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Alasdair J G Gray ELIXIR-UK
Heriot-Watt University
Carole Goble
University of Manchester
Rafael C Jimenez ELIXIR-Hub
Bioschemas
WHAT
1 Nov 2017 #bioschemas 2
Structured data markup
for web pages
1 Nov 2017 #bioschemas 3
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
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
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
Structured data markup for web pages
1 Nov 2017 #bioschemas 7
1 Nov 2017 #bioschemas 8
1 Nov 2017 #bioschemas 9
HOW
1 Nov 2017 #bioschemas 10
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
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
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
Mapping SpecificationUse cases
Mockup
Adoption
Testing Application
Bioschemas Process
1 Nov 2017 #bioschemas 16
Bioschema Profiles
1 Nov 2017 #bioschemas 17
#bioschemas
UniProt
• Name
• Description
• License
• Release
• Citation
• Metrics
• Tools
• …
1 Nov 2017 18
New Biological Types for Schema.org
1 Nov 2017 #bioschemas 20
ADOPTION
1 Nov 2017 #bioschemas 21
Data Catalog
1 Nov 2017 #bioschemas 22
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
BioSamples
1 Nov 2017 #bioschemas 24
Training Material
1 Nov 2017 #bioschemas 25
TeSS: Discovering Training Material
1 Nov 2017 #bioschemas 26
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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Bioschemas overview

  • 1. Alasdair J G Gray ELIXIR-UK Heriot-Watt University Carole Goble University of Manchester Rafael C Jimenez ELIXIR-Hub Bioschemas
  • 2. WHAT 1 Nov 2017 #bioschemas 2
  • 3. Structured data markup for web pages 1 Nov 2017 #bioschemas 3
  • 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
  • 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. Structured data markup for web pages 1 Nov 2017 #bioschemas 7
  • 8. 1 Nov 2017 #bioschemas 8
  • 9. 1 Nov 2017 #bioschemas 9
  • 10. HOW 1 Nov 2017 #bioschemas 10
  • 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. 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 1 Nov 2017 #bioschemas 14
  • 14. Mapping SpecificationUse cases Mockup Adoption Testing Application Bioschemas Process 1 Nov 2017 #bioschemas 16
  • 15. Bioschema Profiles 1 Nov 2017 #bioschemas 17
  • 16. #bioschemas UniProt • Name • Description • License • Release • Citation • Metrics • Tools • … 1 Nov 2017 18
  • 17. New Biological Types for Schema.org 1 Nov 2017 #bioschemas 20
  • 18. ADOPTION 1 Nov 2017 #bioschemas 21
  • 19. Data Catalog 1 Nov 2017 #bioschemas 22
  • 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. BioSamples 1 Nov 2017 #bioschemas 24
  • 22. Training Material 1 Nov 2017 #bioschemas 25
  • 23. TeSS: Discovering Training Material 1 Nov 2017 #bioschemas 26
  • 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