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BioSharing - Mapping the landscape of Standards, Database and Data Policies in the Life Sciences

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A 20 minute talk on BioSharing, presented at the COST CHARME data standards conference in Warsaw, Poland, on June 21th 2016

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BioSharing - Mapping the landscape of Standards, Database and Data Policies in the Life Sciences

  1. 1. BioSharing.org Mapping the landscape of Standards, Databases and Data Policies in the Life Sciences Peter McQuilton, PhD (@drosophilic) @BioSharing content lead
  2. 2. Outline • What is BioSharing? • How do we describe and link standards? • Exploring the landscape of standards, databases and data policies in the life sciences
  3. 3. Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences 1,400 records and growing 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.
  4. 4. Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences What is BioSharing? Launched in 2011, as an evolution of the MIBBI portal (2008-2011) Manually curated Community driven Growing userbase and visibility Promoting the FAIR principles 1,400 records and growing
  5. 5. also operates as a WG in Run at is also an Resource that The BioSharing community 1,400 records and growing
  6. 6. Is there a database, implementing standards, where I can deposit my metagenomics dataset? My funder’s data sharing policy recommends the use of established standards, but which ones are widely endorsedand applicable to my toxicological and clinical data? Am I using the most up-to-date version of this terminology to annotate cell-based assays? I understand this format has been deprecated; what has been replaced by and how is leading the work? Are there databases implementing this exchange format, whose development we have funded? What are the mature standardsand standards-compliant databases we should recommend to our authors? Helping people make the right decision
  7. 7. How do we describe and link standards?
  8. 8. de jure de facto grass-roots groups standard organizations Nanotechnology Working Group Community mobilisation to develop content standards Formats Terminologies Guidelines
  9. 9. 193 85 346 miame MIAPA MIRIAM MIQASMIX 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 There are over 600 standards in the life sciences Formats Terminologies Guidelines
  10. 10. Guidelines = Minimum information reporting requirements, checklists o Report the same core, essential information o e.g. ARRIVE guidelines Terminologies = Controlled vocabularies, taxonomies, thesauri, ontologies etc. o Use the same word and refer to the same ‘thing’ o e.g. Gene Ontology Models/Formats = Conceptual model, conceptual schema, exchange formats o Allow data to flow from one system to another o e.g. FASTA Enablers: to better describe, share and query data Formats Terminologies Guidelines
  11. 11. Model/format formalizing reporting guideline --> <-- Reporting guideline used by model/format Cross-linking standards to standards and databases
  12. 12. Model/format formalizing reporting guideline --> <-- Reporting guideline used by model/format Cross-linking standards to standards and databases
  13. 13. Linking standards and databases to training material Linking standards and databases to training material
  14. 14. Data - Indicators of life cycle status Ready for use, implementation, or recommendation In development Status uncertain Deprecated as subsumed or superseded Manually curated, approved by the community
  15. 15. Data - Indicators of life cycle status Ready for use, implementation, or recommendation In development Status uncertain Deprecated as subsumed or superseded Manually curated, approved by the community
  16. 16. Exploring the landscape
  17. 17. The International Conference on Systems Biology (ICSB), 22-28 August,2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project Search, filter, and refine using our faceted search Search, filter, and refine using our faceted search
  18. 18. Collections and RecommendationsCollections and Recommendations 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.
  19. 19. BioSharing – what we do Inform – what’s out there, which databases use which standards. Map the landscape. Educate– what databases are recommended by your funder, or journal of choice, which standards should you be using, which standards and databases should you recommend? Explore the landscape.
  20. 20. Acknowledgements Eamonn Maguire, DPhil Software Engineer (contractor) Philippe Rocca-Serra, PhD Senior Research Lecturer Alejandra Gonzalez-Beltran, PhD Research Lecturer Milo Thurston, DPhil Research SW Engineer Massimiliano Izzo, PhD Research SW Engineer Peter McQuilton, PhD Senior Knowledge Engineer Allyson Lister, PhD Knowledge Engineer David Johnson, PhD Research SW Engineer Susanna-Assunta Sansone, PhD Centre’s Associate Director, Principal Investigator and Springer Nature’s Consultant for Scientific Data
  21. 21. Use us! • Add/link your standard to BioSharing • Add/link your database • Use us to inform your data policy (and add/link your policy) • Make a collection or recommendation for your group/society https://biosharing.org @biosharing

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