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FAIR Cookbook


The official site

Visit https://fairplus.github.io/the-fair-cookbook to see the web friendly work-in-progress version of the FAIR Cookbook.

:oil_drum::construction: This project is still in early phase and this is work in progress :construction::oil_drum:


The FAIR Cookbook overview

  • The FAIR Cookbook is an activity of the FAIRplus project funded by the Innovative Medicine Initiative (IMI)
    drawing under grant agreement #802750 (2019-22).
  • The FAIR Cookbook is a project aiming at collating protocols for making data FAIR and provide examples of IMI dataset FAIRification.
  • The FAIR Cookbook is open source and licensed under CC-BY-4.0
  • The FAIR Cookbook is written using Markdown and deployed using jupyter-book
  • the FAIR Cookbook is hosted on github. The repository hosts documentation, known as FAIR recipes, and supporting code in the form of jupyter notebooks about FAIRification processes and the content will be released regularly (quarterly) in order to reflect the progress made by the project and the various working groups, which bring together academic and industry partners.

Persona-based content browsing

:construction: This section is under development :construction:

Helmut

Architect & Engineer

Jean

Data Scientist

Fulvia

Data Curator

Wang Ju

Head of Clinical Research

Content and learning objectives

Learn how to FAIRify a number of exemplar IMI datasets, putting the FAIR principles in practices; learn about levels and indicators of FAIRness; the maturity model, the technologies and tools available to assess and improve FAIRness; learn about the skills required, as well as the challenges.

The FAIRification Process

drawing

The FAIR principles & key recipes:

:construction: This section is under development :construction:

FINDABILITY

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Search Engine Optimitization

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Open Archive Deposition

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Annotation

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ACCESSIBILITY

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Access condition

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License selection

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Standards

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INTEROPERABILITY

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Metadata Standards

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Open Syntax

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Ontology

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REUSABILITY

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Standards

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Ontology

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SMART API

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Development Roadmap

The FAIRcookbook development process currently operates on a quarterly release cycle. Each cycle sees 2 scrums where specific use cases or themes are chosen and task forces assigned. The outcome of these efforts are new FAIRification protocols, or FAIR recipes which, after review, are integrated to the main FAIR Cookbook and tagged for release in the github main branch, which is used to build the web-friendly version of the book.

:heavy_check_mark: FAIR Cookbook development roadmap Gantt chart for the year 2020

:heavy_check_mark: The envisioned table of content for the FAIR Cookbook can be found here This Google Document is publicly available in view mode, and with edit mode for all FAIRplus members.


Meet the developers:

  • The FAIR Cookbook content was contributed by the following FAIRplus Consortium Members:
Name Affiliation Name Affiliation
Chuang Kee Ong AZ Ibrahim Emam ICL
Colin Wood AZ Francesco Ronzano IMIM
Ola Engkvist AZ Laura Furlong IMIM
Ratnesh Sahay AZ Herman Van Vlijmen Janssen
David Henderson Bayer Jean-Marc Neefs Janssen
Robert Giessmann Bayer Paul Peeters Janssen
Kurt Dauth BI Rudi Verbeeck Janssen
Karsten Quast Boehringer Scott Lusher Janssen
Emiliano Reynares Boehringer Derek Marren Lilly
Eva Navarrete BSC Andrea Splendiani Novartis
Salvador Capella Gutierrez BSC Dorothy Reilly Novartis
Hannah Hurst EMBL-EBI Nick Lynch PHACTS
Fuqi Xu EMBL-EBI Vitaly Sedlyarov RESOLUTE
Melanie Courtot EMBL-EBI Ulrich Goldmann RESOLUTE
Tony Burdett EMBL-EBI Manuela Pruess SIB
Andrea Zaliani Fraunhofer Mark Ibberson SIB
Andreas Pippow Fraunhofer Vassilios Ioannidis SIB
Franziska Kroh Fraunhofer Danielle Welter UL
Gesa Witt Fraunhofer Venkata P. Satagopam UL
Manfred Kohler Fraunhofer Wei Gu UL
Oya Deniz Beyan Fraunhofer Chris Evelo UM
Philip Gribbon Fraunhofer Egon Willighagen UM
Ashni Sedani GSK Nuno (Ryan) Silva Nunes UM
Femi Akintobi GSK Carole Goble UNIMAN
George Papadotas GSK Ebtisam Alharbi UNIMAN
Peter Woollard GSK Nick Juty UNIMAN
Alasdair J G Gray HWU Dominique Batista UOXF
Petros Papadopoulos HWU Philippe Rocca-Serra UOXF
Ilaria Maresi HYVE Susanna-Assunta Sansone UOXF
Jolanda Strubel HYVE Alejandra Delfin Rossaro UPS
Emma Vos HYVE Anne Cambon-Thomsen UPS

Technology stack

The FAIR Cookbook is built using jupyter-book, following the practice used by the Alan Turing's Institute Book of Data Science.

  • github is used to version control and hosting
  • Markdown is used for the write-up
  • HackMD is used as Markdown Editor thanks to its integration with github and its browser extensions
  • jupyter notebook can be used to provide executable code
  • binder is enabled which allows in web execution of any jupyter notebook distributed with the FAIR Cookbook
  • mermaid javascript library is used to produce flowcharts, Gantt charts and pie charts used in the book.

  • Jekyll Themes provide the style for the web friendly version. The name of this theme is saved in the Jekyll _config.yml configuration file found in. repository settings.


Support or Contact

Having troubles? Check out our issue tracker or contact support and we’ll help you sort it out.


Acknowledgements

The FAIR Cookbook is produced thanks to Jupyter Book