Manager 5August2015

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Agenda

GAF Naming Conventions - Standardization? (Kimberly)

  • As mentioned a few weeks ago, WB and WB-ParaSite are preparing to start submitting additional GAFs for other nematode species and for platyhelminthes.
  • We need to decide on appropriate file names for these GAFs.
  • Looking at examples of what is currently submitted by groups that submit multiple files:
    • gene_association.GeneDB_Lmajor.gz
    • gene_association.PAMGO_Atumefaciens.gz
    • gene_association.goa_chicken.gz
    • gene_association.goa_ref_cow.gz
    • gene_association.goa_uniprot_noiea.gz
  • Wondering if we could come up with standardized naming for GAFs. In practice we could perhaps create a decision tree based on content of the file, i.e. single vs. multiple species? I haven't yet tried to address content, like noiea. Some possibilities with an attempt at case-sensitivity:
    • gene_association.submittinggroup_Gspecies.gz where submitting group is all lower case and G = Genus (wouldn't cover all GAFs, though)
      • gene_association.genedb_Lmajor.gz
      • gene_association.wb_Celegans.gz
    • gene_association.submittinggroup_commonname.gz where common name would be the commonly used name of the highest level of taxonomic classification in the file
      • gene_association.goa_cow.gz
      • gene_association.wb_platyhelminthes.gz
    • gene_association.submittinggroup_taxonid.gz
      • gene_association.goa_9913.gz where 9913 = Bos taurus
      • gene_association.wb.6231.gz where 6231 = Nematoda
    • gene_association.submittinggroup_taxonid_Gspecies.gz
      • gene_association.goa_9913_Btaurus.gz
      • gene_association.wb_6239_Celegans.gz
    • gene_association.submittinggroup_taxonid_commonname.gz
      • gene_association.goa_9913_cow.gz
      • gene_association.goa_6157_platyhelminthes.gz

Minutes