What is biotoolsSchema?¶
biotoolsSchema is a formalised XML schema (XSD) which defines a description model for bioinformatics software. It can be used to describe bioinformatics tools - application software with well-defined data processing functions (inputs, outputs and operations). This includes simple tools with one or a few closely related functions, and complex, multimodal tools with many functions, tools available available for immediate use as online services, or in a form which which you can download, install, configure and run yourself.
biotoolsSchema defines over 50 important scientific, technical and administrative attributes that support cataloguing, discovery, use and interoperability of software. It concentrates upon the salient common features, with a minimal core of 3 attributes only (name, short description and homepage), to provide maximum flexibility for applications. To enable concise information, standard identifiers are used where possible, including EDAM ontology concept IDs for specialised scientific aspects. biotoolsSchema defines 18 controlled vocabularies for technical tool aspects. Verbose information is referred to by URL.
biotoolsSchema together with the EDAM ontology provide the foundation for an information standard for the description of tools. This standard is being adopted by bio.tools and defines the attributes that must be defined within a 5-tier scale of entry completeness and quality.
biotoolsSchema is used by the ELIXIR Tools & Data Services Registry (bio.tools).
How to contribute to biotoolsSchema¶
Contributions to biotoolsSchema are very welcome. Github being our primary communication channel, please do not hesitate to open issues, or comment on them. Pull requests are also welcome! The list of repositories hosting biotoolsSchema and its documentation are listed below. All materials are available under the CC-BY-SA 4.0 license.
Documentation¶
These docs describe the latest stable version (currently 3.0.0) and are maintained in GitHub. Additional documentation is available:
- Technical docs maintained in GitHub where you’ll find example data files
- Usage guidelines including the bio.tools Curators Guide and API Usage Guide
Note
Version 3.0.0 is currently supported in bio.tools.
Status¶
biotoolsSchema is a mature schema having undergone a lot of community-driven revision (e.g. see bio.tools events). Development is use-case driven, primarily by bio.tools. Future versions will not depart fundamentally from the current elements or structure. The development of biotoolsSchema can be followed at GitHub. From version 2.0.0, version numbers follow the MAJOR.MINOR.PATCH pattern:
- MAJOR version for incompatible API changes
- MINOR version for addition of functionality in a backwards-compatible manner
- PATCH version for backwards-compatible bug fixes
Please contribute via GitHub. See also the bio.tools Contributors Guide.
Motivation¶
Bioinformaticians routinely use a large and diverse set of tools and data, and demand powerful and convenient means to organise, find, understand, compare, select, use and connect the available resources. These tasks rely on consistent, machine-understandable resource descriptions. The need - filled by biotoolsSchema - is for an information model that puts the description of a broad range of resources on a consistent syntactic basis.
Citing biotoolsSchema¶
If you use biotoolsSchema, please cite:
Ison J. et al. (2021) biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience, 10 (1)
The article is freely available.