Table 6:
Role of bio.tools and biotoolsSchema in the evaluation of software FAIRness
| Criterion | FAIR principle for software | Provided by bio.tools | Provided by biotoolsSchema |
|---|---|---|---|
| F1 | Software and its associated metadata have a global, unique, and persistent identifier for each released version. | bio.tools assigns persistent and unique identifiers to registered software. | Attributes for bio.tools-specific software identifiers (“biotoolsID” and “biotoolsCURIE”) and other identifiers (“otherID”) including doi, rrid, and cpe. |
| F2 | Software is described with rich metadata. | biotoolsSchema defines >50 important scientific, technical, and administrative attributes that support cataloguing, discovery, use, and interoperability of software. | |
| F3 | Metadata clearly and explicitly include identifiers for all the versions of the software they describe. | biotoolsSchema supports the annotation of all versions of the software applicable to a bio.tools entry. Version information can also be attached to specific identifier, download, or publication attributes. | |
| F4 | Software and its associated metadata are included in a searchable software registry. | bio.tools information includes all metadata supported by biotoolsSchema. | biotoolSchema supports links to where software source code and binaries can be downloaded. |
| A1 | Software and its associated metadata are accessible by their identifier using a standardized communications protocol. | Metadata can be retrieved from bio.tools using an API. | |
| A1.1 | The protocol is open, free, and universally implementable. | bio.tools API is a fully documented REST API (see [53]). | |
| A1.2 | The protocol allows for an authentication and authorization procedure, where necessary. | Authentication and authorizations management are handled by the REST API (see, e.g., [54]). | |
| A2 | Software metadata are accessible, even when the software is no longer available. | Curation practice for bio.tools is to set the maturity to “legacy” instead of removing an entry; entries are never deleted. | biotoolsSchema supports annotation of software as “legacy” (“maturity” attribute). |
| I1 | Software and its associated metadata use a formal, accessible, shared, and broadly applicable language to facilitate machine readability and data exchange. | Schema.org semantic markup is available through the API. | biotoolsSchema is specified as both XSD and JSON Schema and is compatible with Schema.org. |
| I2S.1 | Software and its associated metadata are formally described using controlled vocabularies that follow the FAIR principles. | biotoolsSchema makes extensive use of controlled vocabularies, all of which are rendered FAIR through ontology portals such as OLS or are publicly available and documented (see Table 3). | |
| I2S.2 | Software uses and produces data in types and formats that are formally described using controlled vocabularies that follow the FAIR principles. | biotoolsSchema supports the data consumed and produced by software to be described using the EDAM ontology. | |
| I4S | Software dependencies are documented and mechanisms to access them exist. | biotoolsSchema provides a controlled vocabulary of documentation types (e.g., Installation instructions), which should describe software dependencies in detail. It also provides a controlled vocabulary for describing dependencies between software resources as relationships between tools (using, e.g., “uses” and “usedBy” of ”relation” attribute). | |
| R1.1 | Software and its associated metadata have independent, clear, and accessible usage licenses compatible with the software dependencies. | bio.tools entries are available under CC BY-4.0 license. | biotoolsSchema itself is licensed under CC BY-SA 4.0. Individual software licenses are documented by the “license” attribute. |
| R1.2 | Software metadata include detailed provenance; detail level should be community agreed. | biotoolsSchema supports links to the software repository where provenance information such as version history, releases, and contributors should be hosted. biotoolsSchema also includes a detailed credit model, which provides contact details for various types of contributing entities (e.g., Person, Institute) and roles (e.g., Developer, Maintainer). | |
| R1.3 | Software metadata and documentation meet domain-relevant community standards. | biotoolsSchema attribute “documentation” supports links to various documentation resources, and specification of documentation type (e.g., “Citation instructions”). |
For each FAIRness criterion for software (in column 1) as proposed in [51], the role of bio.tools (column 2) and biotoolsSchema (column 3) are summarized. Some of these criteria, such as the assignment of an identifier, are satisfied by a bio.tools registration, while other criteria such as the license depend upon the curation of a biotoolsSchema attribute within bio.tools.