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Bioschemas.org
BioSchemas Schema.org development for life
sciences Niall BeardScientific Web Technologist, University of Manchester
ELIXIR: European infrastructure for biological informationData infrastructure for Europe’s life-science research:
www.elixir-europe.org
@ELIXIREurope
Data
Interoperability
Tools
Compute
Training
Marine metagenomics
Human data
Crop and forest plants
Rare diseases
• 17 Members • 2 Observers
ELIXIR Hub based alongside EMBL-EBI in Hinxton
• 17 Members• 2 Observers
Data & Interoperability
• (Meta)Data Standards• Interoperability services• API’s
• Identifiers• Minting, Mapping,
Resolving• Secure access to data• BYOD, Use Case driven
FAIRFindable
Accessible
Interoperable
ReusableIntelligible
Reproducible
Citable
Track & Countable
Grand Challenge of Data-Intensive Science• “…to improve knowledge discovery by assisting
both humans and their computational agents, in the discover of, access to and integration and analysis of, task-appropriate scientific data and other scholarly digital objects.”
The long tail, collections sets and small science
Slide courtesy of Todd Vision, Dryad
https://www.explainxkcd.com/wiki/images/6/60/standards.png
Metadata modelie. Recipe type
<div itemscope itemtype="http://schema.org/Recipe">
<div itemprop="nutrition” itemscopeitemtype="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> . . .
Content Integration Approach
Content Content Content
Schema.org Schema.org Schema.org
Minimum informationControlled vocabularies
Cardinality
Data model
New properties
BioSchemas.orgminimal, maximal, extensible
Trainingmaterials
Events Organizations
Data
Standards
Software
Minimum information
for one content type
Trainingmaterials
Events Organizations
DataSoftware
Standards
Common properties
among content types
Content Integration Approach
Content Content Content
Schema.org Schema.org Schema.org
integration
TeSS, ELIXIR Training Portal - Aggregates Life Science Training Materials
Large Training Sites• Well-formed APIs• XML Dumps • RSS feeds
Medium/Small Sites• No structured data
http://www.france-bioinformatique.fr/en/training_material
https://search.google.com/structured-data/testing-tool
Applied Drupal 7 schema.org extensionTook about 2 hours
Included in TeSS in an hour
Value chain for content providers and aggregators using schema.org• Low barrier to adoption
• Simple embedding in web pages and off the shelf CMS • Builds on a shared core and data structure• Improves scalability of integration operations
• Widespread tooling, harvesters and indexing• Search engines and Integration tools
• Structured Data parsers and Rich Snippets• 10 billion Web Pages surveyed, approx 1/3rd of web
pages use schema.org• Persistent – Web already too invested for schema.org to just
go away
Find | Cite | Credit
DepthDATS
Reach
How we develop specifications
Getting Involved
• Join our mailing lists• [email protected]• Visit our website• http://bioschemas.org
Acknowledgements
Acknowledgments
• TeSSAleksandra Nenadic
• BioSharingSA Sansone, A Gonzalez-Beltran, P McQuilton, P Rocca-Serra
• NIH BD2K bioCADDIESA Sansone, A Gonzalez-Beltran, Jeff Grethe
• CommunityPremysl Velek
• EventMartin Cook
• Training materialsAleksandra Nenadic & Gabriella Rustici
Organization representatives
Group chairs
BioSchemas community
• ELIXIRPremysl Velek
• Pistoia AllianceRichard Holland
• GOBLETTerri Attwood
• BBMRIMichaela Mayrhofer
• OrganizationRichard Holland & Rafael C Jimenez
• PersonNiall Beard
• StandardA Gonzalez-Beltran & P McQuilton
Contributors• Aleksandra Nenadic• Adam Hospital • Gabriella Rustici• Carlos Horro• Martin Cook• Niall Beard• Rafael C Jimenez• Andy Jenkinson• Manuel Corpas• Roberto Preste• Richard Holland• Alejandra Gonzalez-Beltran• Andrew Lonie• Carole Coble• Peter McQuilton• Premysil Velek• Ian Dunlop• Jef Grethe• Milo Thurston• Niklas Blomberg
• Isabelle Perseil• Jaap Heringa• Jon Ison• John Hancock• Simon Jupp• John (Jack) D. Van Horn • Ivana Krenkova• Laura Furlong• Morris Swertz• Mateusz Kuzak• Mario Alberich• Mark Thompson• Maria Martin• Mikael Borg• Montserrat González• Norman Morrison• Núria Queralt-Rosinach• Olivier Sallou• Robert Pergl• Pedro Fernandes
• Yasset Perez-Riverol• Sarala Wimalaratne• Nick Juty• Jose Luis Ambite• Brane Leskošek• Celia van Gelder• Christa Janko• Christine Staiger• Dan Brickley• Daniel Faria• Dmitry Repchevsky• Daniel Sobral• Daniel Vaughan• Ian Fore• Frederik Coppens• Josep Ll. Gelpi• ChuQiao Gong• Hedi Peterson• Hervé Ménager• Nina Hrtonova
• Pierre Larmande• Rob Finn• Renzo Kottmann• Rodrigo Lopez• Sameer Velankar• Sara Light• Carol Shreffler • Silvano Squizzato• Susanna Sansone• Tony Burdett• Terri Attwood• Cath Brooksbank• Hedi Peterson• Luc Deltombe• Michaela Mayrhofer• Philippe Rocca-Serra
