controlled_vocabularies.rst

Controlled vocabularies

biotoolsSchema defines 17 controlled vocabularies - as standarised enumerations of terms - for description of technical software aspects (see below).

Vocabulary	Description
tool type	The type of application software.
operating system	The operating system supported by a downloadable software package, e.g. 'Linux'.
programming language	Name of programming language the software source code was written in, e.g. 'C'.
license	Software or data usage license, e.g. 'GPL-3.0'
maturity	How mature the software product is, e.g. 'Mature'.
cost	Monetary cost of acquiring the software, e.g. 'Free of charge'.
accessibility	Whether there are non-monetary restrictions on accessing an online service, e.g. 'Open access'.
link type	The type of data, information or system that is obtained when the link is resolved, e.g. 'Helpdesk'.
download type	Type of download that is linked to, e.g. 'Source code'.
documentation type	Type of documentation that is linked to, e.g. 'API documentation'.
publication type	Type of publication, e.g. 'Review'.
relation type	Type of relation between this and another registered software, e.g. 'isNewVersionOf'.
entity type	Types of entities that may be credited, e.g. 'Person'.
entity role	Roles that may be assigned to creditable entities, e.g. 'Developer'.
ID type	Type of tool identifier, e.g. 'rrid'.
ELIXIR Platform	Name of the ELIXIR Platform that is credited, e.g. 'Tools'
ELIXIR Node	Name of the ELIXIR Node that is credited, e.g. 'Norway'
ELIXIR Community	Name of relevant ELIXIR (or associated) community, e.g. 'Galaxy'

Tool type

The type of application software: a discrete software entity can have more than one type, e.g. "Command-line tool, Web application"

Type	Description
Bioinformatics portal	web site providing a platform/portal to multiple resources used for research in a focused area, including biological databases, web applications, training resources and so on.
Command-line tool	A tool with a text-based (command-line) interface.
Database portal	A Web site providing a portal to a biological database, typically allowing a user to browse, deposit, search, visualise, analyse or download data.
Desktop application	A tool with a graphical user interface that runs on your desktop environment, e.g. on a PC or mobile device.
Library	A collection of components that are used to construct other tools. bio.tools scope includes component libraries performing high-level bioinformatics functions but excludes lower-level programming libraries.
Ontology	A collection of information about concepts, including terms, synonyms, descriptions etc.
Plug-in	A software component encapsulating a set of related functions, which are not standalone, i.e. depend upon other software for its use, e.g. a Javascript widget, or a plug-in, extension add-on etc. that extends the function of some existing tool.
Script	A tool written for some run-time environment (e.g. other applications or an OS shell) that automates the execution of tasks. Often a small program written in a general-purpose languages (e.g. Perl, Python) or some domain-specific languages (e.g. sed).
SPARQL endpoint	A service that provides queries over an RDF knowledge base via the SPARQL query language and protocol, and returns results via HTTP.
Suite	A collection of tools which are bundled together into a convenient toolkit. Such tools typically share related functionality, a common user interface and can exchange data conveniently. This includes collections of stand-alone command-line tools, or Web applications within a common portal.
Web application	A tool with a graphical user interface that runs in your Web browser.
Web API	An application programming interface (API) consisting of endpoints to a request-response message system accessible via HTTP. Includes everything from simple data-access URLs to RESTful APIs.
Web service	An API described in a machine readable form (typically WSDL) providing programmatic access via SOAP over HTTP.
Workbench	An application or suite with a graphical user interface, providing an integrated environment for data analysis which includes or may be extended with any number of functions or tools. Includes workflow systems, platforms, frameworks etc.
Workflow	A set of tools which have been composed together into a pipeline of some sort. Such tools are (typically) standalone, but are composed for convenience, for instance for batch execution via some workflow engine or script.

Operating system

The operating system supported by a downloadable software package, e.g. "Linux"

Maturity	Description
Linux	All flavours of Linux/UNIX operating systems.
Windows	All flavours of Microsoft Windows operating system.
Mac	All flavours of Apple Macintosh operating systems (primarily Mac OS X).

Programming language

Name of programming language the software source code was written in, e.g. "C"

See the technical docs for a list of valid terms.

License

Software or data usage license, e.g. "GPL-3.0"

See the technical docs for a complete list of valid terms. Noteworthy terms are below:

License	Description
Proprietary	Software for which the software's publisher or another person retains intellectual property rights - usually copyright of the source code, but sometimes patent rights.
Freeware	Proprietary software that is available for use at no monetary cost. In other words, freeware may be used without payment but may usually not be modified, re-distributed or reverse-engineered without the author's permission.
Not licensed	Software which is not licensed and is not proprietary.
Other	Software under license not currently supported by biotoolsSchema.

Maturity

How mature the software product is, e.g. "Mature"

Maturity	Description
Emerging	Nascent or early release software that may not yet be fully featured or stable.
Mature	Software that is generally considered to fulfill several of the following: secure, reliable, actively maintained, fully featured, proven in production environments, has an active community, and is described or cited in the scientific literature.
Legacy	Software which is no longer in common use, deprecated by the provider, superseded by other software, replaced by a newer version, is obsolete etc.

Cost

Monetary cost of acquiring the software, e.g. "Free of charge (with retritions)"

Cost	Description
Free of charge	Software which available for use by all, with full functionality, at no monetary cost to the user.
Free of charge (with restrictions)	Software which is available for use at no monetary cost to the user, but possibly with limited functionality, usage restrictions, or other limitations.
Commercial	Software which you have to pay to access.

Accessibility

Whether there are non-monetary restrictions on accessing an online service, e.g. "Open access"

Accessibility	Description
Open access	An online service which is available for use to all, but possibly requiring user accounts / authentication.
Open access (with restrictions)	An online service which is available for use to all, but possibly with some usage limitations and other restrictions.
Restricted access	An online service which is available for use to a restricted audience, e.g. members of a specific institute.

Link type

The type of data, information or system that is obtained when the link is resolved, e.g. "Mailing list"

Link type	Description
Discussion forum	Online forum for user discussions about the software.
Galaxy service	An online service providing the tool through the Galaxy platform.
Helpdesk	A phone line, web site or email-based system providing help to the end-user of the software.
Issue tracker	Tracker for software issues, bug reports, feature requests etc.
Mailing list	Mailing list for the software announcements, discussions, support etc.
Mirror	Mirror of an (identical) online service.
Software catalogue	Some registry, catalogue etc. other than bio.tools where the tool is also described.
Repository	A place where source code, data and other files can be retrieved from, typically via platforms like GitHub which provide version control and other features, or something simpler, e.g. an FTP site.
Social media	A website used by the software community including social networking sites, discussion and support fora, WIKIs etc.
Service	An online service (other than Galaxy) that provides access (an interface) to the software.
Technical monitoring	Information about the technical status of a tool.
Other	Other type of link for software - the default if a more specific type is not available.

Download type

Type of download that is linked to, e.g. "Binaries"

Download type	Description
API specification	File providing an API specification for the software, e.g. Swagger/OpenAPI, WSDL or RAML file.
Biological data	Biological data, or a web page on a database portal where such data may be downloaded.
Binaries	Binaries for the software; compiled code that allow a program to be installed without having to compile the source code.
Command-line specification	File providing a command line specification for the software.
Container file	Container file including the software.
Icon	Icon of the software.
Screenshot	Screenshot of the software.
Source code	The source code for the software, that can be compiled or assembled into an executable computer program.
Software package	A software package; a bundle of files and information about those files, typically including source code and / or binaries.
Test data	Data for testing the software is working correctly.
Test script	Script used for testing testing whether the software is working correctly.
Tool wrapper (CWL)	Tool wrapper in Common Workflow Language (CWL) format for the software.
Tool wrapper (galaxy)	Galaxy tool configuration file (wrapper) for the software.
Tool wrapper (taverna)	Taverna configuration file for the software.
Tool wrapper (other)	Workbench configuration file (other than taverna, galaxy or CWL wrapper) for the software.
VM image	Virtual machine (VM) image for the software.
Downloads page	Web page summarising general downloads available for the software.
Other	Other type of download for software - the default if a more specific type is not available.

Documentation type

Type of documentation that is linked to, e.g. "Citation instructions"

Documentation type	Description
API documentation	Human-readable API documentation.
Citation instructions	Information on how to correctly cite use of the software; typically which publication(s) to cite, or something more general, e.g. a form of words to use.
Code of conduct	A set of guidelines or rules outlining the norms, expectations, responsibilities and proper practice for individuals working within the software project.
Command-line options	Information about the command-line interface to a tool.
Contributions policy	Information about policy for making contributions to the software project.
FAQ	Frequently Asked Questions (and answers) about the software.
General	General documentation.
Governance	Information about the software governance model.
Installation instructions	Instructions how to install the software.
Quick start guide	A short guide helping the end-user to use the software as soon as possible.
User manual	Information on how to use the software, tailored to the end-user.
Release notes	Notes about a software release or changes to the software; a change log.
Terms of use	Rules that one must agree to abide by in order to use a service.
Training material	Online training material such as a tutorial, a presentation, video etc.
Other	Some other type of documentation not listed in biotoolsSchema.

Publication type

Type of publication, e.g. "Primary"

Publication type	Description
Primary	The principal publication about the tool itself; the article to cite when acknowledging use of the tool.
Method	A publication describing a scientific method or algorithm implemented by the tool.
Usage	A publication describing the application of the tool to scientific research, a particular task or dataset.
Benchmarking study	A publication which assessed the performance of the tool.
Review	A publication where the tool was reviewed.
Other	A publication of relevance to the tool but not fitting the other categories.

Relation type

Type of relation between this and another registered software, e.g. "isNewVersionOf"

Relation type	Description
isNewVersionOf	The software is a new version of an existing software, typically providing new or improved functionality.
hasNewVersion	(inverse of above)
uses	The software provides an interface to or in some other way uses the functions of other software under the hood, e.g. invoking a command-line tool or calling a Web API, Web service or SPARQL endpoint to perform its function.
usedBy	(inverse of above)
includes	A workbench, toolkit or workflow includes some other, independently available, software.
includedIn	(inverse of above)

Entity type

Type of entity that is credited, e.g. "Person"

Entity type	Description
Person	Credit of an individual.
Project	Credit of a community software project not formally associated with any single institute.
Division	Credit of or a formal part of an institutional organisation, e.g. a department, research group, team, etc
Institute	Credit of an organisation such as a university, hospital, research institute, service center, unit etc.
Consortium	Credit of an association of two or more institutes or other legal entities which have joined forces for some common purpose. Includes Research Infrastructures (RIs) such as ELIXIR, parts of an RI such as an ELIXIR node etc.
Funding agency	Credit of a legal entity providing funding for development of the software or provision of an online service.

Entity role

Role performed by entity that is credited, e.g. "Developer"

Role	Description
Developer	Author of the original software source code.
Maintainer	Maintainer of a mature software providing packaging, patching, distribution etc.
Provider	Institutional provider of an online service.
Documentor	Author of software documentation including making edits to a bio.tools entry.
Contributor	Some other role in software production or service delivery including design, deployment, system administration, evaluation, testing, documentation, training, user support etc.
Support	Provider of support in using the software.
Primary contact	The primary point of contact for the software.

ID type

Type of tool identifier, e.g. "rrid"

Role	Description
doi	Digital Object Identifier of the software assigned (typically) by the software developer or service provider.
rrid	Research Resource Identifier as used by the NIH-supported Resource Identification Portal (https://scicrunch.org/resources).
cpe	Common Platform Enumeration (CPE) identifier as listed in the CPE dictionary (https://cpe.mitre.org/dictionary/).
biotoolsCURIE	bio.tools CURIE (secondary identifier).

ELIXIR Platform

Name of the ELIXIR Platform that is credited, e.g. "Tools"

ELIXIR Platform	Description
Data	ELIXIR Data Platform
Tools	ELIXIR Tools Platform
Compute	ELIXIR Compute Platform
Interoperability	ELIXIR Interoperability Platform
Training	ELIXIR Training Platform

ELIXIR Node

Name of the ELIXIR Node that is credited, e.g. "Norway"

ELIXIR Node
Belgium
Czech Republic
Denmark
EMBL
Estonia
Finland
France
Germany
Greece
Hungary
Ireland
Israel
Italy
Luxembourg
Netherlands
Norway
Portugal
Slovenia
Spain
Sweden
Switzerland
UK

ELIXIR Community

Name of relevant ELIXIR (or associated) community, e.g. "Galaxy"

ELIXIR Node
3D-BioInfo
Federated Human Data
Galaxy
Human Copy Number Variation
Intrinsically Disordered Proteins
Marine Metagenomics
Metabolomics
Microbial Biotechnology
Plant Sciences
Proteomics
Rare Diseases