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Dawn Field: the Genomics Standards Consortium (GSC)


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

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Dawn Field: the Genomics Standards Consortium (GSC)

  1. 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 Standards Driving Science
  2. The rise of the megasequencing project... Standards Driving Science
  3. From Genomes to Interactions to Communities to Models Standards Driving Science
  4. 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 Standards Driving Science
  5. 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 Standards Driving Science
  6. 2012 2014 2016 2018 2020 2022 Standards Driving Science
  7. 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 Standards Driving Science
  8. Standards Driving Science
  9. From Genomes to Interactions to Communities to Models Standards Driving Science
  10. Standards Driving Science
  11.  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 Standards Driving Science
  12. Communication Community Collaboration Communal Table Standards Driving Science
  13. Standards Driving Science
  14. Standards Driving Science
  15. Standards Driving Science
  16. The Data SuperMarket Norman Morrison Standards Driving Science
  17. Standards Driving Science
  18. Standards Driving Science
  19.  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. Standards Driving Science
  20. 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’ Standards Driving Science
  21. 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 Standards Driving Science
  22.  the implementation of new genomic standards  methods of capturing and exchanging metadata  harmonization of metadata collection and analysis efforts across the wider genomics community Standards Driving Science
  23. •Organizing meetings •Forming working groups •Creating Consensus Products Standards Driving Science
  24. Standards Driving Science
  25. 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 Standards Driving Science
  26. <MIxS> Standards Driving Science
  27. 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 Standards Driving Science
  28. Standards Driving Science
  29.  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 Standards Driving Science
  30.  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 Standards Driving Science
  31. 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) Standards Driving Science
  32. GSC Funding RCN4GSC Coordination, workshops, working groups, infrastructure and exchange visits Additional workshop funds Local Hosts of GSC workshops Sponsors of GSC Events Standards Driving Science
  33. 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 Standards Driving Science
  34. Large-Scale Data Journal/DatabaseGigaScience aims to revolutionize data dissemination, organization, understanding, and use.An online open-access open-data journal, we publish big-data studies from the entirespectrum of life and biomedical sciences. A novel publication format links standardmanuscript publication with an extensive database that hosts all associated data, providesdata analysis tools, cloud-computing resources, and gives all datasets a DOI as a citable andtrackable data publication mark. For more information: @gigascience Standards Driving Science
  35. 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 Standards Driving Science