TY - JOUR

T1 - biotoolsSchema

T2 - a formalized schema for bioinformatics software description

AU - Ison, Jon

AU - Ienasescu, Hans

AU - Rydza, Emil

AU - Chmura, Piotr

AU - Rapacki, Kristoffer

AU - Gaignard, Alban

AU - Schwämmle, Veit

AU - Van Helden, Jacques

AU - Kalaš, Matúš

AU - Ménager, Hervé

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - Bioinformatics software

KW - Data sharing

KW - Standards

KW - Tools

U2 - 10.1093/gigascience/giaa157

DO - 10.1093/gigascience/giaa157

M3 - Journal article

C2 - 33506265

AN - SCOPUS:85100532852

VL - 10

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 1

M1 - giaa157

ER -