biotoolsSchema: a formalized schema for bioinformatics software description

Jon Ison (1) , Hans Ienasescu (2) , Emil Rydza (3) , Piotr Chmura (3) , Kristoffer Rapacki (2) , Alban Gaignard (1, 4) , Veit Schwämmle (5) , Jacques van Helden (1, 6) , Matúš Kalaš (7) , Hervé Ménager (1, 8)

1 IFB-CORE - Institut Français de Bioinformatique
2 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
3 UCPH - University of Copenhagen = Københavns Universitet
4 ITX - ITX - unité de recherche de l'institut du thorax
5 SDU - University of Southern Denmark
6 AMU - Aix Marseille Université
7 UiB - University of Bergen
8 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

Background: Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information used to describe life-scientific digital resources presents an obstacle to their utilization. Although several standardization efforts are emerging, no information schema has been sufficiently detailed to enable uniform semantic and syntactic description-and cataloguing-of bioinformatics resources. Findings: Here we describe biotoolsSchema, a formalized information model that balances the needs of conciseness for rapid adoption against the provision of rich technical information and scientific context. biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with >17,000 machine-readable and human-understandable descriptions of software and other digital life-science resources. We compare our approach to related initiatives and provide alignments to foster interoperability and reusability. Conclusions: biotoolsSchema supports the formalized, rigorous, and consistent specification of the syntax and semantics of bioinformatics resources, and enables cataloguing efforts such as bio.tools that help scientists to find, comprehend, and compare resources. The use of biotoolsSchema in bio.tools promotes the FAIRness of research software, a key element of open and reproducible developments for data-intensive sciences.

Mots clés: Bioinformatics software; Data sharing; Standards; Tools

Domaines: Bio-informatique [q-bio.QM]

Jon Ison, Hans Ienasescu, Emil Rydza, Piotr Chmura, Kristoffer Rapacki, et al.. biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience, 2021, 10 (1), pp.giaa157. ⟨10.1093/gigascience/giaa157⟩. ⟨hal-03145289⟩