CVGOAI 2010

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Cardiovascular GO Annotation Initiative Targets 2010 meeting

Thursday 25th February 12noon to 1:30pm

Location: 3rd floor seminar room of the Rayne Institute, London

Conference call facilities available.


Chair

Professor Philippa Talmud (attending)

Gene Ontology annotators

Dr Ruth Lovering (attending)

Dr Varsha Khodiyar (attending)

Collaborators

Professor Peter Scambler (attending)

Dr Mike Hubank

Dr Rolf Apweiler (attending remotely)

International Scientific Advisory Panel

  • Professor Shoumo Bhattacharya - Oxford University (unable to attend)
  • Professor Francois Cambien - INSERM Paris
  • Professor Anna Dominiczak - Glasgow University (unable to attend)
  • Professor Philippe Froguel - Imperial College
  • Dr Brendan Keating - University of Pennsylvania (attending remotely)
  • Professsor Aldons Lusis - University of Califonia Los Angeles (unable to attend)
  • Dr Manuel Mayr - King's College London
  • Professor Mark McCarthy - Oxford University (unable to attend)
  • Professor William McKenna - University College London Hospital
  • Professor Daniel Rader - University of Pennsylvania
  • Emily Dimmer - GOA team Coordinator - EBI (attending)

Annotation targets

355 annotations per month to human proteins.

  • Varsha’s target will be to create 145 annotations to human proteins each month (Varsha works 70%FTE).
  • Ruth’s target will be to create 210 annotations to human proteins each month.

Try this approach for 2 months to make sure this is feasible.

The annotation targets will be:

  • To annotate proteins involved in heart development to take advantage of these new terms.
  • To continue to annotate with a process specific approach limited to every other month.
  • To annotate proteins on both the Reference genome and BHF target lists, every other month.
  • Consider next year aiming to increase the number of genes annotated with some GO term

The process approach to annotation is leading to a decrease in the number of annotations we are creating, due to the additional time spent creating more specific GO terms and identifying the appropriate genes to annotate. We have therefore suggested that we should aim to change the annotation approach on a monthly basis to ensure that the numbers of annotations created remains high.

Improving GO annotations

  • Submit a list of 60 proteins relevant to heart development to the Reference Genome to enable these proteins to be annotated across 12 species.
  • Meet up with the co-grant holders and specialist advisors to discuss project progress and future direction.
  • Chase up collaborations
  • Decide on topic for next CV GO workshop
  • Decide on how to increase the participation of expert scientists in GO annotation. In grant had suggested holding an annotation jamboree to fast track annotation of CV relevant proteins. An alternative would be to annotate recent papers from a specific group, along with papers referenced from these papers, then arrange to visit the group, give a GO presentation and then talk to members of the group individually about whether the annotations reflect the data in the papers and the accumulated knowledge of these genes. As a pilot study annotate papers from the Cardiovascular genetics group. Also record what changes are made during these discussions so that we can gauge whether or not this is a worthwhile investment of time.
  • Provide more detailed annotation information using Column 16, including cell type, tissue type, protein targets.

Funding applications

  • Wellcome Trust Crohn’s-focused annotation project (2 curators)
  • 1-2 other applications, (possibly sight and neuronal) annotation projects.

Papers

  • Heart Development GO workshop summary.
  • Progress of this project and the impact of the project on analysis of genes associated with cardiovascular systems.
  • "The importance of focused Gene Ontology curation of specific mammalian systems" for a new BioCuration on-line journal.

Teaching

Following the success of this module last term, organise an MSc GO module for 2010.

Meetings

  • Gene Ontology Consortium meeting, Stanford, March (Ruth and Varsha remote attendance)
  • Gene Ontology Consortium meeting, unknown location, Autumn (Ruth in person funding permitting, Varsha remote attendance)
  • Quarterly GO annotation jamborees (3 a year in EBI, one a year at UCL) (Ruth and Varsha to attend in person)
  • Reference Genome Annotation Camp, Geneva, June (Ruth and Varsha to attend in person, funding permitting)
  • Local cardiovascular and bioinformatics meetings, London, eg:
    • Computational Biology Town meeting-Use and potential of computational methods in the biomedical sciences, January (Varsha)