An overview of Bioschemas presented to the ELIXIR-UK All Hands Meeting in Edinburgh, November 2017

1. Alasdair J G Gray ELIXIR-UK
Heriot-Watt University
Carole Goble
University of Manchester
Rafael C Jimenez ELIXIR-Hub
Bioschemas

2. WHAT
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3. Structured data markup
for web pages
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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. 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

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<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. Structured data markup for web pages
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8. 1 Nov 2017 #bioschemas 8

9. 1 Nov 2017 #bioschemas 9

10. HOW
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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)
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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. 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
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14. Mapping SpecificationUse cases
Mockup
Adoption
Testing Application
Bioschemas Process
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15. Bioschema Profiles
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16. #bioschemas
UniProt
• Name
• Description
• License
• Release
• Citation
• Metrics
• Tools
• …
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17. New Biological Types for Schema.org
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18. ADOPTION
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19. Data Catalog
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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
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21. BioSamples
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22. Training Material
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23. TeSS: Discovering Training Material
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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
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