FAIR Cookbook

The official site


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

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

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The FAIR principles & key recipes:

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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Access condition

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License selection

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Standards

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REUSABILITY

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License selection

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Standards

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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.

☑️ FAIR Cookbook development roadmap Gantt chart for the year 2020

☑️ 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:

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.