Manager 5August2015

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 below; I favor including the taxon ID and corresponding Genus Species or common name, whichever matched the label on the taxon ID:
  • 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 OR gene_association.submittinggroup_taxonid_commonname.gz depending upon single vs multiple species
    • gene_association.goa_9913_Btaurus.gz
    • gene_association.wb_6239_Celegans.gz
    • gene_association.goa_6157_platyhelminthes.gz