Manager 7May2014

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David, Rachael, Paul T., Judy, Kimberly, Rama, Chris, Huaiyu, Paul S., Pascale.


GO meeting organization

  • I'll keep people updated as soon as there is more information coming up.

- Pascale

Proposed priorities for GOC working groups

Ontology development

  1. term requests
  2. OWLification
  3. support for LEGO (MF restructuring, …)
  4. begin and end functions for cellular processes
  5. logical definitions for terms that include cell type, anatomy terms
  6. MF and RHEA

Literature annotation

  1. QC metrics for annotations
  2. defining annotation standards, training, documentation
  3. focus on planned PAINT annotation families

Phylogenetic annotation

  1. Jamboree until Barcelona meeting: GO-funded curators should spend GO-funded time on this project through end of Sept.? [5 curators full time for 6 weeks or 20% time for 5-6 curators]= 5-10 families per week
  2. paper on QC assessment using PAINT


  1. Drupal Web Site & AmiGO (Seth needs to move on, Moni + Stanford?)
  2. migrate all remaining cron jobs to Jenkins (Heiko)
  3. LEGO annotation tool prototype release (Seth)
  4. Complete migration of ontology editing to full OWL (protege plug-ins, Heiko, Chris, Simon)
  5. jsPAINT in view-only mode made public (Seth)
  6. jsPAINT roll-out (Seth, Suzi)
  7. mySQL/LEAD retirement (will take a while)
  8. Amazon Cloud for GO website and AmiGO (Mike/Stuart/Seth)
  9. CANTO deployment (Chris, Seth, Kim, Rama)
  10. LEGO mirrors of graphRDF/OWL
  11. GAF-GPAD roundtripping (Mary?)
  12. LEGO/OWL ←→ GPAD converters (Mary?)
  13. Graphic display of enrichment results (Mary?)
  14. Term Genie templates for CL and UBERON (Heiko, Chris)
  15. Paper Viewer release-able (i.e. connected to grid/table annot tool, Owl) [Hans-Michael, Juancarlos, Yuling]
  16. Stabilized enrichment tool (??USC)
  17. GO-mine retirement, unplugging (Stanford)
  18. Getting Textpresso to work with MF (in addition to CCC) [Hans-Michael, Kimberly]
  19. authentication/authorization (software group mutual choice)
  20. Orion/LEGO import from Reactome


  1. Annotation training material on web site
  2. Annotation/help forum

Quarterly GOC conference call

  1. Once a quarter, report on each to the ‘priorities' and ‘next steps’ for each group. We would have two main objectives for each quarter.
  2. Next meeting (teleconference) would be in June.
  3. All GO invited to ‘listen in’, managers, directors, selected others would carry most of reporting and discussion.
Our proposal for first meeting, which necessarily would be a ‘start’.
  • Litrerature Annotation and Corrodination (Rama?)
    • management and coordination and standards
    • Annotation efforts
  • Phylogenetic Annotations (Huaiyu?)
    • management and coordination
    • annotation report
  • Software
    • Web presence
    • annotation and ontology QC and files
    • maintain db and resources


GO meeting organization

Pascale is local host and will send announcement to GOC list.

Proposed priorities for GOC working groups

GO tops have drawn up priorities for each group and would like to implement quarterly reporting to keep track of these. This priority list above is for the year. Comments/suggestions are welcome.

Would ideally have quantitative measures for each priority.

Working groups should go through these and discuss with GO directors about what their priorities are. It's not clear that we have the right balance of people on each project, we can address this by using these priorities and quarterly reporting.

We want to suggest closer contact between phylogenetic and literature annotation and move towards integration of QC, literature, phylogenetic annotation as a cyclic process.

Suggestion to use JIRA to keep track of overall priorities; would be a top-level view of priorities, the details would remain in SourceForge, GitHub, GO help, etc.

The GO PIs should assign people to each task (and timelines) and invite other relevant people to contribute if needed.

Quarterly calls

Twice a year meetings is not enough to track priorities, therefore we should have quarterly calls involving the whole GO Consortium. The first meeting is proposed for June (18th?). The call will last 1.5 hours and each group would have 10 minutes to report progress and aims for next quarter. Would need to be top level priorities rather than details. The focus should be on items that need feedback from the wider GOC.