Manager 19August2015

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Agenda

GO user survey

  • Any feedback on the latest survey revision? https://www.surveymonkey.com/r/WM93W63
  • Next steps? At the last call it was suggested to send the survey to the SAB ahead of the GOC meeting. Is it ready to go now? Send it to the full go-consortium mailing list too?
    • Opinion: once ready, the survey should be sent to researchers outside the GO lists. Maintaining an inward look could limit the amount of useful feedback we receive. We should include researchers who consume the GO yet are not necessary aware of communications within the consortium. Some examples of target communities outside GOC-lists are: evolutionary biology lists (e.g. evoldir), genomics research communities (e.g. arthropod genomics and manakin genomics community), other curation lists (e.g. ISB).

GAF and gp2protein file Naming Conventions

  • To be discussed at the Consortium meeting in DC
  • Proposal to standardize GAF names to include appropriate NCBI taxon ID and text string to indicate what organism(s) are included in the file
  • Also, remove multiple periods in file names (and include appropriate file extension?)
  • Would like to confirm proposed naming convention before meeting
  • Generic name: lower case submitting group abbreviation from GO.xrf_abbs_NCBI taxon id_NCBI taxon id name.gaf.gz
    • NCBI taxon id name would be the corresponding taxonomic name or lower case genus species name abbreviated as: gspecies
  • Examples:
    • wb_6239_celegans.gaf.gz
    • wb_6157_platyhelminthes.gaf.gz
  • Outstanding issues:
    • Is there an appropriate NCBI taxon ID for all GAF files we currently offer?
    • Will there be an appropriate NCBI taxon ID for all future GAF files, i.e. strain-specific files?
    • Should we continue to use other descriptors like 'ref' or 'noieas' in the file names? Is there another way to indicate this info or organize the downloads page to make it clearer to users what is available? Can/Should we offer more file versions, i.e. a gene-centric file, a transcript-centric file, a proteome-centric file?
  • gp2protein file naming convention
  • Should also standardize how we name gp2protein files
  • Generic name: gp2protein_lower case submitting group abbreviation from GO.xrf_abbs.gz
  • Example:
    • gp2protein_wb.gz
  • Related question - how are isoforms handled in the gp2protein file, e.g., P34708-1 and P34708-2

Software Updates

Review DC Meetings Agenda - What needs to be prepared?

  • Consortium Meeting - agenda; details for arrival
  • Workshop - advertisement; GO-directors: please send message to your contacts in the area, especially NIH researchers.
  • SAB

Minutes

  • In attendance: Paola, Kimberly, Judy, Paul T., Rama, David, Chris, Huaiyu, Suzi, Melanie, Moni

GO user survey

  • Ready to go??
    • Paola incorporated comments from PIs and David
  • When and who should receive the request to fill it out?
    • GO consortium vs GO friends?
    • Send to SAB before the meeting to get their engagement
  • Try out on a few people to get focused feedback - Jane, Val, and a GO user outside the consortium

File Naming Conventions Proposal

  • GAF: wb_6239_celegans.gaf.gz
  • GAF: wb_6157_platyhelminthes.gaf.gz
  • gp2protein files:
    • How generated?
    • How used?
    • Obsolete according to some timeline
    • QofO directory to get mappings
    • AmiGO will need to be re-factored
    • MODs will need to check the mappings and communicate with UniProt to ensure QC
    • What about gpad/gpi?
    • What about GCRP set? - would there be loss if we just used that set?
    • Future plan should also consider ncRNAs (RNACentral mappings).

DC Meeting

  • GO-top will review agenda items
  • Check agendas for consortium meeting - add items, if needed - try to be as focused as possible
  • Workshop - advertise!!
    • Wave fee for students? other participants?
  • SAB - PIs will go over agenda today and ask for material for presenting
  • Need head count from registration to help estimate participants