Difference between revisions of "WBConfCall 2014.02.06-Agenda and Minutes"

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== Models schedule ==
 
== Models schedule ==
 
== Generating gene association files that conform to the GAF 2.0 format (Ranjana, Raymond)==
 
== 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 files (GAFs) are generated by Hinxton for GO, phenotype and anatomy data, but they currently don't conform to the [http://www.geneontology.org/GO.format.gaf-2_0.shtml GAF 2.0 format] which is the industry standard, and required for the ontology browser that Raymond and Juancarlos are working on.
 
(Looks like an easy fix, since they seem to be just missing two required columns).
 
(Looks like an easy fix, since they seem to be just missing two required columns).
 +
 +
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)
 
*We need to generate a GAF for gene-disease data (Ranjana and Paul D can talk offline about this)
  
 
= Minutes =
 
= Minutes =

Revision as of 22:01, 5 February 2014

Agenda

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

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.

(Looks like an easy fix, since they seem to be just missing two required columns).

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)

Minutes