"Standards landscape" NIF Big Data 2 Knowledge (BD2K) Initiative, Sep, 2013

"Standards landscape" NIF Big Data 2 Knowledge (BD2K) Initiative, Sep, 2013

• 1.
  Data Consultant, Honorary AcademicEditor Susanna-Assunta Sansone, PhD Associate Director, Principal Investigator NIH BD2K Workshop: Frameworks for Community-Based Standards Efforts, Sept 25-26, 2013 Mapping the Landscape of Community Standards Challenges and Opportunities www.slideshare.net/SusannaSansone
• 2.
  §  Researchers andbioinformaticians in both academic and commercial arenas, along with funding agencies and publishers, embrace the concept that community-developed, standards are pivotal to structure, enrich the description and share •  entities of interest e.g., genes, metabolites, phenotypes, models •  experimental steps e.g., provenance of study materials, technology and measurement types Growing movement for reproducible research
• 3.
  A community mobilizationto develop standards, e.g.: §  Structural and operational differences •  organization types (open, close to members, society, WG etc.) •  standards development (how to formulate, conduct and maintain) •  adoption, uptake, outreach (link to journals, funders and commercial sector) •  funds (sponsors, memberships, grants, volunteering) de jure de facto grass-roots groups standard organizations Nanotechnology Working Group
• 4.
  Types of reportingstandards Nanotechnology Working Group Including minimum information reporting requirements, or checklists to report the same core, essential information Including controlled vocabularies, taxonomies, thesauri, ontologies etc. to use the same word and refer to the same ‘thing’ Including conceptual model, conceptual schema from which an exchange format is derived to allow data to flow from one system to another
• 5.
  Technologically-delineated views of theworld Biologically-delineated views of the world Generic features ( common core ) - description of source biomaterial - experimental design components Arrays Scanning Arrays & Scanning Columns Gels MS MS FTIR NMR Columns transcriptomics proteomics metabolomics plant biology epidemiology microbiology Fragmentation, duplications and gaps To compare and integrate data we need interoperable standards
• 6.
  Growing number ofreporting standards + 130 + 150 + 303 Source:BioPortal Databases, annotation, curation tools implementing standards miame! MIAPA! MIRIAM! MIQAS! MIX! MIGEN! CIMR! MIAPE! MIASE! MIQE! MISFISHIE….! REMARK! CONSORT! MAGE-Tab! GCDML! SRAxml! SOFT! FASTA! DICOM! MzML! SBRML! SEDML…! GELML! ISA-Tab! CML! MITAB! AAO! CHEBI! OBI! PATO! ENVO! MOD! BTO! IDO…! TEDDY! PRO! XAO! DO VO! Source:BioSharing Source:BioSharing
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  But how muchdo we know about these standards
• 9.
  •  A coherent,curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
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  •  A coherent,curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains •  Progressively associate standards to data policies and databases •  Develop assessment criteria for usability and popularity of standards •  Help stakeholders to make informed decisions on e.g. what standards or databases to use or recommend; identify efforts they have funded
• 11.
  The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 11
• 12.
  The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 12 Users can claim records and maintain them
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  The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 13 Criteria to be used in evaluating standards for adoption
• 14.
  The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 14 Help prospective users to select and use appropriate one
• 15.
  The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 15 Classify, links standards and visualize relations
• 16.
  Example The relationship amongpopular standard formats for pathway information BioPAX and PSI-MI are designed for data exchange to and from databases and pathway and network data integration. SBML and CellML are designed to support mathematical simulations of biological systems and SBGN represents pathway diagrams. CREDIT: Demir, et al., The BioPAX community standard for pathway data sharing, 2010.
• 17.
  Drug Discovery TodayVolume 16, Numbers 21/22 November 2011 research with The information landscape in the industrial sector Big Life Science Company Yesterday Today Tomorrow Big Life Science Company Proprietary content provider Public content provider Academic group Software vendor CRO Service provider Regulatory authorities …evolving… Credit: Pistoia Alliance Michael Braxenthaler, Roche
• 18.
  Not just technologicalbut also social challenges §  Ownership of open standards can be problematic in broad, grass-root collaborations •  legal framework is still embryonic •  it requires improved models, to encourage maintenance of and contributions to these efforts, supporting their evolutions •  Extensive community liaison needs to be •  managed and funded •  rewards and incentives need to be identified for all contributors
• 19.
  Acknowledgements •  Jessica Tenenbaum • Michael Braxenthaler •  Lee Harland •  Bryn Williams-Jones •  Ian Dix •  Trish Whetzel •  Mark Musen •  Collaborators in •  OBO Foundry •  COSMOS •  ISA Commons (especially ISA-Tab-Nano team) •  GSC •  Metabolomics Society •  Data Dryad •  Pistoia Alliance •  Elixir UK •  and many more….