ISMB BioSchemas Presentation

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• all@bioschemas.org• 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

http://bioschemas.org

@BioSchemas

Thank you!Mailing List: all@bioschemas.org

@niall_beard