2014 Barcelona GOC Meeting Agenda

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Daily schedule

  • Start: 9 AM
  • Morning coffee break: 10:30 to 11:00
  • Lunch: 13:00 + break until 16:00
  • Afternoon session: 16:00 to 20:00


Coffee and snacks will be served at 16:00

We will be updating the trello board as we go.

  • Please ensure that all outstanding items from the trello board are covered here in the agenda under the appropriate heading.

We realize the midday break is long. This was done for two reasons. First because all three days are quite full we wanted to give people some opportunity to walk about the city, and second because dinner in Barcelona is usually quite late and this puts us on the local schedule. We can discuss further on Monday morning if anyone feels strongly there is a need to change this approach. Bear in mind that whatever is decided we still require three full working days.

Monday 13 October

User support and interaction

  1. Site content (Moni)
    • GO site/docs development. (Moni, Seth) trello
      • Review list of missing website content, ACTION: get volunteers to complete each missing item
      • Video tutorials, ACTION: discuss suggestions for other tutorials
    • Google analytics (trello) (Seth/Rama)
  2. AmiGO feedback and development (Seth)
  3. Infrastructure improvements (Seth)
    • Shared QuickGO graphics
    • Migration of all cron jobs to Jenkins - status
    • RHEA pipeline - no change
    • mySQL retirement (Chris)
    • Cloud deployment (trello)
    • Golr refactoring (trello)
  4. Public consumption of GO content
    • Linked data version of GO. trello (Chris)
    • Other
      • What types of files can/should we provide?
      • How should we distribute annotations to protein complexes and/or other entities, e.g. ncRNAs?
    • Improving documentation
      • ontology downloads
      • documentation on annotations needs to be more user-friendly
  5. GO Help Desk (trello)
    • Adding people to the rota
    • Assigning the help desk
    • adding to FAQ
  6. Public submission of annotations (trello)
    • Documentation reviewed (Moni)
    • Users able to syntactically validate submissions online (Heiko)
    • CANTO deployment
    • Preparation for synapse meeting at Stanley Institute
      • Who will go, use of Noctua, ease of submission, etc.
  7. GO Enrichment Analysis (Judy, Paul, Chris, Suzi)
    • Summary of discussion on mail list - ppt (Chris)
    • report on needs/ improvements in AmiGO tool (Seth, Paul)
      • intersection with Panther db often down
    • What are the right tools/algorithms to use for different types of input data?
      • E.g. microarray vs RNA-seq; dealing with bias
    • Benchmarking data sets
    • ISMB Workshop
      • Judy working on white paper 'Gene Enrichment Analysis using the GO: the good, the bad, the ugly.' I will have early draft at meeting.

Tuesday 14 October

Phylogenetic Annotation

  1. PAINT curation updates, analysis and Jamboree debrief (Huaiyu, Pascale, 30')
  2. Autophagy in PAINT: lessons learned (Marc F, Pascale)
  3. Annotations, including NOTs, to isoforms; different functions for isoforms (Karen remotely? [could this be done 2 pm or later if both Karen and Darren Natale are to call in] Judy/David can present)
    • can we identify these from annotation files? do we exclude these genes from PAINT curation?
  4. Family tree quality assessment/improvement with curated orthologs from PomBase & ZFIN (Paul)
  5. Jenkins running of PAINT GAF file updates (Suzi)
  6. jsPaint status

Literature Annotation

  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 30-45 min)
  3. Cross-species entries in Annotation Extensions - is there any value in this information for GO? (Re-visiting an earlier discussion we had about this in Cambridge, 2013.) (Kimberly 15-20 min)
  4. Use of expanded evidence codes and interactions with ECO (Kimberley, with input from others - 15-20 minutes)
    • Are any groups currently using expanded ECO codes for GO annotation?
    • Can existing tools (Protein2GO, GO web site, AmiGO) accommodate the codes?
    • Any reasons not to start using expanded ECO codes? Is turn around time for new ECO term requests sufficent?
  5. Discussion of catabolism and biosynthesis (Pascale)
  6. Discussion on 'protein dimerization activity' vs. e.g. 'protein homotetramerization' (MF vs BP).
  7. Refresher/overview of available TG templates (Jane)
  8. GO annotations for IntAct complexes
  9. Capturing assays in a controlled fashion - example, rubidium assays - SF11241 and ontology meeting agenda 2014-10-09
  10. Annotation QA
    • Jenkins GAF QC checks and inferences (Heiko, Rama)
    • Monique Zahn: Quality control process in neXtProt (about 15 minutes)
    • Val's annotation matrix


Wednesday 15 October

Common Curation Environment and LEGO annotations

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)
    • Progress Report and Timeline for releases and annotation usage - [1] (Chris/Suzi)
    • LEGO Specification - an updated version. (TENTATIVE - pending discussions Huaiyu, 20')
    • LEGO models of annotation extensions (David OS)
    • BioPax imports
      • Reactome import progress (trello)
    • Export to legacy formats (trello) http://build.berkeleybop.org/job/export-lego-to-legacy/
      • Translation scripts (GAF<-->GPAD, LEGO/OWL<-->GAF/GPAD)
  2. Textpresso Central/Capella (Michael Mueller)
  3. Update on Protein2GO, including annotation to IntACT IDs (Tony 15-20mins)

Ontology Production and R&D

  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 doc (Chris)
  3. GO and human disease (Chris) <-- this now incorporated into GO-analysis section
  4. High-level protein family classification and application to annotation deepening (trello) (Jane)
  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)
  9. inference of 'part_of' relationships (Chris)