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Bioschemas findability and interoperability

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Bioschemas findability and interoperability

  1. 1. Alasdair J G Gray Heriot-Watt University/ELIXIR-UK Bioschemas Community http://bioschemas.org/people/ Bioschemas: Enabling Findability & Interoperability
  2. 2. Schema.org: Semantic markup for web pages http://bioschemas.org Picture: Carole Goble, Turing Lecture 2018 4 June 2018 2
  3. 3. Bioschemas • Schema.org for life sciences –Introduce life sciences types • Use case driven –Finding data –Presenting search results –Metadata exchange • Minimum properties – 6 • Link to domain ontologies Specification on top of schema.org Layer of constrains + documentation + extensions Specification Data model Minimum information Controlled vocabularies Cardinality Documentation Examples New (properties | types) 4 June 2018 http://bioschemas.org 3
  4. 4. 4 June 2018 http://bioschemas.org 4
  5. 5. 200+ People35PMs (funding) 18Working groups 18Events 15Specifications 12Code repositories 229GitHub issues 468Community emails 30Live deploys 6M+Pages Bioschemas Community
  6. 6. Mapping SpecificationUse cases Mockup Adoption Testing Application Bioschemas Process 4 June 2018 http://bioschemas.org 6
  7. 7. Bioschemas Deployments http://bioschemas.org/liveDeploys/ 4 June 2018 http://bioschemas.org 7 30Live deploys 6M+Pages
  8. 8. TeSS: Bioschemas in action http://bioschemas.org
  9. 9. Prototype: MarRef  BioSamples Without an API 4 June 2018 http://bioschemas.org 9 https://github.com/EBIBioSamples/bioschemas_marref_demo/blob/master/Summary.md
  10. 10. Exploiting Bioschemas Markup: Tooling • buzzbang –Crawl markup –Search interface • GoWeb –Specification generation • Validata –Validate markup 4 June 2018 http://bioschemas.org 10
  11. 11. Bioschemas 2018 and Beyond • Increase Adoption –Core Data Resources –Deposition Databases –Node Resources –Community Resources • Staff Exchange Programme –Travel fund for Bioschema events –Staff transfer • Training and Events –ECCB Tutorial –NetTab –Biohackathon http://bioschemas.org4 June 2018 11 Bioschemas Tutorial 15:30–17:30 Wednesday Peking Room
  12. 12. Acknowledgements http://bioschemas.org/people/ 4 June 2018 http://bioschemas.org 12 Join Bioschemas bioschemas.org/ howtojoin/ Join Bioschemas Steering Committee https://goo.gl/forms/ brrkVCmsDAAqkNJU2

Editor's Notes

  • IMDb page for True Grit: looks like normal web page
    Markup in the page makes it interpretable by machines
    Allows content consumers to develop smart apps
    T B-L believes this is the Semantic Web
    40% of web pages contain markup
  • Currently no rich search results
    Would like something more like this
  • Thriving grassroots community
    Over 200 people
    18 Events
    15 Profiles
    30 Live deployments
    6 Million+ pages

  • Define use case
    Metadata crosswalk and mapping to schema.org
    Metadata providers
    Metadata registries
    Standards defining metadata
    Bioschemas specification
    Define minimum properties based on “finding” use cases
    Define cardinality and suggested controlled vocabularies
    Test with existing entries
    Adoption by data repositories and registries
    Applications
  • Similar work in
    FAIRsharing
    Identifiers.org
    Biosamples
  • Bioschemas markup added to MarRef pages
    Markup crawled using BuzzBang
    Data included as a BioSample Curation
    Depicted by the External Links

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