Overview of standards/stakeholders in life science (RDA Engagement Interest Group)

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Overview of standards/stakeholders in life science (RDA Engagement Interest Group)

  1. 1. Data Consultant, Honorary Academic Editor Susanna-Assunta Sansone, PhD Associate Director, Principal Investigator RDA Engagement IG, Sept, 2013 Mapping the landscape of stakeholders and standards in the life sciences @
  2. 2. §  Researchers and bioinformaticians in both academic and commercial arenas, along with funding agencies and publishers, embrace the concept that community-developed, open, common reporting standards are pivotal to structure and enrich the annotation of •  entities of interest (e.g., genes, metabolites, phenotypes) and •  experimental steps (e.g., provenance of study materials, technology and measurement types) Standards for describing and reporting datasets
  3. 3. A ‘general mobilization’ to develop standards, e.g.: report the same core, essential information use the same word and refer to the same ‘thing’allow data to flow from one system to another
  4. 4. A ‘general mobilization’ to develop standards…..BUT §  Fragmentation of the standards is a major issue ! •  Being focused on particular communities’ interests, be their individual technologies or biological/biomedical disciplines, leads to duplication of effort, and more seriously, the development of (largely arbitrarily) different standards •  This severely hinders the interoperability of databases and tools and ultimately the integration of datasets
  5. 5. Growing number of reporting standards + 130 Estimated + 150 Source:MIBBI, EQUATOR + 303 Source:BioPortal Databases, annotation, curation tools 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! To track provenance of the information and ensure richness of data and experimental metadata descriptions, to maximize reusability
  6. 6. But how much do we know about these standards
  7. 7. •  A coherent, curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
  8. 8. •  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
  9. 9. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 9
  10. 10. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 10
  11. 11. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 11 Users can claim entries and maintain them
  12. 12. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 12
  13. 13. §  Existence of a formal specification, with: •  good level of documentation, with scope and use cases •  ease of implementation •  human and machine readability §  Broad adoption and implementation, outside the initial group by: •  community databases (hence existence of standards-annotated datasets) •  software (e.g. for reporting, editing, curating, submitting to databases) §  Active user community, also providing: •  support •  responsiveness to community requests •  examples §  Interoperability with and extensibility to other standards, ranging from: •  compatibility with other standards •  flexibility to cover new domains •  conversion and mapping, if applicable §  Openness Criteria to be used in evaluating standards for adoption: Jessica D. Tenenbaum Duke Translational Medicine Institute Melissa Haendel OHSU Library Susanna-Assunta Sansone University of Oxford also as part of the NIH Clinical and Translational Science Award (CTSA) program
  14. 14. §  Database name §  Main resource URL §  Contact information §  Date resource established (year) §  Conditions of use (free, or type of license) §  Scope: data types captured, curation polic §  Standards implemented: checklists, terminologies, formats §  Taxonomic coverage §  Data accessibility/output options §  Data release frequency §  Versioning period and access to historical files §  Documentation available §  User support options §  Data submission policy §  Relevant publications §  Tools available Core attributes to describe databases and assist in evaluating scope and relevance as well as access to data: Gaudet et al. NAR Database, 2011
  15. 15. Beside grass-roots initiatives and formal standardization initiatives, which other stakeholders are relevant and operative in the data area?
  16. 16. Data publication platforms, e.g.:
  17. 17. §  Pharma R&D has invested heavily in procedures and tools that integrate external information with their own data to enhance the decision-making process §  Now pre-competitive initiatives and private-public partnerships are blooming as solutions towards reducing costs, associated to data management and curation, and maximize data interoperability Pre-competitive initiative
  18. 18. Big Life Science Company Yesterday Today Tomorrow Yesterday Today Tomorrow Innovation Model Innovation inside Searching for Innovation Heterogeneity of collaborations; part of the wider ecosystem IT Internal apps & data Struggling with change security and trust Cloud, services Data Mostly inside In and out Distributed Portfolio Internally driven and owned Partially shared Shared portfolio Credit to: Pistoia Alliance Big Life Science Company Proprietary content provider Public content provider Academic group Software vendor CRO Service provider Regulatory authorities The information landscape in the industrial sector …evolving…
  19. 19. Our industry needs a Disruptive Innovation. That Disruption...is Pistoia Credit to: Pistoia Alliance If you want to go fast, go alone If you want to go far, go together

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