in progress]
@@ Line 38: / Line 37: @@
 * best would be total number of gene predictions.
 * Judy: look at Sue Rhee's recent paper
-[ACTION ITEM]: DONE: Mary will include IC in the graphs
-[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]: REJECTED. The two lists do not have that much overlap. Mike (pascale) merge two email lists (reference genome and annotation) into  'annotation'
 ==Ongoing action items==