Dawn Field's opening presidential address to the 13th Genomics Standards Consortium workshop in Shenzhen, 5th March 2012

2. The GSC is an open membership community
working towards better descriptions of our
collection of genomes, metagenomes and
marker gene sets
The GSC is running a range of consensus-driven
projects and is now making a call for community
compliance/community involvement
http://gensc.org Standards Driving Science

3. The rise of the
megasequencing
project...
http://gensc.org Standards Driving Science

4. From
Genomes to
Interactions to
Communities to
Models
http://gensc.org Standards Driving Science

5. 1950 1960 1970 1980 1990 2001
Watson & Crick Sequencing
discover the double helix Invented
1980
PCR
1953 Invented
1989 2001
Similarity
Searching
Developed
(Blast) Internet
Develops
1996
1994 1995
http://gensc.org Standards Driving Science

6. 2001 2003 2005 2007 2009 2011
Sargasso Sea
Metagenome
Global Ocean Survey
Metagenomes 1k
Human
(62 genomes
Next-generation genomes)
sequencing
GEBA Synthetic
(56
genomes) life
http://gensc.org Standards Driving Science

7. 2012 2014 2016 2018 2020 2022
http://gensc.org Standards Driving Science

8. A network of sites working to generate genomic
observations that are well-contextualized and
compliant with global data standards
Sustained, DNA Centric, Place-Based Research
http://gensc.org Standards Driving Science

9. http://gensc.org Standards Driving Science

10. From
Genomes to
Interactions to
Communities to
Models
http://gensc.org Standards Driving Science

11. http://gensc.org Standards Driving Science

12.  Sept 17-19, 2012, Oxford e-Research
Centre, University of Oxford
 Launch of Genomic Observatories
Network; Focus on highly
contextualized site-based research,
defining what a genomic observatories
is, GSC standards compliance, data
integration, RDF, modelling and
Biocode Commons
http://gensc.org Standards Driving Science

13. Communication
Community
Collaboration
Communal Table
http://gensc.org Standards Driving Science

14. http://gensc.org Standards Driving Science

15. http://gensc.org Standards Driving Science

16. http://gensc.org Standards Driving Science

17. The Data SuperMarket Norman Morrison
http://gensc.org Standards Driving Science

18. http://gensc.org Standards Driving Science

19. http://gensc.org Standards Driving Science

20.  A standard is a convention that gives
uniformity to an area of research or
innovation.
 Standards unite groups and enable
collective change.
 Standards provide the language in which
innovation is written.
http://gensc.org Standards Driving Science

21. Standards
Not everything should be ‘standardized’
Aggregation of data, information, and knowledge
requires standard ways of doing things
Standards provide foundations; Standards should drive
innovation (think of electrical plugs or the internet)
Pick the right concepts to standardize – at the right
time, with the right people
Requires good ‘group think’ – or ‘systems thinking’
http://gensc.org Standards Driving Science

22. GSC 10
Argonne, 2010
GSC 11,
Hinxton, 2010
Taking the ‘Common Path’ towards
building consensus:
GSC 12
Bremen, 2011
•Identify the problem
•Define a community to address it
•Define scope of the solution
•Implement solution GSC 13
•Gain adoption of solution BGI 2012
http://gensc.org Standards Driving Science

23.  the implementation of new
genomic standards
 methods of capturing and
exchanging metadata
 harmonization of metadata
collection and analysis
efforts across the wider
genomics community
http://gensc.org Standards Driving Science

24. •Organizing meetings
•Forming working groups
•Creating Consensus Products
http://gensc.org Standards Driving Science

25. http://gensc.org Standards Driving Science

26. Please provide this minimum
information when you publish
•a genome
•a metagenome
•a gene marker study (i.e. ribosomal genes)
Genbank, EMBL and DDBJ now accept this
information and encourage its submission to their
public DNA databases
http://gensc.org Standards Driving Science

27. <MIxS>
http://gensc.org Standards Driving Science

28. The Genomic Contextual Data Markup Language (GCDML)
The Genomic Rosetta Stone (GRS)
Standards in Genomic Sciences (SIGS) journal
The Microbial Earth Project (MEP)
The GSC’s Compliance and Interoperability (Developers)
Working Group
M5: Metagenomics, Metadata, Meta-analysis, Models and Meta-
infrastructure
The GSC’s Biodiversity Working Group
http://gensc.org Standards Driving Science

29. http://gensc.org/
http://gensc.org Standards Driving Science

30.  The era of genomics is just beginning…
 Self-organization by the scientific
community can pay dividends (i.e. consensus
building, large-scale co-ordination)
 Standards are keys to unlocking data
http://gensc.org Standards Driving Science

31.  The GSC is running a range of consensus-
driven projects and is now making a call for
community compliance/community
involvement
 Now possible to submit compliant metadata
for MIGS/MIMS/MIMARKS to
DDBJ/EMBL/GenBank, GOLD, MG-Rast,
CAMERA, BII, VAMPS and more
http://gensc.org Standards Driving Science

32. The GSC efforts are contributed on a volunteer basis by a wide range of participants,
including GSC authors, working group members, workshop participants and adopters.
Special Thanks to the GSC Board:
Linda Amaral-Zettler, MBL Nikos Kyrpides, DOE, JGI
Guy Cochrane, EMBL-EBI Folker Meyer, Argonne National Lab
Jim Cole, MSU Norman Morrison (University of Manchester)
Inigo San Gil , LTER
Neil Davies (Berkeley)
Susanna Sansone, University of Oxford
Peter Dawyndt, University of Ghent
Lynn Schriml, University of Maryland (Treasurer of GSC)
Dawn Field, CEH (Chair of GSC)
Peter Sterk, GSC (Secretary of GSC)
George Garrity, MSU Dave Ussery DTU
Jack Gilbert, Argonne National Lab Owen White, University of Maryland
Frank Oliver Glöckner, MPI-Bremen John Wooley, UCSD (PI of RCN4GSC)
Lynette Hirschman, MITRE
Hans-Peter Klenk, DSMZ Institutional Liasons to the GSC Board
Renzo Kottmann, MPI-Bremen Ilene Mizrachi (NCBI/GenBank)
Rob Knight (University of Colorado Tatiana Tatusova (NCBI/RefSeq)
http://gensc.org Standards Driving Science

33. GSC Funding RCN4GSC
Coordination, workshops, working groups,
infrastructure and exchange visits
Additional workshop funds
Local Hosts of
GSC workshops
Sponsors of
GSC Events
http://gensc.org Standards Driving Science

34. Now taking submissions…
Large-Scale Data
Journal/Database
In conjunction with:
Editor-in-Chief: Laurie Goodman, PhD
Editor: Scott Edmunds, PhD
Assistant Editor: Alexandra Basford, PhD
http://gensc.org Standards Driving Science

35. Large-Scale Data Journal/Database
GigaScience aims to revolutionize data dissemination, organization, understanding, and use.
An online open-access open-data journal, we publish 'big-data' studies from the entire
spectrum of life and biomedical sciences. A novel publication format links standard
manuscript publication with an extensive database that hosts all associated data, provides
data analysis tools, cloud-computing resources, and gives all datasets a DOI as a citable and
trackable data publication mark.
www.gigasciencejournal.com
For more information: editorial@gigasciencejournal.com @gigascience
http://gensc.org Standards Driving Science

36. Seeking submissions highlighting best practice in genomics
research: • Discussion/comment/white papers
• Cloud computing, software for data handling
• Research highlighting best practice
• Rapid review - rolling publication after launch issue
• High-visibility – published/promoted by BMC/GigaScience
• Article Processing Charge covered by BGI
• Hosting of any test datasets in GigaDB
@gigascience
Contact: editorial@gigasciencejournal.com
http://gensc.org Standards Driving Science