Manager 5August2015

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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. I propose a version including the taxon ID and a name that matches the label associated with the taxon ID:
    • gene_association.submittinggroup_taxonid_gspecies.gz
    • gene_association.submittinggroup_taxonid_classificationname.gz
      • gene_association.goa_9913_btaurus.gz
      • gene_association.wb_6239_celegans.gz
      • gene_association.wb_6231_nematoda.gz
      • gene_association.wb_6157_platyhelminthes.gz
  • Other suggestions?
  • Does this work for strain-specific files?
  • What about files like the 'noieas' file that UniProt submits?
  • Corresponding identifier mapping files would stay the same, e.g., gp2protein.wb?

Symposium day in Washington DC

  • Donna Slonim has agreed to give a talk and we are currently waiting an update from Trey Ideker.
  • There is not a tentative count for participants, and the symposium has not yet been announced outside the GOC lists.
  • Will there be time for side meetings?

Agenda for main GOC meeting

GO user survey

Please let Paola know if you have any feedback.

Trello board


GAF Naming Conventions - Standardization? (Kimberly)

  • Keep taxon id with file name.
    • Rama: is the taxon ID for a specific strain/Ref.proteome or the generic taxon id for the species?
    • should ref.proteome be part of the file name?
    • Rama: while we are renaming files we should rename the GOA files too. For e.g. the file name with 'noiea' may not mean much to users
    • Chris: regarding the format of the file name, the period should be used only to separate the file extension. Rest of the file name should have underscore. Don't mix periods and underscore.
    • We should also rename the gp2protein files to parallel this new convention
  • Kimberly will present a proposal at the GOC meeting

GOC meeting

  • Trey is looking to reschedule his flight.
  • We haven't planned any side meetings so far
  • Chris: Noctua presentation is appropriate for symposium day
    • Rama: Aren't we going to talk about Noctua in the main GOC meeting?
    • Chris: will give an overview of the system etc at the symposium and do the detailed discussion at GOC meeting
  • Moni-Workshop can imply that we are planning to do something hands-on. So change the name.
  • Ruth is doing Synapse training. Check with her to see if she can present an overview of the project (Annotating new areas in biology)
  • Melanie and Moni will come up with a schedule for the Symposium day and assign people for presentations. They will include Noctua, Synapse as topics.


  • PIs will discuss and get back to Paola on when the survey should be sent out
  • Rama: should we send the survey to the SAB ahead of time (rather than showing it at the meeting) to get their feedback? Yes.
  • Moni- the progress bar moves very slowly, can we put more questions on one page?