2014 Barcelona GOC Meeting Agenda

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Day1-Curation and Annotations

Curation paradigms and documentations

  1. With/From field cardinality proposal(Rachael 30-45min) (Decisions: what is the cardinality of the with field for each evidence code? Can we use pipes/commas consistently as we do for extensions? If an 'AND is converted to an 'OR' is this really a weaker statement or a different statement-do we need a 3rd delimiter?)
  2. Annotation extension relationships: how to use them (Ruth)
  3. Discussion of catabolism and biosynthesis (Pascale)
  4. Discussion on 'protein dimerization activity' vs. e.g. 'protein homotetramerization' (MF vs BP). See summary here: http://sourceforge.net/p/geneontology/ontology-requests/11087/ (Paola)

and https://sourceforge.net/p/geneontology/ontology-requests/10909/

  1. Refresher/overview of available TG templates (Jane)
  2. Use of expanded evidence codes and interactions with ECO (Kimberley, with input from others - 15-20 minutes)
    1. Are any groups currently using expanded ECO codes for GO annotation?
    2. Can existing tools (Protein2GO, GO web site, AmiGO) accommodate the codes?
    3. Any reasons not to start using expanded ECO codes? Is turn around time for new ECO term requests sufficent?

Not directly GO related

  1.  Monique Zahn: Quality control process in neXtProt (about 15 minutes)

Common Curation Environment

The objective is to have environment into which all curators can enter data and from which each group can extract data files.

  1. Noctua development (Chris, Seth, Heiko, Suzi?)
    1. LEGO models of annotation extensions (David OS)
  2. Textpresso Central/Capella (Michael Mueller)
  3. Update on Protein2GO, including annotation to IntACT IDs (Tony 15-20mins)


  1. PAINT Jamboree debrief, future directions (Huaiyu, Pascale)
  2.  Autophagy in PAINT: lessons learned (Marc F, Pascale)

Day2-Ontology Development and Priorities

  1. Sourceforge back-log; how to address?
    Sourceforge jamboree worked, but now we are near 300 again
  2. Pilot project to replace NCI thesaurus 'biological process' branch with GO biological process (Chris)
  3. GO and human disease (Chris)
  4. High-level protein family classification (Jane)
    Can we use PRO classes for protein families?
  5. Proposed changes to Molecular Function (Jane)
  6. Progress in moving GO editing and annotation extension relations to OWL. (David OS)
  7. Clarity vs Expressiveness in GO - striking a balance (David OS working on a white paper on this).
  8. Roche/GO project (David OS)

Day3-UserSupport including AmiGO and Enrichment Analysis

  1. GO site/docs development (Moni, Seth)
  2. AmiGO feedback and development (Seth)
  3. GO Help Desk
    1. Adding people to the rota
    2. Assigning the help desk
    3. adding to FAQ
  4. GO Enrichment Analysis (Judy, Paul, others)
    1. report on needs/ improvements in AmiGO tool (Seth, Paul, Rama)
      1. intersection with Panther db often down
    2. Judy working on white paper 'Gene Enrichment Anaysis using the GO: the good, the bad, the ugly.' I will have early draft at meeting.