8 JUN 2010 RefGen Phone Conference (Archived)

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Present

  • GOA: Emily, Yasmin
  • BHF-UCL: Ruth, Varsha
  • MGI:
  • RGD: Stan
  • Flybase:
  • dictyBase: Pascale
  • TAIR:
  • AgBase: Lakshmi
  • SGD: Rama, Julie
  • pombe
  • Ecoli:
  • Wormbase: Kimberly Van Auken, Ranjana Kishore
  • ZFIN:
  • PPOD: Mike

Preparation of GO camp

  • Progress by each working group - 5-10 minute summary
  1. Regulation : Jane Lomax and Kimberly VanAuken (2010_GO_camp_Use_of_Regulation_issues)
    • IMP experiments can be misinterpreted as regulation (because of the definition of regulation)
    • Ontology needs to improve beginning and end points of pathways
    • Older annotations sometimes need to be checked and removed
  2. Downstream events: Rachael Huntley and Varsha Khodiyar (Wiki Page: 2010_GO_camp_downstream_effect)
  3. Protein binding: Ruth Lovering and Ursula Hinz ( Wiki Page: 2010_GO_camp_binding_documentation_issues
  4. Protein complexes: Pascale Gaudet and Bernd Roechert (Wiki page: 2010_GO_camp_Annotation_of_complexes_issues)
  5. Response to : Rebecca Foulger and Pascale Gaudet (Wiki Page: 2010_GO-camp_Response_to_terms_issues)
    • The documentation needs to distinguish between 'mediators' of the response and 'targets' of the response.
    • Annotations to high level terms should be removed
  6. Annotation Propagation: Alan Bridge and Paul Thomas (Wiki Page: 2010_GO_camp_Annotation_propagation_rules)
  7. HTP: Rama Balakrishnan (Wiki page: 2010_GO_camp_Annotation_of_HTP_data)
    • Read SGD guidelines on the above wiki page
    • Propose to use extended evidence codes 'reviewed' - ' unreviewed'

PAINT-generated GAF file

Samples are avilable for download here:

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/paint/

ACTION ITEMS: Software/PAINT groups to look into the following points brought up by curators:

  • Issue (Doug): many IDs in the 'with' column - this creates a display problem
  • Issue: (Ranjana, Doug): hard to manage downloading all the individual families; especially once we'll have many families
  • Databases must make sure that they accept and display annotations here data_source =ref genome
  • Where will the reference be displayed from?
  • For the cvs repository: it would be helpful if there was a file that would contain ALL annotations (not just by family) with only the 12 MODs
  • GO ref genome xref description should be expanded on the webpage.
  • Need to also confirm that ref_genome is the correct string for this column.