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Tool DRAFT Profile

Version: 0.3-DRAFT-2019_07_18 (18 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.


Key to specification table

CD = Cardinality

Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
@context URL Used to provide the context (namespaces) for the JSON-LD file.
Not needed in other serialisations.
ONE
@type Text Schema.org/Bioschemas class for the resource declared using JSON-LD syntax. For other serialisations please use the appropriate mechanism.
While it is permissible to provide multiple types, it is preferred to use a single type.
MANY Schema.org, Bioschemas
@id IRI Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach. ONE
dct:conformsTo IRI Used to state the Bioschemas profile that the markup relates to. The versioned URL of the profile must be used.
Note that we use a CURIE in the table here but the full URL for Dublin Core terms must be used in the markup (http://purl.org/dc/terms/conformsTo), see example.
ONE Bioschemas profile versioned URL
description Text
Schema:

A description of the item.


Bioschemas:

A short description of the tool.

ONE
name Text
Schema:

The name of the item.


Bioschemas:

Name of the tool.

ONE
url URL
Schema:

URL of the item.


Bioschemas:

Homepage of the tool.

ONE
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

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
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

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
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

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/

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
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
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
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
inputData URL
Bioschemas:

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

MANY

EDAM:Data

inputFormat URL
Bioschemas:

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

MANY

EDAM:Data

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
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
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

outputData URL
Bioschemas:

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

MANY

EDAM:Data

outputFormat URL
Bioschemas:

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

MANY

EDAM:Data

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

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
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
thumbnailUrl URL
Schema:

A thumbnail image relevant to the Thing.


Bioschemas:

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

ONE
Bioschemas - 0.3 Draft 2019_07_18 Skip to content
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Tool DRAFT Profile

Version: 0.3-DRAFT-2019_07_18 (18 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.


Key to specification table
  • Green properties/types are proposed by Bioschemas, or indicate proposed changes by Bioschemas to Schema.org
  • Red properties/types exist in the core of Schema.org
  • Blue properties/types exist in the pending area of Schema.org
  • Black properties/types are reused from external vocabularies/ontologies

CD = Cardinality

Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
@context URL Used to provide the context (namespaces) for the JSON-LD file.
Not needed in other serialisations.
ONE
@type Text Schema.org/Bioschemas class for the resource declared using JSON-LD syntax. For other serialisations please use the appropriate mechanism.
While it is permissible to provide multiple types, it is preferred to use a single type.
MANY Schema.org, Bioschemas
@id IRI Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach. ONE
dct:conformsTo IRI Used to state the Bioschemas profile that the markup relates to. The versioned URL of the profile must be used.
Note that we use a CURIE in the table here but the full URL for Dublin Core terms must be used in the markup (http://purl.org/dc/terms/conformsTo), see example.
ONE Bioschemas profile versioned URL
description Text
Schema:

A description of the item.


Bioschemas:

A short description of the tool.

ONE
name Text
Schema:

The name of the item.


Bioschemas:

Name of the tool.

ONE
url URL
Schema:

URL of the item.


Bioschemas:

Homepage of the tool.

ONE
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

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
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

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
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

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/

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
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
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
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
inputData URL
Bioschemas:

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

MANY

EDAM:Data

inputFormat URL
Bioschemas:

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

MANY

EDAM:Data

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
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
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

outputData URL
Bioschemas:

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

MANY

EDAM:Data

outputFormat URL
Bioschemas:

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

MANY

EDAM:Data

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

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
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
thumbnailUrl URL
Schema:

A thumbnail image relevant to the Thing.


Bioschemas:

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

ONE


Person within Tool DRAFT Profile

Version: 0.3-DRAFT (16 November 2018)

Crosswalk

Schema.org hierarchy

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

Thing > Person

Description

Use to describe a person associated with a tool


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

Family name. In the U.S., the last name of an Person. This can be used along with givenName instead of the name property.


ONE
givenName Text
Schema:

Given name. In the U.S., the first name of a Person. This can be used along with familyName instead of the name property.


ONE
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 for Person (DOI) An identifier of the organisation. Preferrably a DOI from Fundref, GRID ID, or Ringgold ID, and in the future Organization ID Initative’s ID, best in a URL form.

MANY
View ≪identifier≫ example
Marginality: Optional.
affiliation Organization
Schema:

An organization that this person is affiliated with. For example, a school/university, a club, or a team.


Bioschemas:

TODO

MANY
View ≪affiliation≫ example
email Text
Schema:

Email address.


ONE
image ImageObject
URL
Schema:

An image of the item. This can be a URL or a fully described ImageObject.


ONE


Organization within Tool DRAFT Profile

Version: 0.3-DRAFT (16 November 2018)

Crosswalk

Schema.org hierarchy

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

Thing > Organization

Description

Use to describe an organization associated with a tool


View all examples
Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Recommended.
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:

An identifier of the organisation. Preferrably a DOI from Fundref, GRID ID, or Ringgold ID, and in the future Organization ID Initative’s ID, best in a URL form.

MANY
View ≪identifier≫ example
name Text
Schema:

The name of the item.


Bioschemas:

A name of the organisation.

ONE
View ≪name≫ example
Marginality: Optional.
logo ImageObject
URL
Schema:

An associated logo.


ONE
View ≪logo≫ example
url URL
Schema:

URL of the item.


ONE
View ≪url≫ example