Sansone bio sharing introduction

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Susanna Sansone's introduction on Biosharing.

Susanna Sansone's introduction on Biosharing.

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  • 1. Susanna-Assunta Sansone, PhD Team Leader, University of Oxford, UK (Updated version of presentation given at) Biocuration, 11 th -14 th October 2010, Tokyo, Japan BioSharing: on Data Policies’s Plans and Reporting Standards  
  • 2. Information intensive research investigations The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
    • Modern studies often run source material through several kinds of assay in parallel
      • E.g. genomic sequencing, protein-protein interaction assays , or the measurement of metabolite concentrations and fluxes
  • 3. Comprehensible, reusable, reproducible research The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
    • Data (descriptions of biological entities of interest, e.g. , genes, targets and their measurements, e.g. , intensity, location) must be shared accompanied by enough, well annotated experimental information ( i.e. - ‘metadata’- provenance of study materials, technology and measurement types, etc .)
  • 4. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
    • Three types of standards enable unambiguous representation , description and communication of the experimental information
      • Minimum core information specifications: checklists
      • Semantics: nomenclatures and terminologies
      • Syntax: exchange formats
    Reporting standards as enablers
  • 5. Strong advocators The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
    • Journals, biocurators and the research community continue to participate in the development of standards, tools and databases
      • to support sharing of sufficiently well annotated datasets
      • to enable comprehensible, reusable, reproducible research
  • 6. ...funders are developing data policies...
    • Several data preservation , management and sharing policies have emerged in response to increased funding for genomics and functional genomics (omics) bioscience domains
  • 7. ....similar trend in the regulatory arena
    • “… lack of standardized data affects CDER’s review processes by curtailing a reviewer’s ability to perform integral tasks such as rapid acquisition, storage, analysis......efficient management of a portfolio of standards projects will require coordinated efforts and clear roles for multiple participants within/outside FDA ”
  • 8. ....and commercial sector
    • R&D has invested heavily in procedures and tools that integrate external information with their own data to enhance the decision-making process
    • Now joining forces to streamline non-competitive elements of the life science workflow by the specification of common standards , business terms, relationships and processes
  • 9. Escalating number of efforts (omics domain), e.g.
  • 10. Navigating a sea of ‘standards’
  • 11. I work on plants, are these just for biomedical applications? Which one are mature enough for me to use or recommend? How can I get involved to propose extensions or modifications? Which tools and databases implement which one? Which one are widely accepted and recognized? What are the criteria to evaluate status and value? ...?.... ...?.... ....?... ...?.... ....?... ...?.... I use HT sequencing technologies, which one are applicable to me? Navigating a sea of ‘standards’ Which tools and databases implement which one? I use HT sequencing technologies, which one are applicable to me?
  • 12. HT sequencing: public databases and ‘standards’ EBI NCBI ENA SRA
  • 13. HT sequencing: public databases and ‘standards’ EBI NCBI ENA SRA
    • checklists: MIAME, MINSEQ
    • formats: MAGE-ML, MAGE-Tab
    • ontologies: MGED Ontology...
    • checklists: MIGS, MIENS
    • format: GCDML
    • ontologies: EnVO light...
    INSDC feature table
  • 14. (2008) Vol 26 No 8 http://mibbi.org
  • 15.
      • Serves researchers , biocurators , journal editors and reviewers , and funders to
        • discover checklist s for a particular domain
        • monitor progress of extant efforts
        • facilitate collaborations
      • Link a sister effort in health research EQUATOR ( www.equator-network.org )
      • Funds for coordination activities and meetings
        • Our next meeting is in Germany, Dec 2010
  • 16. Linking checklists to terminologies http://www.ebi.ac.uk/ontology-lookup/ http://bioportal.bioontology.org/ http://www.obofoundry.org/
  • 17. Science (2009), Vol 326, 234-236 http://biosharing.org
  • 18.
    • Aim to protect cumulative data outputs, recognizing
      • data sharing as a way to accelerate subsequent exploitation
      • the right of first use for data provides and right to appropriate accreditation
      • the importance of ‘standards’ in annotation and reporting process, but...
  • 19.
    • Often inconsistent and/or unclear on the standards and methods to be used for preserving, managing and sharing data
      • “ .. recommend use of appropriate standards ..”, “.. where these exists ..”, “... mature, stable efforts ..”, “.. MIAME format ..”, “.. accredited standards organizations ..”, “.. deposition to public repositories.. ”, “.. release on websites ..”...etc
  • 20.
    • Urgent need for fostering communications between policy makers, the ‘standards’ groups
      • including researchers, biocurators and developers
  • 21. ‘ Social engineering’ http://biosharing.org
  • 22.
    • It is NOT
      • a top down initiative to harmonize the standards
      • another society to develop another standard
      • a data or tool resource
    • Started as a blog (supplementary materials for the article in Science ).......
    http://biosharing.org
  • 23.  
  • 24.  
  • 25.  
  • 26. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 27. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 28. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
  • 29. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project Launch of prototype in December Iterative development, also based on feedback (enrichment, enhancement and links to other existing/new resources)