WBConfCall 2014.02.06-Agenda and Minutes

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New WormBase team member

Plans for WS243

  • Topic curation for WS243 & WS244: Repsonse to Pathogens, Signaling in Innate Immunity
    • Take papers and genes from two WormBook chapters:
  1. Interactions with microbial pathogens (2005) - Creg Darby
  2. Signaling in the immune response (2006) - Jonathan J. Ewbank

Upcoming Species

  • Necator americanus <= WS242
  • Pristionchus exspectatus
  • Pristionchus pacificus <= waiting for ENA submission
  • Romanomermis culicivorax <= ParaSite
  • Trichuris suis
  • Meloidogyne incognita

Models schedule

  • Decide on WS243 upload date (Friday)
  • Models Tagging -2 weeks
  • Models proposal deadline -3 weeks

Not tied to a call.

Generating gene association files that conform to the GAF 2.0 format (Ranjana, Raymond)

  • Gene association files (GAFs) are generated by Hinxton for GO, phenotype and anatomy data, but they currently don't conform to the GAF 2.0 format which is the industry standard, and required for the ontology browser that Raymond and Juancarlos are working on.

gene_association         all good
anatomy_association column 6  => "WB_REF:WBPaperDDDDDDDDD"
                    column 9  => leave empty, no aspect choice for our anatomy ontology.
                    column 12 => "gene"
                    column 13 => "taxon:DDDD"
phenotype_association    same as anatomy
  • We need to generate a GAF for gene-disease data (Ranjana and Paul D can talk offline about this)