Introduction¶

Your guide in the FAIRification journey¶

The FAIR Cookbook is a collection of birds-eye view recipes on the FAIR components, the infrastructure needed, and a set of applied examples in the Life Sciences, offering a deep dive in technical aspects of FAIR data management. This is a ‘live resource’, because recipes are added and improved, collaboratively and iteratively, in an open manner. The objective of the FAIR Cookbook is to develop and disseminate guidance and processes needed to make and keep data FAIR in the Life Sciences.

Well-managed research data from academia and the industry sectors generate value far beyond the initial research purpose. Current Life Sciences data resources are extensively used by the research community across all sectors e.g. from generating evidence of a mechanism of disease through to toxicology. However, a large proportion of data generated across all sectors of Life Sciences are neither easily discoverable nor accessible and interoperable, making (re)use challenging. Our ambition is to contribute to the development of public and private capacity for high quality data management, by providing recipes that see FAIR Principles embedded in the actual generation of data.

Who is it for?¶

The FAIR Cookbook’s recipes are a combination of guidance, technical, hands-on, background and review types to cover the operation steps of FAIR data management, and are classified according to the audience types, to serve all those involved in the data management life cycle. The FAIR Cookbook is for anyone working in the Life Sciences who needs guidance on applying the FAIR Principles in practice.

For researchers, data scientists, and principal investigators examples of key recipes are those on how to handle data access, choose licenses for datasets, package data for transfer, and provide sufficient descriptive metadata.
For data stewards, data managers, and data curators examples of key recipes are those providing applied FAIRification with clinical trial, epidemiological, and molecular data, as well as those on how to deal with sensitive, patient-centric data.
For software developers, and terminology managers examples of key recipes are the technical ones focused on implementing and using a number of FAIR-enabling tools and services, which can complement their own resources.
Lastly, the FAIR Cookbook is a resource for policy makers, including funders, and trainers that can use it in their guidance material, to incentivize the practice of FAIR data management in the Life Sciences, via examples that are meaningful to the intended audience.

A live resource: present and future¶

The FAIR Cookbook is developed by a thriving community of Life Sciences professionals, in the academia and the industry sectors, including members of the ELIXIR community. Currently funded by the IMI FAIRplus project, a private-public partnership that comprises a coalition of Europe’s leading experts in data interoperability, standards, pre-clinical to clinical translation and long-term sustainable data repositories - with decades of experience in making data available to a wide scientific community for reuse. In addition to expanding its content, we will continue to add links to relevant community, mature and complementary resources in the Life Sciences, including but not limited to those part of the ELIXIR ecosystem, such as the RDMkit, FAIRsharing, biotools and TeSS; also the Pistoia Alliance’s FAIR Toolkit for Life Science Industry, and more generic resources, such as ‘The Turing Way’ handbook for reproducible data science, which the FAIR Cookbook already leverages on. Last but not least, the FAIR Cookbook is a community-driven resource that is being populated and improved, iteratively, in an open manner. If you want to contribute, see how to, or contact us at faircookbook-ed@elixir-europe.org.

The FAIR Cookbook Webinar¶

In May 2021, Our team presented the FAIR Cookbook during a very successful Elixir Webinar which saw more 480 participants connect. You can now watch the recording of the webinar on this channel:

How to cite it¶

Citing us

The FAIR Cookbook: a deliverable of the FAIRplus project (grant agreement 802750), funded by the IMI programme, a private-public partnership that receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA Companies.

To cite the FAIR cookbook FAIRplus deliverable D2.1:

@misc{rocca_serra_philippe_2022_6783564,
  author       = {Rocca-Serra, Philippe and
                  Sansone, Susanna-Assunta and
                  Gu, Wei and
                  Welter, Danielle and
                  Abbassi Daloii, Tooba and
                  Portell-Silva, Laura},
  title        = {D2.1 FAIR Cookbook},
  month        = jun,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.6783564},
  url          = {https://doi.org/10.5281/zenodo.6783564}
}

To cite the FAIR Cookbook GitHub repository:

@software{Rocca-Serra_The_FAIR_Cookbook_2022,
author = {Rocca-Serra, Philippe and J G Gray, Alasdair and Delfin Rossaro, Alejandra and Splendiani, Andrea and Zaliani,
 Andrea and Pippow, Andreas and Cambon-Thomsen, Anne and Sedani, Ashni and Goble, Carole and Evelo, Chris and Kee Ong,
 Chuang and Wood, Colin and Pommier, Cyril and J. B. Clarke, Daniel and Welter, Danielle and Henderson, David 
 and Batista, Dominique and Reilly, Dorothy and Alharbi, Ebtisam and van der Horst, Eelke and Willighagen, Egon 
 and Reynares, Emiliano and Vos, Emma and LeFloch, Erwan and Marin del Pico, Eva and Ronzano, Francesco and 
 Kroh, Franziska and Xu, Fuqi and Backianathan, Gabriel and Papadotas, George and Witt, Gesa and 
 Hurst, Hannah and Van Vlijmen, Herman and Emam, Ibrahim and Liyanage, Isuru and Neefs, Jean-Marc and
 Strubel, Jolanda and Quast, Karsten and van Bochove, Kees and Dauth, Kurt and Furlong, Laura and Garcia, Leyla
 and Giovanni, Lucas and Kohler, Manfred and Pruess, Manuela and Ibberson, Mark and Cook, Martin and 
 Courtot, Melanie and d'Arcy, Mike and Juty, Nick and Lynch, Nick and Engkvist, Ola and Deniz Beyan, Oya
 and Peeters, Paul and Woollard, Peter and Papadopoulos, Petros and Gribbon, Philip and Sahay, Ratnesh and
 Giessmann, Robert and Verbeeck, Rudi and Capella Gutierrez, Salvador and Lusher, Scott and Beier, Sebastian and
 Singh, Sukhi and Sansone, Susanna-Assunta and Plasterer, Tom and Burdett, Tony and Abbassi-Daloii, Tooba and
 Goldmann, Ulrich and Grouès, Valentin and Ioannidis, Vassilios and P. Satagopam, Venkata and Sedlyarov, Vitaly
 and Gu, Wei and Gaidya, Yojana and Warnes, Zachary},
license = {CC-BY-4.0},
month = {4},
title = {{The FAIR Cookbook}},
url = {https://github.com/FAIRplus/the-fair-cookbook/},
version = {0.1.0},
year = {2022}
}

To cite the FAIR Cookbook manuscript:

@article{Rocca-Serra2023-hk,
    author      = {Rocca-Serra, Philippe and Gu, Wei and Ioannidis, Vassilios and
              Abbassi-Daloii, Tooba and Capella-Gutierrez, Salvador and
              Chandramouliswaran, Ishwar and Splendiani, Andrea and Burdett,
              Tony and Giessmann, Robert T and Henderson, David and Batista,
              Dominique and Emam, Ibrahim and Gadiya, Yojana and Giovanni,
              Lucas and Willighagen, Egon and Evelo, Chris and Gray, Alasdair J
              G and Gribbon, Philip and Juty, Nick and Welter, Danielle and
              Quast, Karsten and Peeters, Paul and Plasterer, Tom and Wood,
              Colin and van der Horst, Eelke and Reilly, Dorothy and van
              Vlijmen, Herman and Scollen, Serena and Lister, Allyson and
              Thurston, Milo and Granell, Ramon and {FAIR Cookbook
              Contributors} and Sansone, Susanna-Assunta},
    title       = {{The {FAIR} Cookbook - the essential resource for and by {FAIR}
              doers}},
    month       = may,
    year        = 2023,
    publisher   = {Sci. Data},
    doi         = {10.1038/s41597-023-02166-3},
    url         = {https://doi.org/10.1038/s41597-023-02166-3}
}