2011 UCL Meeting Agenda

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Agenda

Coffee from 9.00am Morning session to start at 9:30am End of sessions: 6pm Monday and Tuesday, 2pm on Wednesday GOC dinner Monday 6:30pm

Software

• Presentation on GOMine (Stanford group)
• Migration of GO to SVN (Proposal) Chris

Milestones Report

• Overview of software group Roadmap ~~ Chris
• AmiGO 2 alpha ~~ Seth
  • amigo2 walkthrough demo
  • overview of architecture, use of Solr
  • opportunities for integration with QuickGO ~~ Tony, Chris
• GOLD beta
• OBO-Edit ~~ Heiko/Chris
  • 2.1 Release
  • 2.2 Plans : mostly maintenance, a few key features, integration of obo2owl code
  • Beyond 2.2. - should there be a 3.0? Proteg4 plugin? Web-based tool? Lego?
• TermGenie 1 beta Heiko
• obo2owl roundtripping Heiko/Shahid
  • OORT
• GPAD specification and tools Amelia
• GO Galaxy
  • http://galaxy.berkeleybop.org:8080/
  • Use by Phenoscape for obo-diffs
  • Wrapping multiple term enrichment tools
  • Use case - miRNA pipeline

Ontology

• Ontology_Release_Files_Proposal Chris

Annotation Working Group (Emily, Rama)

• Progress Report
  • Development of GO annotation guidelines. (Geneva and Transcription factors).
  • Progress on the Community Annotation Tool (PomBase) See wiki
  • ECO codes for GO annotation. See wiki
  • Annotation QCs, including taxon constraints.

• • Column 16 usage and development by groups

• Annotation Proposals and Discussions
  • IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
    • The annotation of the stoichiometry of binding by GO groups. Under the spotlight: protein homodimerization, protein tetramerization etc.

• • • Annotation to Protein Complex objects: a suggested annotation format. see wiki page.

• • • Use of the new relationship Ontology to describe relationships between entities in an annotation, and for the generation of detailed, composite GO terms
      • specific use for column 16 (annotation extension field
      • specific use proposed for explicitly defining a gp to GO term relationship. see wiki

Software Group: Annotation Display and Support activities?

- presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters? - presentation on AmiGO2 and column 16 display intentions?