ComputationalTool DRAFT Profile

Version: 0.5-DRAFT (26 November 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.

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.

Summary of Changes

Changes since the 0.4-DRAFT of the tools profile:

Profile name changed from Tool to ComputationalTool
outputData and outputFormat replaced with serviceOutput
Expected types of additionalType changed from Text to URL
Expected types of applicationCategory extended to include URL
Expected types of applicationSubCategory extended to include URL
inputData and inputFormat replaced with edam:has_input
Expected types of featureList extended to include Text
Expected types of provider extended to include Person

Latest profiles

Latest release: 1.0-RELEASE

Latest draft: 1.1-DRAFT

Previous profiles

Previous version: 0.4-DRAFT-2019_07_19

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

Group	Use Cases	Cross Walk	Task & Issues	Examples	Live Deploys
Tools

You can read the release version of this specification here.

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: additionalType
{
  "@context": "http://schema.org",
  "@id": "https://example.com/tool",
  "@type": "SoftwareApplication",
  "additionalType": [
    "Command-line tool",
    "Web application",
    "Web API"
  ]
}
  

//Property: applicationCategory
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "applicationCategory": "Computational science tool"
}

//Property: applicationSubCategory
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "applicationCategory": "Computational science tool",
  "applicationSubCategory": [
    "Sequence analysis"
  ]
} 

//Property: author
@id either ORCiD if available(!) or otherwise http://resource#authorname. Inside name, maybe homepage. In dump also email???

//Property: citation
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "citation": "https://doi.org/10.1038/nbt.3109"
}



//Property: codeRepository
{
  "@context": "http://schema.org",
  "@type": ["SoftwareApplication", "SoftwareSourceCode"],
  "codeRepository": "https://github.com/compomics/peptide-shaker"
}


//Property: description
{
   "@context": "http://schema.org",  "@type": "SoftwareApplication",
  "description": "PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!"
}

//Property: downloadUrl
{
   "@context": "http://schema.org",  "@type": "SoftwareApplication",
  "downloadURL": "https://github.com/sacdallago/cellmap"
}

//Property: edam:has_input
EDAM Data, EDAM Format or/and IANA media type inside

//Property: featureList
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "featureList": ["http://edamontology.org/operation_3645", "http://edamontology.org/operation_3649"]
}

//Property: identifier
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "@id": "https://bio.tools/peptideshaker",
  "identifier": "https://bio.tools/peptideshaker"
}

//Property: isAccessibleForFree
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "isAccessibleForFree": "True"
}

//Property: keywords
{ "@context": "http://schema.org", "@type": "SoftwareApplication", "keywords": "Biology, chemistry, medicine" }

//Property: license
Example with standard license:

{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "license": "https://spdx.org/licenses/Apache-2.0"
}


Example with "custom" (i.e. made-up) license:

{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "license": {
    "@type": "Comment",
    "text": "This software is free for everybody, unless kittens are hurt."
  }
}

//Property: operatingSystem
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "operatingSystem": ["Linux", "Windows", "Mac"]
}

//Property: programmingLanguage
{
  "@context": "http://schema.org",
  "@type": ["SoftwareApplication", "SoftwareSourceCode"],
  "programmingLanguage": "Java"
}


//Property: provider
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "provider": {
    "@type": "Organization",
    "name": "Bioinfra.Prot",
    "url": "http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics/bioinfraprot/"
  }
}

//Property: serviceOutput
EDAM Data, EDAM Format or/and IANA media type inside

//Property: softwareHelp
{
   "@context": "http://schema.org",  "@type": "SoftwareApplication",
  "softwareHelp": "https://biotools.readthedocs.io/en/latest/"
}

//Property: softwareVersion
{
   "@context": "http://schema.org",  "@type": "SoftwareApplication",
  "softwareVersion": "1.11, 1.12 - 1.13.6"
}

//Property: thumbnailUrl
{
  "@context": "http://schema.org",
  "@type": "SoftwareApplication",
  "thumbnailUrl": "https://compomics.github.io/favicon.ico"
}

//Property: url
{
   "@context": "http://schema.org",  "@type": "SoftwareApplication",
  "url": "http://compomics.github.io/projects/peptide-shaker.html"
}

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		Property ≪@context≫ example `{ "@context": "https://schema.org/" }`
@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	Property ≪@type≫ example `{ "@type": "SoftwareApplication" }`
@id	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	ONE		Property ≪@id≫ example `{ "@id": "http://example.com/entity/A12345" }`
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	Property ≪dct:conformsTo≫ example `{ "http://purl.org/dc/terms/conformsTo": { "@id": "https://bioschemas.org/profiles/ComputationalTool/0.5-DRAFT", "@type": "CreativeWork" } }`
description	Text	Schema: A description of the item. Bioschemas: A short description of the tool.	ONE		Property ≪description≫ example { "@context": "http://schema.org", "@type": "SoftwareApplication", "description": "PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!" }
name	Text	Schema: The name of the item.
url	URL	Schema: URL of the item. Bioschemas: Homepage of the tool.	ONE		Property ≪url≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "url": "http://compomics.github.io/projects/peptide-shaker.html" }`
Marginality: Recommended.
additionalType	URL	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	Property ≪additionalType≫ example `{ "@context": "http://schema.org", "@id": "https://example.com/tool", "@type": "SoftwareApplication", "additionalType": [ "Command-line tool", "Web application", "Web API" ] }`
applicationCategory	Text URL	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		Property ≪applicationCategory≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "applicationCategory": "Computational science tool" }`
applicationSubCategory	Text URL	Schema: Subcategory of the application, e.g. ‘Arcade Game’. Bioschemas: Use an EDAM:Topic to describe the category of application	MANY	EDAM:Topic	Property ≪applicationSubCategory≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "applicationCategory": "Computational science tool", "applicationSubCategory": [ "Sequence analysis" ] }`
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		Property ≪author≫ example `@id either ORCiD if available(!) or otherwise http://resource#authorname. Inside name, maybe homepage. In dump also email???`
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		Property ≪citation≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "citation": "https://doi.org/10.1038/nbt.3109" }`
featureList	Text 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	Property ≪featureList≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "featureList": ["http://edamontology.org/operation_3645", "http://edamontology.org/operation_3649"] }`
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/	Property ≪license≫ example `Example with standard license: { "@context": "http://schema.org", "@type": "SoftwareApplication", "license": "https://spdx.org/licenses/Apache-2.0" } Example with "custom" (i.e. made-up) license: { "@context": "http://schema.org", "@type": "SoftwareApplication", "license": { "@type": "Comment", "text": "This software is free for everybody, unless kittens are hurt." } }`
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		Property ≪softwareVersion≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "softwareVersion": "1.11, 1.12 - 1.13.6" }`
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		Property ≪codeRepository≫ example `{ "@context": "http://schema.org", "@type": ["SoftwareApplication", "SoftwareSourceCode"], "codeRepository": "https://github.com/compomics/peptide-shaker" }`
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		Property ≪downloadUrl≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "downloadURL": "https://github.com/sacdallago/cellmap" }`
edam:has_input	MediaObject	Bioschemas: This is equivalent to edam:has_input. It should be modelled as a MediaObject.	MANY		Property ≪edam:has_input≫ example `EDAM Data, EDAM Format or/and IANA media type inside`
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 an item or CreativeWork that is part of this item, or CreativeWork (in some sense). 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		Property ≪identifier≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "@id": "https://bio.tools/peptideshaker", "identifier": "https://bio.tools/peptideshaker" }`
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		Property ≪isAccessibleForFree≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "isAccessibleForFree": "True" }`
isBasedOn	CreativeWork Product URL	Schema: A resource from which this work is derived or from which it is a modification or adaption. 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 an item or CreativeWork that this item, or CreativeWork (in some sense), is 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		Property ≪keywords≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "keywords": "Biology, chemistry, medicine" }`
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	Property ≪operatingSystem≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "operatingSystem": ["Linux", "Windows", "Mac"] }`
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	Property ≪programmingLanguage≫ example `{ "@context": "http://schema.org", "@type": ["SoftwareApplication", "SoftwareSourceCode"], "programmingLanguage": "Java" }`
provider	Organization Person	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		Property ≪provider≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "provider": { "@type": "Organization", "name": "Bioinfra.Prot", "url": "http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics/bioinfraprot/" } }`
serviceOutput	MediaObject	Schema: The tangible thing generated by the service, e.g. a passport, permit, etc. Supersedes produces. Bioschemas: This is equivalent to edam:has_output. It should be modelled as a MediaObject.	MANY		Property ≪serviceOutput≫ example `EDAM Data, EDAM Format or/and IANA media type inside`
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		Property ≪softwareHelp≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "softwareHelp": "https://biotools.readthedocs.io/en/latest/" }`
thumbnailUrl	URL	Schema: A thumbnail image relevant to the Thing. Bioschemas: A small image representing the tool, such as an icon.	ONE		Property ≪thumbnailUrl≫ example `{ "@context": "http://schema.org", "@type": "SoftwareApplication", "thumbnailUrl": "https://compomics.github.io/favicon.ico" }`