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The Diversity of Biomedical Data, Databases and Standards (Research Data Alliance (RDA) 8th plenary)

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The Diversity of Biomedical Data, Databases and Standards (Research Data Alliance (RDA) 8th plenary)

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A 10 minute presentation given in Denver (CO) on the 15th September as part of the IG Elixir Bridging Force, WG Biosharing Registry,WG Data Type Registries,WG Metadata Standards Catalog joint session of the Research Data Alliance 8th Plenary (part of International Data Week).

This presentation covers the proliferation of data, databases, and data standards in biomedicine, and how BioSharing can help inform and educate users on this landscape and relationships between data, databases and data standards.

A 10 minute presentation given in Denver (CO) on the 15th September as part of the IG Elixir Bridging Force, WG Biosharing Registry,WG Data Type Registries,WG Metadata Standards Catalog joint session of the Research Data Alliance 8th Plenary (part of International Data Week).

This presentation covers the proliferation of data, databases, and data standards in biomedicine, and how BioSharing can help inform and educate users on this landscape and relationships between data, databases and data standards.

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The Diversity of Biomedical Data, Databases and Standards (Research Data Alliance (RDA) 8th plenary)

  1. 1. The Diversity of Biomedical Data, Databases and Standards Peter McQuilton BioSharing Content Lead https://www.biosharing.org @biosharing IG Elixir Bridging Force, WG Biosharing Registry,WG Data Type Registries,WG Metadata Standards Catalog International Data Week, RDA, Denver, 15th September, 2016
  2. 2. A growth in data, a growth in databases, a growth in standards Number of databases in the NAR database issue, up to 2015 (from @AlexBateman1)
  3. 3. • Data/content standards: • Structure, enrich and report the description of the datasets and the experimental context under which they were produced • Facilitate the discovery, sharing, understanding and reuse of datasets • ensure all digital research outputs are Findable, Accessible, Interoperable and Reusable (FAIR) Data has to be structured for sharing – we need standards
  4. 4. Content standards – enablers Formats Terminologies Guidelines Minimum information reporting requirements, checklists o Report the same core, essential information o e.g. MIAME guidelines Controlled vocabularies, taxonomies, thesauri, ontologies etc. o Use the same word and refer to the same ‘thing’ o e.g. Gene Ontology Conceptual model, conceptual schema, exchange formats etc o Allow data to flow from one system to another o e.g. FASTA
  5. 5. de jure de facto grass-roots groups standard organizations Nanotechnology Working Group Over 700 content standards in biomedical sciences miame MIAPA MIRIAM MIQAS MIX MIGEN ARRIVE 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 Formats Terminologies Guidelines …….... …….... ……....
  6. 6. Technologically-focused content standards Biologically-focused content standards Even if common features exists, e.g.: - description of source biomaterial - experimental design components these are inconsistently duplicated Arrays Scanning Arrays & Scanning Columns Gels MS MS FTIR NMR transcriptomics proteomics metabolomics plant biology epidemiology microbiology Diversity in Standards
  7. 7. What is BioSharing? A web-based, curated and searchable portal that monitors the development and evolution of standards, their use in databases and the adoption of both in data policies, to inform and educate the user community.
  8. 8. What is BioSharing? Standards are digital objects too and we make them FAIR
  9. 9. Data policies by funders, journals and other organizations (>100) Database, tools and services (>1000) Content standards (>700) Complex and evolving landscape Formats Terminologies Guidelines
  10. 10. Working with and for the community
  11. 11. NCBI Taxon ~1400 tags Some hierarchy Synonyms 4 axes – - Process - Material - Datatype - Property What data do we capture?
  12. 12. Collections group together one or more types of resource by domain, project or organization. Recommendations are a core-set of resources that are selected and recommended by a funder or journal data policy. Grouping records for different use cases
  13. 13. “BioSharing and its interactive browser will allow us to discover which databases and standards are not currently included in our author guidelines, enabling us to regularly monitor and refine our policies as appropriate, in support of our mission to help our authors enhance the reproducibility of their work.” – Holly Murray, F1000Research
  14. 14. Advisory Board Operational Team

Notas do Editor

  • More data
    More interest in accessing/reusing that data
    Greater need to structure and store the data

    We need to map the landscape
    Repositories
    Standards

  • Tricky to integrate data for example medical experts may be interested in microbiology – do they share standards?
    Middle: If standards developed with common elements shared across disciplines and some standards should be across technologies (e.g. array)
  • NOT GOING TO TALK ABOUT FUNCTIONALITY - SEARCHING ETC.
  • Different stakeholders have different questions
  • Recommendations based on a 3rd party policy document
  • Mention emma by name as PLOS data policy manager

    This is the educational side

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