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eGenomics IV 6-8th June 2007

General Information

The “eGenomics: Cataloguing our Complete Genome Collection IV” workshop is the third NIEeS funded workshop and the fourth workshop of the Genomic Standards Consortium GSC. This workshop will be a mix of short presentations and group discussions which will build heavily on the roadmap developed at the 3rd GSC workshop held at NIEeS in Sept 2006.

The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes and metagenomes. Established in September 2005, after an exploratory workshop hosted by NIEeS, the goal of this international community is to promote mechanisms for standardizing the description of genomes and the exchange and integration of genomic data. Genomic and metagenomic sequencing projects are being completed at a rapid pace that will only increase as the application of ultra-high-throughput methods becomes commonplace. The primary aim of developing a new standard is to ensure that those researchers generating genomes and metagenomic contribute to an increase in the quality and quantity of metadata, so that interpretation and analyses of the genome collection can be carried out in a comprehensive and unhindered manner, especially from an ecological and environmental perspective. More background information about the GSC can be found at its website.

This meeting is being co-organised by Dawn Field, George Garrity, Frank Oliver Glöckner, Tanya Gray, and Tatiana Tatusova

Aim of the meeting

This 4th workshop of the Genomic Standards Consortium GSC will be a mix of short presentations and group discussions which will build heavily on the roadmap developed at the 3rd GSC workshop held at NIEeS in Sept 2006.

Programme

Wednesday 6th June

08.00-10.00

Pre-Workshop optional session:

MIGS/MIMS Technical Session - Active work on next version of checklist and schema with a view to implementation by CAMERA

Workshop opens

10.00

Registration and coffee

10.30

Welcome, background and goals of workshop. Workshop Organizers

10.45

The National Institute for Environmental eScience.
Stuart Ballard, NIEeS

Session I: GSC Activities: scope, syntax and semantics.
Session Chair: Dawn Field

11.00

Overview of GSC activities: The GSC roadmap.
Dawn Field, NERC Centre for Ecology and Hydrology

11.15

INSDC Update – report from the Annual Collaborators meeting.
Guy Cochrane, EMBL

11.30

INSDC update – genome project database and genome project ids.
Tatiana Tatusova, NCBI

11.45

Update on GSC participation in MIBBI (“Minimum Information about Biomedical and Biological Investigations”).
Peter Sterk, EBI

12.00

The Genome Catalogue.
Tanya Gray, NERC Centre for Ecology and Hydrology

12.15

Towards a MIGS/MIMS Object Model based on FuGE.
Allyson Lister, University of Newcastle

12.30

NSF RCN application.
Eugene Kolker, Seattle Children’s Hospital

13.00

Lunch

Session II: Scope and Syntax: MIGS/MIMS Case studies
Session Chair: Frank-Oliver Glöckner

14.00

The need for MIMS (“Minimum Information about a Megagenomic Sequence”) and its origins.
Renzo Kottman, MPI-Bremen

Three case studies

14.15

Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research (CAMERA): Towards MIG/MIMS compliance.
Saul Kravitz, JCVI

14.30

Environmental egenomics databases, the alpine microbial observatory, and developing MIMS/MIGS compliant informatics products.
Rob Guralnick, University of Colorado

14.45

Prospects for MIGS/MIMS in the Integrated Microbial Genomes (IMG/IMG/m).
Victor Markowitz, Lawrence Berkeley National Laboratory and Joint Genome Institute

15.00

Coffee

15.30

MIMS Roundtable discussion
Frank-Oliver Glöckner

Developing MIMS
The relationship fo MIMS to MIGS
Definition of “Minimum”
Review of changes from MIGS/MIMS 1.1 to 1.2

17.30

Thursday 7th June

8.00

RCN Breakfast meeting

Session II Continuted: (“MIMS Information about a Metagenomic Sequence”)
Session Chair: Frank-Oliver Glöckner

09.00

Wrap up of MIGS/MIMS and the way forward for MIMS.
Frank-Oliver Glöckner, MPI Bremen

09.45

RCN Application.
Eugene Kolker, Seattle Children’s Hospital

10.00

Coffee

Session III: Semantics - Controlled vocabularies (CVs) and ontologies
Chair: Trish Whetzel, University of Pennsylvania

10.30

CVs and Ontologies in Gemina - a web based system to retrieve epidemiological and genomic data associated with microbial pathogens.
Neil Hall, University of Liverpool

10.45

Controlled vocabulary and Ontology Requirements of GCat: Supporting the completion of compliant MIGS/MIMS reports.
Tanya Gray, NERC Centre for Ecology and Hydrology

11.00

Text mining options for MIGS/MIMS compliance: Extracting genomic metadata from the literature.
Lynette Hirshman, MITRE

11.15

Open discussion.
Trish Whetzel, University of Pennsylvania and Tanya Gray, NERC Centre for Ecology and Hydrology

13.00

Lunch

Session IV: Towards a single, global list of genomes and metagenomes
Chair: Nikos Kyrpides, Joint Genome Institute

14.00

Overview of the GSC’s Genomic Rosetta Stone: Towards a mapping of all local genomic and metagenomic identifiers.
Dawn Field, NERC Centre for Ecology and Hydrology and Nikos Kyrpides, Joint Genome Institute

14.15

Identifiers available from the SEED database.
Rob Edwards, San Diego State University

14.30

Permanent, unique identifiers in the straininfo.net portal.
Peter Dawyndt, University of Ghent

14.45

Open Discussion - Building the Genomic Rosetta Stone.
Nikos Kyrpides, Joint Genome Institute

15.30

Coffee

Session V: Data exchange and web services
Chair: Anil Wipat

16.00

Introduction to web services, workflows and the power of the ComparaGrid.
Matt Powcock, University of Newcastle.

16.15

Producing and conusming web services in the genome catalogue.
Tanya Gray, NERC Centre for Ecology and Hydrology

16.30

Open Discussion – Collecting and exchanging metadata about genomes and metagenomes. Anil Wipat

17.30

Friday 8th June

8.00

RCN breakfast meeting

Session IV: GSC Roadmap

9.00

Research Co-ordination Network. MIMS-MIGS Technical session application

10.30

Coffee

11.00

MIGS-MIMS technical session review.
Frank-Oliver Glöckner, MPI Bremen

13.00

Lunch

14.00

Wrap up: Review of Actions.
Workshop Co-organizers

15.00

Formal close of workshop (Organizers) and Coffee

15.30

Departure

Location

The meeting and accommodation will be in New Hall, University of Cambridge.

Registration

Registration details will be made available shortly.
Registration is free and includes the accommodation and conference dinner. NIEeS will also fund sensible UK travel expenses for UK scientists.

Contact and further information

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