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Tool DRAFT Profile

Version: 0.4-DRAFT (19 July 2019)

Bioschemas specification for describing a SoftwareApplication in the Life Sciences


If you spot any errors or omissions with this type, please file an issue in our GitHub.


Contributors

The following people have been involved in the creation of this specification document. They are all members of the Tools group.

Group Leader(s)
Other team members

Schema.org hierarchy

This Profile fits into the schema.org hierarchy as follows:

Thing > CreativeWork > SoftwareApplication

Description

The Life Science Tools specification provides a way to describe bioscience tools and software on the World Wide Web. It defines a set of metadata and vocabularies, built on top of existing technologies and standards, that can be used to represent such tools in Web pages and applications. The goal of the specification is to make it easier to discover, exchange and integrate information about life science tools across the Internet.





Key to specification table

Schema.org properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are green.

Schema.org properties/types are red.

Pending Schema.org properties/types are blue.

External (i.e., from 3rd party ontology) properties/types are black.


CD = Cardinality


View all examples
Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
description Text
Schema:

A description of the item.


Bioschemas:

A short description of the tool.

ONE
View ≪description≫ example
name Text
Schema:

The name of the item.


Bioschemas:

Name of the tool.

ONE
View ≪name≫ example
url URL
Schema:

URL of the item.


Bioschemas:

Homepage of the tool.

ONE
View ≪url≫ example
Marginality: Recommended.
additionalType Text
Schema:

An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the ‘typeof’ attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.


Bioschemas:

Type of tool e.g. Command-line tool, Web application etc. Note: Bioschemas have changed URL to Text in the Expected Types. This will be reverted once Bio.Tools provides stable URIs for tool types.

MANY

Please use terms from the ‘Tool type’ table in the biotools documentation

View ≪additionalType≫ example
applicationCategory Text
Schema:

Type of software application, e.g. ‘Game, Multimedia’.


Bioschemas:

The high-level category in the global context, please always use “Computational science tool”.

ONE
View ≪applicationCategory≫ example
applicationSubCategory Text
Schema:

Subcategory of the application, e.g. ‘Arcade Game’.


Bioschemas:

Use an EDAM:Topic to describe the category of application

MANY

EDAM:Topic

View ≪applicationSubCategory≫ example
author Organization
Person
Schema:

The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.


Bioschemas:

TODO

MANY
citation CreativeWork
Text
Schema:

A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.


Bioschemas:

Publication about this tool.

MANY
View ≪citation≫ example
featureList URL
Schema:

Features or modules provided by this application (and possibly required by other applications).


Bioschemas:

Functionality provided by the tool. Note: Bioschemas have removed Text from the Expected Types

MANY

EDAM:Operation

View ≪featureList≫ example
license CreativeWork
URL
Schema:

A license document that applies to this content, typically indicated by URL.


Bioschemas:

The license of a software, curated dataset, etc.

MANY

Use SPDX list of licenses in form https://spdx.org/licenses/

View ≪license≫ example
softwareVersion Text
Schema:

Version of the software instance.


Bioschemas:

Version(s) of the tool, which this information is valid for. Can also be a comma-delimited list and include hyphen-separated ranges of versions.

ONE
View ≪softwareVersion≫ example
Marginality: Optional.
applicationSuite Text
Schema:

The name of the application suite to which the application belongs (e.g. Excel belongs to Office).


Bioschemas:

A suite of tools, to which the tool belongs.

MANY
codeRepository URL
Schema:

Link to the repository where the un-compiled, human readable code and related code is located (SVN, github, CodePlex).


Bioschemas:

Link to the source code repository of the tool.

MANY
View ≪codeRepository≫ example
contributor Organization
Person
Schema:

A secondary contributor to the CreativeWork or Event.


Bioschemas:

TODO

MANY
discussionUrl URL
Schema:

A link to the page containing the comments of the CreativeWork.


Bioschemas:

TODO

MANY
downloadUrl URL
Schema:

If the file can be downloaded, URL to download the binary.


Bioschemas:

A link to the downloadable(s).

MANY
View ≪downloadUrl≫ example
funder Organization
Person
Schema:

A person or organization that supports (sponsors) something through some kind of financial contribution.


Bioschemas:

TODO

MANY
hasPart CreativeWork
Schema:

Indicates a CreativeWork that is (in some sense) a part of this CreativeWork. Inverse property: isPartOf.


Bioschemas:

TODO

MANY
identifier PropertyValue
Text
URL
Schema:

The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.


Bioschemas:

TODO

MANY
View ≪identifier≫ example
inputData URL
Bioschemas:

The input data of the tool. Must be one or more of the EDAM:Data concept URIs.

MANY

EDAM:Data

View ≪inputData≫ example
inputFormat URL
Bioschemas:

A supported format of the input data. Must be one or more of the EDAM:Format concept URIs.

MANY

EDAM:Data

View ≪inputFormat≫ example
isAccessibleForFree Boolean
Schema:

A flag to signal that the item, event, or place is accessible for free. Supersedes free.


Bioschemas:

A flag to signal that the tool or the service are available to be used for free.

ONE
View ≪isAccessibleForFree≫ example
isBasedOn CreativeWork
Product
URL
Schema:

A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.


Bioschemas:

A tool or another work which this tool is based on, or is an extension, distribution, or deployment of.

MANY
isPartOf CreativeWork
Schema:

Indicates a CreativeWork that this CreativeWork is (in some sense) part of. Inverse property: hasPart.


Bioschemas:

A collection, other than a suite of tools, to which the tool belongs.

MANY
keywords Text
Schema:

Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.


Bioschemas:

Additional keywords or tags important for this tool. Multiple entries are delimited by commas.

ONE
View ≪keywords≫ example
operatingSystem Text
Schema:

Operating systems supported (Windows 7, OSX 10.6, Android 1.6).


Bioschemas:

Operating systems on which the tool can be used (without additional wrapping).

MANY

Please use terms from the ‘Operating systems’ table in the biotools documentation

View ≪operatingSystem≫ example
outputData URL
Bioschemas:

The output data of the tool. Must be one or more of the EDAM:Data concept URIs.

MANY

EDAM:Data

View ≪outputData≫ example
outputFormat URL
Bioschemas:

A supported format of the output data. Must be one or more of the EDAM:Format concept URIs.

MANY

EDAM:Data

View ≪outputFormat≫ example
programmingLanguage ComputerLanguage
Text
Schema:

The computer programming language.


Bioschemas:

The main programming language(s) used to build or execute the tool.

MANY

Please use terms from the ‘Programming language’ table in the Bio.Tools documentation

View ≪programmingLanguage≫ example
provider Organization
Schema:

The service provider, service operator, or service performer; the goods producer. Another party (a seller) may offer those services or goods on behalf of the provider. A provider may also serve as the seller. Supersedes carrier.


Bioschemas:

The provider organization of a web application, database portal, web service, etc. Note: Bioschemas have removed Person from the Expected Types.

MANY
View ≪provider≫ example
softwareAddOn SoftwareApplication
Schema:

Additional content for a software application.


Bioschemas:

Additional sub-tools (add-ons, plug-ins, tools in a suite, etc.) that are included in the tool or workflow.

MANY
softwareHelp CreativeWork
Schema:

Software application help.


Bioschemas:

A documentation of the tool.

MANY
View ≪softwareHelp≫ example
thumbnailUrl URL
Schema:

A thumbnail image relevant to the Thing.


Bioschemas:

A small image representing the tool, such as an icon.

ONE
View ≪thumbnailUrl≫ example

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