eGenomics: cataloguing our complete genome collection

1
eGenomics cataloguing our complete genome
collection

• The National Institute for Environmental
  E-Science
• Cambridge, UK
• Sept 7-9, 2005
• Co-organizers Dawn Field and Tatiana Tatusova

2
Challenges and Opportunities

• Rapidly growing collection of genomes
• Increasing need for researchers to access,
  combine and analyze data sets containing genomic,
  taxonomic, ecological and environmental data
• Increasing number of initiatives capturing
  metadata
• Additional information about complete genome
  sequences would be beneficial

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Cataloguing our Complete Genome Collection

• Proposal Field D, Hughes J (2005). Cataloguing
  our current genome collection. Microbiology.
  Pubmed
• Hughes J Field D (2005) Ecological Perspectives
  on our complete genome collection Ecology
  Letters (in press).
• Workshop Cataloguing our current genome
  collection Sept 7-9, 2005 Cambridge, UK NIEeS
• Website Cataloguing our current genome
  collection (NERC International Opportunities
  Fund Award NE/3521773/1)

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Workshop Goals

• Identify the science questions that are driving
  the need for more metadata
• Learn more about current effort to capture and
  use genomic metadata look for ways to harmonize
  across efforts
• Discuss our vision for a future genome catalog
  (research tool, reference site, facilitate re-use
  of genome strains and genomic information, should
  be well linked to related resources)

5
Workshop Organization

• Talks have been organized into five sessions over
  three days
• Time specifically set aside for discussion

6
Day 1

• I Overview of our current and future genome
  collection
• Discussion
• II Databases and Metadata capture efforts
• III Allied Projects

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Day 2

• IV Case Studies
• Small Group Meetings and External visits
• Draft specification
• Controlled vocabularies / ontology
• Case Studies
• Harmonization Efforts / Collaborations

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Day 3

• V Discussion
• Towards a standard
• Towards a metadata exchange format
• A roadmap for the future

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Discussion Document

• Table of Contents
• Executive summary
• The need for a new genomic standard
• The process of consensus building
• The specification checklist
• The specification draft version available
• Issues and challenges
• Considerations
• Case Studies
• Implementation options
• Genomic metadata exchange

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Open call for Case Studies

• Contributing a first-pass description of your
  genome(s) will help provide input into the design
  of the specification
• Both descriptions and comments are collected from
  each contributor and these lead to the refinement
  of the specification

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Grand Questions Towards a new genomic standard

• What does the community want to see happen in
  this domain?
• What is possible?
• How does this project related to other projects
  in the community?
• Who needs to be involved to make it work? (e.g.
  culture collections)
• What will make the community agree to submit
  information?
• Who are the consumers of the end product? (i.e.
  researchers interested in or a few genomes or
  hundreds of genomes, as this speaks to degree to
  which information must be standardized across
  genomes)

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Logistics

• Stuart Ballard (NIEeS Science Director)
• Many, many thanks to NIEeS (Stuart Ballard,
  Martin Dove and Helen Wells)