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)

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

    • 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 @
    • §  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
    • 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
    • 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
    • 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
    • But how much do we know about these standards
    • •  A coherent, curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
    • •  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
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 9
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 10
    • 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
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 12
    • §  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
    • §  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
    • Beside grass-roots initiatives and formal standardization initiatives, which other stakeholders are relevant and operative in the data area?
    • Data publication platforms, e.g.:
    • §  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
    • 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…
    • 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