biotoolsSchema elements

A summary of elements in biotoolsSchema is below. For more detailed information, please see the technical documentation.

Important

When producing XML files compliant to the schema, it is essential to stick to the element order (including nested elements) as described below. See the sample XML files.

Element groups

biotoolsSchema includes scientific, technical and administrative software attributes, organised for convenience into 8 logical groupings (see below).

_images/tool.png
Group XSD element Description
Summary summary Basic information about the software.
Function function Details of the function(s) (i.e. modes of operation) the software provides, expressed in terms from the EDAM ontology.
Labels label Miscellaneous scientific, technical and administrative details of the software, expressed in terms from controlled vocabularies.
Links lnk Miscellaneous links for the software e.g. repository, issue tracker or mailing list.
Downloads download Links to downloads for the software, e.g. source code, virtual machine image or container.
Documentation documentation Links to documentation about the software e.g. manual, API specification or training material.
Publications publication Publications about the software.
Credits credit Individuals or organisations that should be credited, or may be contacted about the software.

Summary group

Basic information about the software.

_images/summary.png _images/otherid.png
Element Description Type Cardinality
name Canonical software name assigned by the software developer or service provider. xs:token (restriction) 1 only
description Textual description of the software. xs:token (restriction) 1 only
homepage Homepage of the software, or some URL that best serves this purpose. URL 1 only
biotoolsID Unique ID (case insensitive) of the tool that is assigned upon registration of the software in bio.tools, normally identical to tool name. URL (restriction) 0 or 1
biotoolsCURIE bio.tools CURIE (compact URI) based on the bio.tools tool ID. xs:token (restriction) 0 or 1
version Version information (typically a version number) of the software applicable to this bio.tools entry. xs:token (restriction) 0 or more
otherID A unique identifier of the software, typically assigned by an ID-assignment authority other than bio.tools. (see below) 0 or more
otherID->value Value of tool identifier. xs:token (restriction) 1 only
otherID->type Type of tool identifier. enum (see docs) 0 or 1
otherID->version Version information (typically a version number) of the software applicable to this identifier. xs:token (restriction) 0 or 1

Note

See the Curators Guide.

Function group

Details of a function (i.e. mode of operation) the software provides, expressed in terms from the EDAM ontology.

Each software entity has one more functions, each corresponding to a mode of operation that the software provides. Each function performs one or more basic operations, and has zero or more primary input and/or output data, each of a specified type and supported format(s). For each operation, data or format element, an EDAM ontology concept URL and/or term are specified.

_images/function.png
_images/operation.png

Data and Format are modelled in the same way as Operation (shown above).

Element Description Type Cardinality
operation The basic operation(s) performed by this software function (EDAM Operation). Ontology concept (restriction) 1 or more
input Details of primary input data.    
input->data Type of primary input data, if any (EDAM data). Ontology concept (restriction) 1 only
input->format Allowed format(s) of the input data (EDAM Format). Ontology concept (restriction) 0 or more
output Details of primary output data.    
output->data Type of primary output data, if any (EDAM Data). Ontology concept (restriction) 1 only
output->format Allowed format(s) of the output data (EDAM Format). Ontology concept (restriction) 0 or more
operation | data | format | topic->url URL of an EDAM Operation | Data | Format concept. URL (restriction) 0 or 1
operation | data | format | topic->term An EDAM Operation | Data | Format term (preferred label or synonym). xs:token 0 or 1
note Concise comment about this function, if not apparent from the software description and EDAM annotations. xs:token (restriction) 0 or 1
cmd Relevant command, command-line fragment or option for executing this function / running the tool in this mode. xs:token (restriction) 0 or 1

Important

The URL must be in the appropriate EDAM Operation | Data | Format namespace, e.g.

The term, e.g. “Multiple sequence alignment” must be either the preferred label of the concept or a synonym of this term, as defined in EDAM.

Note

See the Curators Guide.

Labels group

Miscellaneous scientific, technical and administrative details of the software, expressed in terms from controlled vocabularies.

_images/labels.png
Element Description Type Cardinality
toolType A type of application software: a discrete software entity can have more than one type. enum (see docs) 0 or more
topic General scientific domain the software serves or other general category: one of EDAM Topic URL or term is specified. Ontology concept (restriction) 0 or more
topic->url URL of an EDAM Topic concept. URL (restriction) 0 or 1
topic->term An EDAM Topic term (preferred label or synonym). xs:token 0 or 1
operatingSystem The operating system supported by a downloadable software package. enum (see docs) 0 or more
language Name of programming language the software source code was written in. enum (see docs) 0 or more
license Software or data usage license. enum (see docs) 0 or 1
collectionID Tag for a collection that the software has been assigned to within bio.tools. xs:token (restriction) 0 or more
maturity How mature the software product is. enum (see link) 0 or 1
cost Monetary cost of acquiring the software. enum (see docs) 0 or 1
accessibility Whether the software is freely available for use. enum (see docs) 0 or more
ELIXIRPlatform Name of the ELIXIR Platform that is credited. enum (see docs) 0 or more
ELIXIRNode Name of the ELIXIR Node that is credited. enum (see docs) 0 or more

Note

See the Curators Guide.

Download group

Links to downloads for the software, e.g. source code, virtual machine image or container.

_images/download.png
Element Description Type Cardinality
url Link to download (or repo providing a download) for the software. URL 1 only
type Type of download that is linked to. enum (see docs) 1 only
note Comment about the download. xs:token (restriction) 0 or 1
version Version information (typically a version number) of the software applicable to this download. xs:token (restriction) 0 or 1

Note

See the Curators Guide.

Documentation group

Links to documentation about the software e.g. manual, API specification or training material.

_images/documentation.png
Element Description Type Cardinality
url Link to documentation on the web for the tool. URL 1 only
type Type of documentation that is linked to. enum (see docs) 1 only
note Comment about the documentation. xs:token (restriction) 0 or 1

Note

See the Curators Guide.

Publications group

Publications about the software

_images/publication.png
Element Description Type Cardinality
pmcid PubMed Central Identifier of a publication about the software. xs:token (restriction) 0 or 1
pmid PubMed Identifier. xs:token (restriction) 0 or 1
doi Digital Object Identifier. xs:token (restriction) 0 or 1
type Type of publication. enum (see docs) 0 or 1
version Version information (typically a version number) of the software applicable to this publication. xs:token (restriction) 0 or 1

Note

See the Curators Guide.

Credits group

Individuals or organisations that should be credited, or may be contacted about the software.

_images/credit.png
Element Description Type Cardinality
name Name of the entity that is credited. xs:token (restriction) 0 or 1
orcidid Unique identifier (ORCID iD) of a person that is credited. xs:token (restriction) 0 or 1
email Email address. email address 0 or 1
url URL, e.g. homepage of an institute. URL 0 or 1
tel Telephone number. xs:token (restriction) 0 or 1
typeEntity Type of entity that is credited. enum (see docs) 0 or 1
typeRole Role performed by entity that is credited. enum (see docs) 0 or more
note A comment about the credit. xs:token (restriction) 0 or 1

Note

See the Curators Guide.