The Tool Information Standards are a stack of community-defined, open and integrated technologies, technical standards and guidelines:
- biotoolsCore is a flat list of over 50 important scientific, technical and administrative software attributes that support cataloguing, discovery, use and interoperability of software. It will soon be made available in JSON format. {repo, learn more}
- EDAM is an ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology. It defines the semantics - a controlled vocabulary - to describe software functionality in terms of operations, types of input and output data and data identifiers, supported data formats, and common topics. {repo, readthedocs}
- biotoolsSchema is a formalised XML schema (XSD) which defines a description model for bioinformatics software. It defines a structure and syntax for the 50 attributes listed in biotoolsCore. To enable concise information, standard identifiers are used where possible, including EDAM ontology for scientific aspects and internally-defined controlled vocabularies for technical aspects such as programming language and license. It defines the scope and content of the bio.tools registry of life science software. {repo, readthedocs}
- Tool information profiles define lists of software attributes (from biotoolsCore) that can, should or must be specified for different types of tools within a set of tool descriptions. An individual profile - a JSON file conforming to toolInfoProfileSchema (JSON schema) - defines an information requirements that is tailored to an individual communities (national, scientific or technical). Tool information profiles provide a practical curation framework and metrics for any corpus of tools. {repo}
- Curation guidelines describe conventions for how each attribute should be specified when describing a tool for registation in catalogues such as bio.tools. These human-readable user-friendly guidelines provide information that goes beyond syntax and semantics provided by biotoolsSchema and EDAM. Beyond the general purpose Curators Guide, a set of tutorials are being tailored to the specific requirements of national, scientific and technical community profiles. {repo}
- Software Best Practice can be abstracted from the curation guidelines, for example, the general recommendations being developed by ELIXIR for the provision and documentation of software.
The standards support the broader bio.tools initative - fostered with support from ELIXIR - which aspires to provide comprehensive and consistent information for all European bioinformatics resources:
- Community curation of bioinformatics software and data resources (2019), Briefings in Bioinformatics, doi:10.1093/bib/bbz075
- The bio.tools registry of software tools and data resources for the life sciences (2019), Genome Biology, doi:10.1093/bioinformatics/btt113.
- Tools and data services registry: a community effort to document bioinformatics resources (2016), Nucleic Acids Research doi:10.1093/nar/gkv1116