Published in chem-bla-ics

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore. But in the past two weeks I did attend two workshops.


The FAIR Cookbook - the essential resource for and by FAIR doers

Published in Scientific Data
Authors Philippe Rocca-Serra, Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, Ishwar Chandramouliswaran, Andrea Splendiani, Tony Burdett, Robert T. Giessmann, David Henderson, Dominique Batista, Ibrahim Emam, Yojana Gadiya, Lucas Giovanni, Egon Willighagen, Chris Evelo, Alasdair J. G. Gray, Philip Gribbon, Nick Juty, Danielle Welter, Karsten Quast, Paul Peeters, Tom Plasterer, Colin Wood, Eelke van der Horst, Dorothy Reilly, Herman van Vlijmen, Serena Scollen, Allyson Lister, Milo Thurston, Ramon Granell, Gabriel Backianathan, Sebastian Baier, Anne Cambon Thomsen, Martin Cook, Melanie Courtot, Mike d’Arcy, Kurt Dauth, Eva Marin del Piico, Leyla Garcia, Ulrich Goldmann, Valentin Grouès, Daniel J. B. Clarke, Erwan Lefloch, Isuru Liyanage, Petros Papadopoulos, Cyril Pommier, Emiliano Reynares, Francesco Ronzano, Alejandra Delfin-Rossaro, Venkata Sagatopam, Ashni Sedani, Vitaly Sedlyarov, Liubov Shilova, Sukhi Singh, Jolanda Strubel, Kees van Bochove, Zachary Warnes, Peter Woollard, Fuqi Xu, Andrea Zaliani, Susanna-Assunta Sansone, the FAIR Cookbook Contributors

AbstractThe notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for “FAIR doers” in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes.

Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management

Published in Journal of Cheminformatics
Authors Alexander S. Behr, Hendrik Borgelt, Norbert Kockmann

AbstractAs scientific digitization advances it is imperative ensuring data is Findable, Accessible, Interoperable, and Reusable (FAIR) for machine-processable data. Ontologies play a vital role in enhancing data FAIRness by explicitly representing knowledge in a machine-understandable format. Research data in catalysis research often exhibits complexity and diversity, necessitating a respectively broad collection of ontologies. While ontology portals such as EBI OLS and BioPortal aid in ontology discovery, they lack deep classification, while quality metrics for ontology reusability and domains are absent for the domain of catalysis research. Thus, this work provides an approach for systematic collection of ontology metadata with focus on the catalysis research data value chain. By classifying ontologies by subdomains of catalysis research, the approach is offering efficient comparison across ontologies. Furthermore, a workflow and codebase is presented, facilitating representation of the metadata on GitHub. Finally, a method is presented to automatically map the classes contained in the ontologies of the metadata collection against each other, providing further insights on relatedness of the ontologies listed. The presented methodology is designed for its reusability, enabling its adaptation to other ontology collections or domains of knowledge. The ontology metadata taken up for this work and the code developed and described in this work are available in a GitHub repository at: