2012 GOC Meeting Caltech

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2012 Caltech GOC Meeting Logistics

Biological relevance - Paul S - Sunday 10:30

  • GO as a biological reference (critique?)
    • Biological utility survey (Rama, Ranjana)
    • Strategy for prioritization of ontology development topics (Paul)
      • Emily summation of needed areas aka textbook
      • Information content approach
  • Objectives for this meeting
    • set quarterly objectives process

Web - Cherry - Sunday afternoon

  • GO Website and user interfaces
    • AmiGO 2 the sequel (Seth)
    • QuickGO (Tony)
    • GO-Mine (Ben/Kalpana)
    • Switch to Drupal (Seth)
      • dynamic monitoring of discussions (biostars, Tweets, etc.)
    • New logo (Mike will just tell us)
    • Need a webmaster?
  • GO Help (Judy)
    • any new approaches?
    • %of questions we can answer with available tools?
  • Dissemination
    • Publication plans
    • Meetings to attend
    • New training material
  • Licensing issues (Seth)

Biological Representation - Paul T - Monday morning to mid-afternoon

  • Management of Ontology Development
    • Jira tracking system (Jane)
    • Automated ontology checks Jenkins (Chris)
      • ontology publishing pipeline
    • Term Genie status (Heiko)
  • Incorporation of External ontologies (David and Jane)
    • Report on migration of NIF subcellular AO to GO-CC (Jane)
    • CHEBI (David)
    • BFO 2.0 - (Chris)
      • do we comply with BFO and split part_of into 2 relations? Need 'official' signoff of GO's stance
  • Extensions to the GO annotation model
    • LEGO data model, an 'annoton' (Chris and Paul)
      • For prototyping: Protege plug-in for annotation (Heiko)
      • Current examples (Kimberly and David)
    • col. 16 extensions (Paul, Chris, Jane, Rachael)
      • GPAD releases
      • relationship to LEGO

Project infrastructure - Suzi - Monday mid-afternoon to Tuesday mid-morning

  • CAT
    • Architecture, services (Suzi)
    • protein2go introduction (Rachael)
    • WormBase experience with protein2go (Kimberly)
    • Wormbase CC tool (Kimberly)
    • Migration plans (Suzi)
      • Short term: towards protein2go
      • Longer term: capabilities to support LEGO
  • PAINT (Paul T)
    • PAINT annotation progress
  • Enrichment (and other) tool improvement plans (Chris)
    • Standardize interface to tools & allow plug in play eg via Galaxy
    • Promote tools that provide access to latest GO, work with those that don't. See GO Tools Registry
    • Getting enrichment tools to leverage ontology and annotation improvements

Annotation Production - Judy Tuesday mid-morning to mid-afternoon

  • Annotation Production Progress/Tracking (Paul S)
    • volume of annotations
    • backlog of papers selected
    • New reporting page
    • Observations/Comments
  • Term requests
    • Current rate of additions & rate of clearance
  • Standard processing of uploaded annotations
    • Automated annotation QC (Chris/Heiko)
    • Annotation "Quality" measurement (Mike)
    • Filtering of taxid that are not supported (Mike)
  • Current ontology development and annotation topics on the table (one slide each, Judy to present)
    • cardio conduction (Ruth)
    • apoptosis (Paola)
    • cell cycle (Val or Judy)
    • tRNA Modification (Harold)
    • review of approach, staging (Judy)
  • Submissions and outreach to outside groups
    • Web page with instructions (Rama)
    • Pulling in external annotations
    • Future work - who has been in contact? any active outreach?

Set objectives for next period (Paul S) Tuesday late afternoon