2011 UCL Meeting Agenda

From GO Wiki
Jump to navigation Jump to search

back to meeting logistics page

Monday

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

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

...order and timings needed for remaining Software items:

  • GO Common Authentication interface ~~ Seth
    • New architecture
  • 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
    • Loading of phylogenetic data ~~ Sven
  • 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
    • Retiring TG0
    • Extensions - additional templates
    • Integration with ontology roadmap
    • Use of TG as SF replacement ("freeform" term creation)
  • obo2owl roundtripping ~~ Heiko
    • Using OORT to produce releases ~~ Chris (!keep this item here - Jane)

16:00-17:00 Annotation Software

  • Annotation Tools
    • PAINT report ~~ Suzi, PaulT

Tuesday

9:30am Annotation

Software Group: Annotation Display and Support activities?

  • 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

Annotation Group

  • Annotation Progress Report [Rama and Emily] 10 mins

to include:

  • Progress of CACAO biocurator training on GONUTS [1]

[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)
  • Annotation to Protein Complex objects: a suggested annotation format??
  • 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

Ontology

  • 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 ~~ David (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

Wednesday

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]

The GO managers would like to have a lunchtime meeting with the GO PIs on Mon or Tues, so if we could have a separate table/room or something?

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



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.