Top Banner
Innovative technology accelerating research Susanna-Assunta Sansone, PhD Team Leader, University of Oxford, UK Biocuration, 11 th -14 th October 2010, Tokyo, Japan Omics Data Sharing BioSharing: on Data Policies’s Plans and Reporting Standards
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
  • 1. Susanna-Assunta Sansone, PhD Team Leader,University of Oxford, UK Biocuration, 11 th -14 thOctober 2010, Tokyo, Japan Omics Data Sharing BioSharing:on Data Policiess Plansand Reporting Standards Innovative technology accelerating research

2. Information intensive research investigations The International Conference on Systems Biology (ICSB) , 22-28 August, 2008Susanna-Assunta

  • Modernstudiesoften run source material through several kinds ofassayin parallel
    • E.g. genomic sequencing, protein-protein interactionassays , or the measurement of metabolite concentrations and fluxes

3. Comprehensible, reusable, reproducible researchThe International Conference on Systems Biology (ICSB) , 22-28 August, 2008Susanna-Assunta

  • 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 annotatedexperimental information( i.e.- metadata- provenance of study materials, technology and measurement types,etc .)

4. The International Conference on Systems Biology (ICSB) , 22-28 August, 2008Susanna-Assunta

  • Three types of standards enableunambiguousrepresentation ,descriptionandcommunicationof theexperimental information
    • Minimum core information specifications:checklists
    • Semantics:nomenclaturesandterminologies
    • Syntax:exchange formats

Reporting standards as enablers 5. Strong advocators The International Conference on Systems Biology (ICSB) , 22-28 August, 2008Susanna-Assunta

  • Journals, biocurators and the research community continue to participate in the development ofstandards, toolsanddatabases
    • to support sharing ofsufficiently well annotated datasets
    • to enable comprehensible, reusable, reproducible research

6. ...funders are developing data policies...

  • Several datapreservation ,managementandsharing policies have emerged in response to increased funding for genomics and functional genomics(omics)biosciencedomains

7. ....similar trend in the regulatory arena

  • lack of standardized data affects CDERs review processes by curtailing a reviewers ability to perform integral tasks such as rapid acquisition, storage, analysis......efficient management of a portfolio ofstandards projectswill 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 ofcommon standards , businessterms, relationships and processes


  • Increased efficiency
    • Metadata remains associated with the results generated
    • Avoids the risk of loss of information through staff turnover
    • Enables time-efficient handover of projects
  • Enhanced confidence in data
    • Enables fully-informed assessment of results (methods used etc.)
    • Supports the discovery of sources of systematic or random errors
    • Facilitates better-informed comparisons or cross analysis of data sets
  • Defined requirements for submission, exchange and/or publication
    • Within multi-sites organization or between collaborators
    • To journals or repositories
    • To regulatory bodies

Reporting standards as a means to an end 10. Escalating number of efforts (omics domain),e.g. 11.

  • Wide variety of authorities
    • Standard organizations
    • International projects
    • Working groups
    • Grass-root movements
  • Multi-stakeholders and multi-disciplinary
    • Researchers, biocurators, software/database developers , modellers
    • Academics, industries, governmental and regulatory bodies
    • Manufacturers, software vendors, journal editors and funders
  • Heterogeneous focus - beyond reporting requirements- e.g.
    • Broader understanding of the use of omics data
    • Agreed world-wide recommendations
    • Measurements and methods validation

Heterogeneity of the efforts 12. Navigating a sea of standards 13. 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 databasesimplementwhich 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 databasesimplementwhich one? I use HT sequencing technologies, which one are applicable to me? 14. HT sequencing: public databases and standards EBI NCBI ENA SRA 15. 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...

INSDCfeature table 16. (2008) Vol 26 No 8 17.

    • Servesresearchers ,biocurators ,journal editors and reviewers , and funders to
      • discover checklist s for a particular domain
      • monitor progressof extant efforts
      • facilitate collaborations
    • Link a sister effort in health research EQUATOR ( )
    • Funds for coordination activities and meetings
      • Our next meeting is in Germany, Dec 2010

18. Linking checklists to terminologies 19. Science (2009), Vol 326, 234-236 20.

  • 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 standardsin annotation and reporting process,but...


  • Ofteninconsistentand/orunclearon 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


  • Urgent need for fostering communications between policy makers, the standards groups
    • including researchers, biocurators and developers

23. Social engineering 24.

  • It isNOT
    • 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 inScience )....... 25. 26. 27. 28.

  • Call for participation
    • We need more..........
    • Suggestions on how to bestcreate and populate the website, list the standards, allow updates, link to other portals etc...
  • Close engagement with the Biocuration Society and the new BioDBcore effort 29. Part of our software development activities Rocca-Serraet al , Bioinformatics , 2010 ISA software suite open source: 30. Science , 2009 Bioinformatics , 2010 Nature Biotech , (invited)