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eGenomics: Cataloguing our complete genome collection

11 -13th Sept 2006

General information

Our complete genome collection, the result of a significant investment of public funds, is one of our most valuable biological resources and also one of the most complex. The value of these data lies in the ability to view, compare and contrast the entire genetic complement of a wide range of organisms. The complexity of these data stems not only from the vast number of biological features within these genomes (i.e. genes, promoters, binding sites etc) but also from the complexity of the evolutionary relationships and ecological lifestyles - factors that play a major role in shaping genome features and content - of the organisms to whom these genomes belong.
The scientific community would benefit significantly from the establishment of a data standard to capture more of this complexity. This standard could provide electronic, machine-readable reports for submission to a public database at the time of publication of each genome (analogous to the submission of genome annotation files). In this way, the experts on each organism would be directly responsible for providing data to the wider community about the detailed features of the organism.
Currently the difficulty of obtaining such metadata in a high quality and easily accessible format is a common bottleneck in large-scale computational studies and a significant source of difficulties in the process of scientific discovery. Likewise, merging ecological and environmental data with complete genome sequences opens up a new area of research possibilities. The creation of this genome catalogue would provide an extensive amount of novel data and a powerful new research tool.

This workshop is being organised by Dawn Field of the Centre for Ecology and Hydrology, Oxford and Tatiana Tatusov of the National Centre for Biotechnology Information.

This is the third meeting of the Genomics Standards Consortium. http://gensc.sf.net

Aim of the workshop

raise awareness of existing projects aimed at merging metadata with genomic sequences within this community.
explore how to harmonize efforts between existing and future projects.
develop the “Minimal Information about a Genome Sequence” checklist
define how the culture and associated physical infrastructure required by an international working group might evolve.
evaluate awareness of how this project can proceed in an e-science arena.
evaluate how webservices, (workflows and LSIDs) may play a role in the implementation of such a standard.

Programme

	Monday 11th September

10:00	Registration/coffee
10:30	Welcome, background and goals of workshop (Dawn Field and Tatiana Tatusov, Oxford Centre for Ecology and Hydrology and the NCBI)
10:45	Introduction to The National Institute for Environmental E-Science (Stuart Ballard, NIEeS)

	Session I: Overview of our current and future genome collection Session Chair: Dave Ussery
11:00	Exploring the Tree of Life through genomics (Sandie Baldauf, Univerity of York)
11:30	The promise of 454 Sequencing in Characterizing Natural Diversity (Rob Edwards, University of San Diego)
12:00	Applying Environmental Genomics to Microbial Ecology (George Kowalchuk)
12:30	CAMERA, TBC
13:00	Lunch

	Session II: Databases and Metadata capture and Exchange efforts Session Chair: George Garrity
14:00	INSDC Sequencing Project Metadata submission protocol: NCBI web service API (Tatiana Tatusova, NCBI)
14:20	The DDJB Perspective on our complete genome collection (Yoshino Tateno, DDBJ)
14:40	The IMG, IMGm, and GOLD V2.0 databases (Nikos Kyripides, JGI)
15:00	PUMA: from genomes to GFF: metadata exchange (Natalia Maltsev, Argonne National Laboratory)
15:20	Coffee
16:00	Evaluation of the “Minimum Information about a Genome Sequence” specification / checklist (Peter Sterk, EBI)
16:20	Evaluation of the checklist to XML schema transformation (Dawn Field, CEH Oxford)
16:40	Demonstration of the Genome Catalogue (Tanya Gray, CEH Oxford)
17:00	Close
	Dinner at Robinson College

	Tuesday 12th September

	Session III: Allied Projects: Ontology Development Session Chair: Dawn Field
09:00	Names for Life and Phenobank (George Garrity, U of Michigan)
09:20	MICheck : bringing the MIxxx community together (Chris Taylor, EBI)
09:40	An Overview of OBO and the OBO Foundry (Michael Ashburner)
10:00	An Overview of FuGO and its relationship to the GSC (Trish Whetzel, U Penn)
10:20	PATO – towards a description of organismal phenotypes (Suzi Lewis, Berkeley)
10:40	MegX and the capture of environmental metadata (Frank-Oliver Glockner, Max Planck Institute for Marine Microbes)
11:00	Coffee

	Session IV: Group work on the MIGS specification, genome reports and the Genome Catalogue
11:30	Open discussion – the MIGS specification
13:00	Lunch
14:00	Open discussion - the Genome Catalogue
15:00	Coffee
15:30	Open discussion – capture of terms
17:00	Close
	Dinner at Robinson College

	Wednesday 13th September

	Session V: Discussion
09:00	INDSC Panel Discussion
10:30	Coffee
11:00	The GSC road map (working group membership, actions, future meetings)
13:00	Lunch
14:00	Wrap up
15:00	Formal close of workshop and Coffee
15:30	Departures

Location

The workshop, accommodation, and workshop dinners will all be in Robinson College, Cambridge. Session IV, on Tuesday afternoon will held in Titan 1 computer room.
A google map for this event is provided here

Follow-on

It is anticipated that the workshop may generate interest in some follow-on activities. We will discuss the sort of follow-on activities that can be arranged, such as visits to NIEeS to demonstrate some of the escience/grid technologies and to provide help with installation and usage.

Registration

Registration has now closed. Registration is free. Registration for UK academic participants includes accommodation in College and meals. The NIEeS will also refund sensible travel and accommodation expenses within the UK for UK academic particpants.

Contact and further information

For information about registration, and all other types of queries, please contact the NIEeS office in the first instance.

This document last modified: Thursday, 07-Sep-2006 09:56:22 BST