Tool Information Standard

The Tool Information Standard is one component of a stack of interrelated technologies and guidelines:

technology_stack

  • biotoolsSchema is a formalised XML schema (XSD) which defines a description model for bioinformatics software. It defines a syntax for over 50 important scientific, technical and administrative attributes that support cataloguing, discovery, use and interoperability of software. 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.
  • EDAM ontology is an ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology. It defines the semantics - a controlled vocabulary - for describing software in terms of types of input and output data and data identifiers, supported data formats, operations and topics.
  • Tool Information Standard lists software attributes (from biotoolsSchema) that must be specified within a 5-tier scale of description completeness and quality. It provides a practical framework and metrics for description of individual tools, and the curation of collections such as bio.tools.
  • Curation Guidelines describe conventions for how each attribute should be specified when registering a tool in bio.tools. These human-readable and user-friendly guidelines provide information that goes beyond syntax and semantics provided by biotoolsSchema and EDAM.
  • Software Best Practice can be abstracted from the Curation Guidelines, for example, general recommendations for the description / documentation of software in contexts other than bio.tools.

Tiers in the standard

The Tool Information Standard is five lists of tool attributes (see Table below) that must be specified for a software description (e.g. a bio.tools entry) to be assigned in a 5 tier ratings of description completeness. Some attributes are grouped (see tables on right) for purposes of determining adherence to the standard. For example “Documentation” is satisfied if at least one of “General” documentation”, “API documentation” or “API specification” is specified.

infographic_attributes

Attributes

General attributes

Attribute Description Format biotoolsSchema Guideline
Name Canonical software name assigned by the software developer or service provider Text <name> link
Description Short and concise textual description of the software function Text <description> link
Homepage Homepage of the software, or some URL that best serves this purpose URL <homepage> link
Unique ID Unique ID of the tool that is assigned upon registration of the software in bio.tools Text (URL-safe version of tool name) <toolID> link
Tool type The type of application software: a discrete software entity can have more than one type. enum (from biotoolsSchema) <toolType> link
Scientific topics General scientific domain the software serves or other general category, e.g. ‘Proteomics’ Term and / or URI of EDAM Topic concept(s) <topic> link
Publications Publications about the software DOI, PMID or PMCID <publication> link
Scientific operations The basic operation(s) performed by the software, e.g. ‘Multiple sequence alignment’ Term and / or URI of EDAM Operation concept(s) <function><operation> link
Operating system The operating system supported by a downloadable software package. enum (from biotoolsSchema) <labels><OperatingSystem> link
Language Name of programming language the software source code was written in, e.g. ‘C’. enum (from biotoolsSchema) <language> link
License Software or data usage license enum (from biotoolsSchema) <labels><license> link
Type of input & output data Type of primary input / output data (if any), e.g. ‘Protein sequences’ Term and / or URI of EDAM Data concept(s) <function><input>/<output><data> link
Supported data formats Allowed format(s) of primary inputs/outputs, e.g. ‘FASTA’ Term and / or URI of EDAM Format concept(s) <function><input>/<output><format> link
Scientific benchmark Scientific benchmarking results. URL <link><type>Scientific benchmark</type> link
Technical monitoring Technical monitoring results. URL <link><type>Technical monitoring</type> link

“Documentation” group

Attribute Description Format biotoolsSchema Guideline
General documentation General documentation URL <documentation><type>General</type> link
Manual Information on how to use the software. URL <documentation><type>Manual</type> link
API documentation Human-readable API documentation. URL <documentation><type>API documentation</type> link
API specification File providing an API specification for the software, e.g. Swagger/OpenAPI, WSDL or RAML file. URL <download><type>API specification</type> link

“Code availability” group

Attribute Description Format biotoolsSchema Guideline
Repository Link to repository where source code, data and other files may be downloaded URL <link><type>Repository</type> link
Source code Software source code. URL <download><type>Source code</type> link
Source package Source package (of various types) for the software. URL <download><type>Source package</type> link

“Accessibility” group

Attribute Description Format biotoolsSchema Guideline
Terms of use Rules that one must agree to abide by in order to use a service. URL <documentation><type>Terms of use</type> link
Accessibility Whether the software is freely available for use. enum (from biotoolsSchema) <labels><Accessibility> link
Cost Monetary cost of acquiring the software. enum (from biotoolsSchema) <labels><Cost> link

“Support” group

Attribute Description Format biotoolsSchema Guideline
Helpdesk Helpdesk providing support in using the software. URL <link><type>Helpdesk</type> link
Issue tracker Link to tracker for software issues, bug reports, feature requests etc. URL <link><type>Issue tracker</type> link
Mailing list Link to mailing list for software announcements, discussions, support etc. URL <link><type>Mailing list</type> link
Contact person Primary contact, e.g. a person, helpdesk or mailing list Name, email, URL and/or ORCID iD <credit><typeRole>Primary contact</typeRole> link

“Downloads” group

Attribute Description Format biotoolsSchema Guideline
Biological data Biological data, or a web page on a database portal where such data may be downloaded. URL <download><type>Biological data</type> link
Binaries Binaries for the software. URL <download><type>Binaries</type> link
Binary package Binary package for the software. URL <download><type>Binary package</type> link
Container file Container file including the software. URL <download><type>Container file</type> link
CWL file Common Workflow Language (CWL) file for the software. URL <download><type>CWL file</type> link
Ontology A file containing an ontology, controlled vocabulary, terminology etc. URL <download><type>Ontology</type> link
VM image Virtual machine (VM) image for the software. URL <download><type>VM image</type> link
Tool wrapper (galaxy) Galaxy tool configuration file (wrapper) for the software. URL <download><type>Tool wrapper (galaxy)</type> link
Tool wrapper (taverna) Taverna configuration file for the software. URL <download><type>Tool wrapper (taverna)</type> link
Tool wrapper (other) Workbench configuration file (other than taverna, galaxy or CWL wrapper) for the software. URL <download><type>Tool wrapper (other)</type> link