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Bioschemas overview

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Bioschemas overview

  1. 1. Alasdair J G Gray ELIXIR-UK Heriot-Watt University Carole Goble University of Manchester Rafael C Jimenez ELIXIR-Hub Bioschemas
  2. 2. WHAT 1 Nov 2017 #bioschemas 2
  3. 3. Structured data markup for web pages 1 Nov 2017 #bioschemas 3
  4. 4. 41 Nov 2017 #bioschemas <div> <h1>Classic potato salad</h1> <div> Nutrition facts: <span>144 kcal</span>, </div> Ingredients: - <span>800g small new potato</span> Structured data markup for web pages Without markup
  5. 5. 1 Nov 2017 #bioschemas 5 <div> <h1>Classic potato salad</h1> <div> Nutrition facts: <span>144 kcal</span>, </div> Ingredients: - <span>800g small new potato</span> Structured data markup for web pages Recipe Nutrition Calories Ingridients Title Without markup
  6. 6. 1 Nov 2017 #bioschemas 6 <div itemscope itemtype="http://schema.org/Recipe"> <h1 itemprop="name">Classic potato salad</h1> <div itemprop="nutrition” itemscope itemtype="http://schema.org/NutritionInformation"> Nutrition facts: <span itemprop="calories">144 kcal</span>, </div> Ingredients: - <span itemprop="recipeIngredient">800g small new potato</span> - <span itemprop="recipeIngredient">3 shallot</span> Structured data markup for web pages RDFa JSON-LD Microdata With markup
  7. 7. Structured data markup for web pages 1 Nov 2017 #bioschemas 7
  8. 8. 1 Nov 2017 #bioschemas 8
  9. 9. 1 Nov 2017 #bioschemas 9
  10. 10. HOW 1 Nov 2017 #bioschemas 10
  11. 11. 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) 1 Nov 2017 #bioschemas 11
  12. 12. ELIXIR/Bioschemas activities planned for 2017 • Specifications and demonstrators –Data repository, Dataset, Sample, Phenotype, Beacons and Protein annotations • Discovery and validation tools • Support and community engagement –Meetings, Hackathons, Knowledge dissemination, Training in adoption Better exposure of metadata to search engines and registries Better search1 Nov 2017 #bioschemas 13
  13. 13. Bioschemas Community Many stakeholders and work streams. Lots of enthusiasm. •Good communication and coordination • Among partners • With Bioschemas community • With schema.org •Two major activities • The Project • The Community ELIXIR Implementation Study EOSCPilot Bioschemas Project Schema.org Bioschemas.org Bioschemas Project Bioschemas Project ELIXIR 1 Nov 2017 #bioschemas 14
  14. 14. Mapping SpecificationUse cases Mockup Adoption Testing Application Bioschemas Process 1 Nov 2017 #bioschemas 16
  15. 15. Bioschema Profiles 1 Nov 2017 #bioschemas 17
  16. 16. #bioschemas UniProt • Name • Description • License • Release • Citation • Metrics • Tools • … 1 Nov 2017 18
  17. 17. New Biological Types for Schema.org 1 Nov 2017 #bioschemas 20
  18. 18. ADOPTION 1 Nov 2017 #bioschemas 21
  19. 19. Data Catalog 1 Nov 2017 #bioschemas 22
  20. 20. Bioschemas Dataset Deployment OmicsDI datasets • Status: in production • Available from: view-source: http://www.omicsdi.org/dataset/pride/PXD001416 Reactome dataset • Status: in production • Available from: view-source: http://reactome.org/content/detail/R-HSA-74160 1 Nov 2017 #bioschemas 23
  21. 21. BioSamples 1 Nov 2017 #bioschemas 24
  22. 22. Training Material 1 Nov 2017 #bioschemas 25
  23. 23. TeSS: Discovering Training Material 1 Nov 2017 #bioschemas 26
  24. 24. bioschemas.org Acknowledgements Haydee Artaza Terri Atwood Phil Barker Dominique Batista Niall Beard Raoul Bonnal Cath Brooksbank Tony Burdett Guillermo Calderon Mantilla Ethy Cannon Justin Clark-Casey Martin Cook Manuel Corpas Michael R Crusoe Pavel Dallakian Luc Deltombe Stephen Ficklin Leyla Garcia Carole Goble Alejandra Gonzalez- Beltran Alasdair Gray Jeffrey Grethe Henning Hermjakob Richard Holland Carlos Horro Jon Ison Christa Janko Andy Jenkinson Rafael C Jimenez Claire Johnson Simon Jupp Nick Juty Lee Larcombe Nicolas Le Novère Mikael Linden Audald Lloret Federico López Gómez Ronald Margolis Maria Martin Michaela Th. Mayrhofer Kenneth McLeod Peter McQuilton Sarah Morgan Chris Mungall Aleksandra Nenadic Helen Parkinson Roberto Preste Giuseppe Profiti Philippe Rocca-Serra Gabriella Rustici Susanna A Sansone Vicky Schneider Serena Scollen Chris Taylor Milo Thurston Dan Timmons John Van Horn Susheel Varma Sameer Velankar Premysl Velek Andra Waagmeester Liz Williams Sarala Wimalaratne Anil Wipat Olga Ximena Giraldo Anita de Waard Peter van Heusden + others to be added 1 Nov 2017 #bioschemas 27

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