biotoolsSchema: a formalized schema for bioinformatics software description

Abstract

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.

Nine best practices for research software registries and repositories

“…To improve the readability of the metadata schema and facilitate its translation to other standards, resources may provide a mapping (from the metadata schema used in the resource) to published standard schemas, through the form of a “cross-walk” ( e.g ., the CodeMeta cross-walk ( )) and include an example entry from the repository that illustrates all the fields of the metadata schema. For instance, extensive documentation ( ) is available for the biotoolsSchema ( Ison et al, 2021 ) format, which is used in the bio.tools registry. Another example is the OntoSoft vocabulary ( ), used by the OntoSoft registry ( Gil, Ratnakar & Garijo, 2015 ; Gil et al, 2016 ) and available in both machine-readable and human readable formats.…”

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

“…A similar question of granularity applies at the workflow tool level [4], particularly for Findability and Accessibility, as we can consider at lowest granularity the scientific method in general (e.g., any algorithm for sequence alignment), followed by an application suite (bio.tools entry [35], homepage, documentation), instantiated as a particular software installation (Debian package, Docker container) with its dependencies at same level. The installation includes one or more software executables (a particular binary, a running service service), providing at the highest detailed granularity level the specific types of software functionality (a particular mode of operation, choice of analysis), for instance using certain command line flags.…”

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

“…In addition, the list of versions, the last update date of the tool, the number of downloads, and all of the additional identifiers (e.g., PubMed and bio.tools 11 identifiers) are shown. In the example (Figure 2), peptide-shaker has been pulled from BioContainers repositories more than 3.6 million times, which can be used as an additional metric 6,11,12 of the usability of a particular bioinformatics or proteomics tool in Cloud and HPC environments.…”