2012 GOC Meeting Caltech: Difference between revisions

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** AmiGO 2 the sequel (Seth)
** AmiGO 2 the sequel (Seth)
** QuickGO (Tony)
** QuickGO (Tony)
** GO-Mine (Mike/Rama) (http://gomine.geneontology.org)
** GOMine InterMine for GO (Mike/Rama) ([http://gomine.geneontology.org GoMine])
** Switch to Drupal (Seth)
** Switch to Drupal (Seth)
*** dynamic monitoring of discussions (biostars, Tweets, etc.)
*** dynamic monitoring of discussions (biostars, Tweets, etc.)
** New logo (contest is happening : http://www.logomyway.com/printLogos.php?print=printlogo&cId=9400)
** New logo (contest is happening : [http://www.logomyway.com/printLogos.php?print=printlogo&cId=9400 LogoMyWay])
** Need a webmaster?
** Need a webmaster?
* GO Help (Judy)
* GO Help (Judy)

Revision as of 13:41, 7 October 2012

2012 Caltech GOC Meeting Logistics

Biological relevance - Paul S - Sunday 10:30

024 Beckman Behavioral Biology Building; [coffee at 09:30; lunch 1at 1230]
  • GO as a biological reference (critique?)
  • Objectives for this meeting
    • set quarterly objectives process

Web - Cherry - Sunday afternoon

  • GO Website and user interfaces
    • AmiGO 2 the sequel (Seth)
    • QuickGO (Tony)
    • GOMine InterMine for GO (Mike/Rama) (GoMine)
    • Switch to Drupal (Seth)
      • dynamic monitoring of discussions (biostars, Tweets, etc.)
    • New logo (contest is happening : LogoMyWay)
    • 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 lunch

coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)

  • Management of Ontology Development
    • Jira tracking system (Jane)
    • Automated ontology checks Jenkins (Chris)
      • ontology publishing pipeline
    • Term Genie status (Heiko - ~6 slides + demo)
  • 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 afternoon to Tuesday mid-morning

coffee at 0830; lunch on your own (Chandler Cafeteria)

  • CAT
    • Architecture, services (Suzi)
    • protein2go introduction (Rachael)
    • WormBase experience with protein2go (Kimberly)
    • Wormbase CC tool (Kimberly)
    • BioCreative Challenge IV - GO Triage and Annotation (Kimberly, James, Donghui, Judy)
    • Migration plans (Suzi)
      • Short term: towards protein2go
      • Longer term: capabilities to support LEGO
  • 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
  • PAINT (Paul T)
    • PAINT annotation progress
    • Strategy for prioritization of ontology development topics (Paul and Judy)
      • Emily summation of needed areas aka textbook
      • Information content approach

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 (Judy/Jane)
    • Current rate of additions & rate of clearance
  • Standard processing of uploaded annotations
    • Automated annotation QC (Chris/Heiko ~5 slides + demo)
    • Annotation "Quality" measurement (Mike)
    • Filtering of taxid that are not supported (Mike)
  • Redundant/non-redundant annotations (Rama will summarize what was discussed during AnnotationCalls)
  • Provenance of evidence (Rama)
  • 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