9 MAR 2010 RefGen Phone Conference (Archived)

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  • GOA:
  • BHF-UCL: Ruth, Varsha
  • MGI: Li, Mary
  • RGD: Stan
  • Flybase: Susan
  • dictyBase: Pascale
  • TAIR:
  • AgBase: Lakshmi Pillai
  • SGD: Rama, Julie
  • pombe
  • Ecoli:
  • Wormbase: Ranjana Kishore, Kimberly Van Auken
  • ZFIN:
  • PPOD: Kara
  • Berkeley: Suzi, Seth

Action items - ALL

  1. Please fill the wiki pages for curation progress of lung targets (9_MAR_2010_RefGen_Phone_Conference#Lung_targets:_progress)
  2. Please add yourself to the working groups for the GO annotation camp (2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed)

Lung targets: progress

Li Ni: Please continue to fill wiki page for curation progress: Note that high priority genes are in red.

Next targets: heart development

Varsha Khodiyar, UCL

GO annotation camp

  • Please fill the attendees list of you already know whether you can attend or not. We'd like at least one person from each group to participate. the goal is to finalize annotation guidelines on several topics and we'd like all groups to participate in discussions and be aware of the finalized guidelines.
  • Focused annotation topics:
  1. Use of regulation
  2. Process beginning/end: Downstream effects /response to
  3. Binding and complexes
    1. Binding documentation
    2. Annotation of complexes

Please add yourself to the working group(s) you would like to be part of. So far everyone who voted for a topic is part of that group. This may be too many groups for everyone and too many members per group.

Ref.Genome in AmiGO

http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search Seth has implemented some enhancements. Check it out.

  • Example query: top and homolset:yes

Ref genome progress report for April 2010 SAB


Please suggest edits if appropriate.

Annotation status reporting tool : progress


Sven Heinicke (developer at Princeton) is working through ID mapping issues:

of the 339448 proteins in the seq2pthr.gz file:

61123 exist in the gene_product table 5126 have entries in the dbxref table but not the gene_product table 273199 new rows in the dbxref table (and gene_product) will have to be created

the script to load these missing rows into the go database has been run.

Sven has just started to work on the web interface and is aiming to send something very simple around toward the end of the week.

Back to Ref Genomes Conference_Calls