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 (http://gensc.sf.net)
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. |
| 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
|
| 17.30 | Close |
8.00 |
RCN Breakfast meeting |
Session II Continuted: ("MIMS Information about a Metagenomic Sequence")
|
|
| 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 |
|
| 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. |
| 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. |
| 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 | Close |
| 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.