ISMB BioSchemas Presentation
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This document provides an overview of ELIXIR, a European infrastructure for biological information. ELIXIR aims to coordinate life science data infrastructure across Europe to support data sharing and interoperability. It has 17 member countries and 2 observer countries. ELIXIR focuses on areas like metadata standards, APIs, identifiers, and secure access to data. It also promotes principles like findability, accessibility, interoperability, and reusability of data. The document discusses ELIXIR's role in supporting areas like marine metagenomics, human data, crops/plants, and rare diseases. It notes that ELIXIR's hub is located alongside the European Molecular Biology Laboratory European Bioinformatics Institute.
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ISMB BioSchemas Presentation
- 1. Bioschemas.org BioSchemas Schema.org development for life sciences Niall Beard ScientificWebTechnologist, University of Manchester
- 2. ELIXIR: European infrastructure for biological information Data 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
- 3. • 17 Members • 2 Observers
- 4. Data & Interoperability • (Meta)Data Standards • Interoperability services • API’s • Identifiers • Minting, Mapping, Resolving • Secure access to data • BYOD, Use Case driven
- 5. FAIR Findable Accessible Interoperable Reusable Intelligible Reproducible Citable Track & Countable
- 6. 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.”
- 7. The long tail, collections sets and small science Slide courtesy of Todd Vision, Dryad
- 9. Metadata model ie. Recipe type
- 11. <div itemscope itemtype="http://schema.org/Recipe"> <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> . . .
- 13. Content Integration Approach Content Content Content Schema.org Schema.org Schema.org
- 14. Minimum information Controlled vocabular Cardinality Data model New properties
- 15. BioSchemas.org minimal, maximal, extensible Training materials Events Organizations Data Standards Software Minimum information for one content type Training materials Events Organizations DataSoftware Standards Common properties among content types
- 16. Content Integration Approach Content Content Content Schema.org Schema.org Schema.org integration
- 17. TeSS, ELIXIRTraining Portal - Aggregates Life ScienceTraining Materials
- 18. Large Training Sites • Well-formed APIs • XML Dumps • RSS feeds Medium/Small Sites • No structured data
- 19. http://www.france-bioinformatique.fr/en/training_material https://search.google.com/structured-data/testing-tool Applied Drupal 7 schema.org extension Took about 2 hours Included in TeSS in an hour
- 20. 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 billionWeb Pages surveyed, approx 1/3rd of web pages use schema.org • Persistent –Web already too invested for schema.org to just go away
- 21. Find | Cite | Credit Depth DATS Reach
- 22. How we develop specifications
- 24. Getting Involved • Join our mailing lists • all@bioschemas.org • Visit our website • http://bioschemas.org
- 25. Acknowledgements
- 26. Acknowledgments • TeSS Aleksandra Nenadic • BioSharing SA Sansone, A Gonzalez-Beltran, P McQuilton, P Rocca- Serra • NIH BD2K bioCADDIE SA Sansone, A Gonzalez-Beltran, Jeff Grethe • Community Premysl Velek • Event Martin Cook • Training materials Aleksandra Nenadic & Gabriella Rustici Organization representatives Group chairs BioSchemas community • ELIXIR Premysl Velek • Pistoia Alliance Richard Holland • GOBLET Terri Attwood • BBMRI Michaela Mayrhofer • Organization Richard Holland & Rafael C Jimenez • Person Niall Beard • Standard A Gonzalez-Beltran & P McQuilton
- 27. 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 • CaroleCoble • Peter McQuilton • PremysilVelek • Ian Dunlop • Jef Grethe • MiloThurston • 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
- 28. http://bioschemas.org @BioSchemas Thank you! Mailing List: all@bioschemas.org @niall_beard
Editor's Notes
- Create standards for Biological Types Proteins Pathways Samples Organizational Types Training Materials Events Researcher Profiles
- Coordinate – Integrate – Sustain Bioinfo rsources from member states five technical platforms: Data, Interoperability, Tools, Compute and Training. Connect tech to the real needs of user communities in the life sciences: Marine metagenomics, Crop and forest plants, Human data, Rare diseases.
- The ELIXIR network currently counts 17 Members and 2 Observers. The Network is coordinated from ELIXIR Hub, based alongside EMBL-EBI in Hinxton, UK
- Data and Interop WP Tasks in APIs and permanent identifiers BioSchemas is relevant to production of data standards to improve interoperability
- F+A+Intelligible -&gt; Reuse Published 15 March 2016 by Mark Wilkinson It’s the law to show this slide. FAIR principles written by prolific scientific leaders Guidelines for producing and managing data Should strive for them
- The data ecosystem appears to be moving away from centralization, is becoming more diverse and less integrated thereby exacerbating the discovery and re-usability problem for both human and computational stakeholders. Rise in smaller sites hosting data rather than large centralized repositories like Genbank and PDB Taken from Todd Vision Dryad
- Cannot introduce a new standard without asking yourself why this isn’t true. Standards to be successful Value Clear need for it to solve problem / produce benefit Uptake by a sizeable portion of the community Leveraging existing widespread standards to make them suitable for life science. The mechanism is well established Value – for people to want to use it Input – from the community in creation - feeling of openness and ownership (or a big stick if it’s dogmatic) Momentum -
- Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet Huge community Microsoft Google Yahoo Momentum – 1/3rd sites use They want to extract data – knowledge is their value Machine learning approach can be good – NER Get providers to structure Recipe type (move on!)
- Hundreds of sites with thousands of recipes Allow users to easily find recipe by specifying difficulty prep time ingredients etc
- Nested types
- Rich Snippets Sort and filter by attributes
- Search engines can integrate content
- Ammend existing schemas to make fit for life science Extend schemas if necessary Schema.org not restrictive Controlled Vocabularies we keep generic – can recommend using certain ones but don’t want to be overly prescriptive
- Try and use the same attributes to describe schema whenever possible
- The end effect of this extra layer of information yields integratable content. Lots of integration platforms like BioCaddie Openphacts and TeSS can use to include
- ELIXIR training mostly – lots of small websites and beyond
- HTML scraping Not robhust Takes a long time Sometimes not possible (non-unique ids of elements)
- Examples of extensive tooling Structured data testing tool by Google Schema.org drupal plugin (also Joomla, Wordpress,
- A considerably more scalable solution to HTML scraping that is easy to adopt for content providers and easy to integrate for content integration platforms
- BioCADDIE is the Rosetta Stone ELIXIR-NL FAIRifier DCAT+ coverage Indexing and harvesting: OAI-PMH COTS Schema.org lightweight and wide reaching and bioschemas offers that but with extra
- Empirical assessment of existing data types Map terms to most similar schema Suggested ammendments (e.g. to CreativeWork) or extend if needed ‘Minimum Information’ is most subjective field
- Produce many examples for each one Schema.org defines attributes – lots of examples in supprted formats – microdata, rdfa, and json-ld