2011 UCL Meeting Agenda

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Main meeting Monday to Wednesday

Wilkins Haldane Room ([1])

GO managers and PIs

Tuesday 1pm to 2:30pm Wilkins JBR Meeting Room ([2])

GO curators and ChEBI

Wednesday 10:30am to 1:30pm Cruciform Foyer Seminar Room 3 ([3])


Morning Coffee from 9.00am

Morning session to start at 9:30am

Philippa Talmud to welcome the GO Consortium to UCL.

PIs to kick off meeting...?

Software (requested: 3 hours)

  1. Overview of software group activities and Roadmap [Chris]
  2. Personnel Updates [Chris]

    • New architecture (30 mins)
  • AmiGO 2 alpha ~~ Seth
    • amigo2 walkthrough demo
    • Example queries using c16
      • CL examples (mouse annotations)
      • POMBE examples
      • Treatment of evidence types
    • overview of architecture, use of Solr. Demo of Solr API
    • opportunities for integration with QuickGO ~~ Tony, Chris
  • OBO-Edit ~~ Heiko/Chris (20 mins)
    • 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 (25 mins)
    • Retiring TG0
    • Extensions - additional templates
    • Integration with ontology roadmap
    • Use of TG as SF replacement ("freeform" term creation)

Annotation Software

  • Annotation Tools
    • PAINT report ~~ Suzi, PaulT

GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html


Separate lunchtime meeting for GO managers and PIs. Wilkins JBR Meeting Room 1pm to 2:30pm

Annotation (requested: 5 hours)

Software and Annotation Group: Annotation Display and Support activities?

  • Annotation Roadmap overview (Rama)
  • Annotation Progress Report [Rama and Emily] 10 mins

to include:

    • GO Consortium outreach activities and integration of external data sources into primary species GAFs.
    • Development of GO annotation guidelines,
    • Community Annotation Tool
    • ECO codes
    • Annotation QCs, including taxon constraints.
  • Progress of CACAO biocurator training on GONUTS [4]

[Jim 10 mins]

  • Annotation Extension Field (column 16)
    • Development of the column 16 format (Val)
    • Discussion:
      • Rules for transferring column 16 via ISS and via F->P inferences.

  • Protein Binding (covering both ontology and annotation issues)
    • Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
    • Level of detail required under GO:0005515 protein binding (Jane)
  • specific use proposed for explicitly defining a gp to GO term relationship. see wiki
  • Progress and Direction of the Reference Genome Project (Pascale)
  • Ways in which PAINT annotation can be carried out to quickly generate annotations as a first draft annotation set (raised on the annotation call 25/10/2011)
  • suitable projects to engage all groups
  • GOLD beta ~~ Chris - on behalf of Shahid
    • GAF services
      • Annotation file QC
      • Inference of new annotations
        • Use of logical definitions to suggest deeper annotations
        • Cross-ontology inference using part_of and occurs_in

[15mins talk + 20min discussion]

  • Common Annotation Framework ((Aim 4 of the Grant) - a centralized curation system to help curators efficiently capture annotations from the literature
    • Brainstorming session on GO curation tool features - what features are essential, what features would be great to have, what do curators not want

Ontology (requested: 3 hours)

  • Roadmap/project overview [Jane/David]
  • Ontology editing workflow
    • Dual mode Obo-Edit and Protege editing ~~ Chris
    • Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
    • MIREOTing subsets of external ontologies into editors version ~~ Chris
    • Report on how the GO editors are using SourceForge: triage, jamborees etc ~~ Jane
  • Aligning with external ontologies
    • Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
      • Integration with Uberon
      • Use in FANTOM5
      • Neuro-cell work
    • Update on GOCHE ~~ David
    • Behaviour alignment and NBO - a proposal [Jane]
  • Content Projects
    • Update on signaling ~~ Rebecca
    • Update on viruses ~~ Jane
    • Update on transcription ~~ Karen (please make this a late time slot so Karen can call in: 3pm UK time at the earliest)
    • Update on GO apoptosis project (Paola and Pablo)
    • Update on generic GO slim (was this done at LA?) [Val]
      • Processes and components
      • Functions
  • Relations
    • Update on RO and BFO ~~ Chris
    • GO subset of RO
    • Coordinating between annotation group and ontology group on GO subset of new RO


On Wed morning, several of us intend to meet with the CHEBI group who are going to come over to UCL. We were thinking perhaps we do the meeting wrap-up first thing on the Wed morning - action items, next meeting date etc. and then we can meet with CHEBI immediately afterwards. We thought perhaps another smaller group meeting might run in parallel (annotation-based? possibly focusing on the Reference Genome effort, group participation issues, next Reference Genome projects, do people want to volunteer to run different projects? and how to work together to meet targets?). Ruth is looking into booking additional rooms. [Jane]

Project Management

- Overall project management under new grant goals
- Manage documentation
- Manage staff
- Discussion on appropriate software tools to help manage and report progress on individual project milestones

  • Jira demo [Tony]

- Discussion on a replacement for the Webex screen sharing tool. - Communication between managers projects.