Manager 20Aug2014

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On call

Judy, Suzi, Chris, Rama, Pascale, Kimberly, David, Paul T.


Trello board

GOC meeting Barcelona

  • People should add items to the wiki

Conf. Call with Phil Bourne (NIH)

NAR Paper

  • Judy reminder about upcoming database issue
  • Moni and Harold are working on a draft
  • Aiming for September 15th deadline, but will likely need a little more time
  • Paper focuses on updates and enhancements to the project, also provides overall summary with key info (e.g., contact)

SourceForge Clearance Jamboree

  • Resolved a number of outstanding SourceForge tickets - Paola is compiling the numbers
  • By end of week, hopefully all of Val's outstanding tickets will also be resolved

Overhaul of Molecular Function

  • Ontology editors looked at the proposal and liked much of the proposed changes
  • Where would the MF overhaul fit in with ontology development priorities?
  • Would be good to have more people trained in ontology development
  • Also testing out web Protege - a more long term goal

Other Areas of Ontology Development

  • Working on Uberon developmental process, perhaps a bigger scope
  • Cell cycle - Jane continues to work on this
  • New terms - TermGenie
  • New terms - SourceForge
  • For SourceForge, may be necessary to move on from items if submitter doesn't respond to follow-up questions
  • Areas where there is poor representation in the ontology, or ontology is confusing - these can be more major projects
  • ACTION ITEM - need to start triaging items, but still need to discuss adding more resources to ontology development
  • Major items could get their own Trello cards (with sub-items, if needed)
  • As an example, the ubiquitination project has now become much larger, now encompasses other small protein transferases (e.g., SUMOylation, NEDDylation) - now a Trello card for this
  • Bring in more experts to help?


  • Chris - new release of Noctua
  • Most visible change is user login
  • Also Noctua annotations are loading into the dev version of AmiGO (will give demo at Barcelona)
  • This is very useful as we get more models; curators can search for annotations in dev version of AmiGO
  • Chris will contact

Text Mining

  • Yuling is training an enzymatic activity document classifier (SVM)
  • Will investigate feasibility of SVM on PMC corpus for prioritizing papers based on data type

Annotation Advocacy

  • Moving to Jenkins - progressing
  • Moni is working with Rachael and Rama on documentation for submitting annotations
  • Annotation extensions - ongoing education; every annotation call things come up, are discussed, and documentation is revised as needed
  • Annotation metrics - any work done on auto-generating reports?
  • Numbers are available on website; but should we also be measuring and reporting information content?
  • Can we tap into software support from other members to help with this?
  • Include GAF errors

Phylogenetic-based Annotation

  • Had in-person component of the tree annotation jamboree
  • Went well, got lots of trees annotated, talked about metrics
  • Still need to have annotations committed, though
  • ACTION ITEM - Need to initiate the Monday Google hangout
  • ACTION ITEM - Remove large-scale experiments from display in PAINT, add to next PAINT call agenda

Outreach and Usability

  • NAR paper in the works
  • Documentation updating


  • Still working on RDF representation of GO
  • TermGenie paper is out