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ComputationalWorkflow DRAFT Profile

Version: 0.5-DRAFT-2020_07_21 (22 July 2020)

Bioschemas specification for describing a computational workflow 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
creator Organization
Person
 Schema:

The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.


 MANY
dateCreated Date
DateTime
 Schema:

The date on which the CreativeWork was created or the item was added to a DataFeed.


 ONE
input FormalParameter
 Schema:

an input required to use the workflow (eg. xl spreadsheet, xml file, …)


 MANY
license CreativeWork
URL
 Schema:

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


 MANY
name Text
 Schema:

The name of the item.


Bioschemas:

The name of the item as input

 ONE
output FormalParameter
 Schema:

an output produced by the workflow


 MANY
programmingLanguage ComputerLanguage
 Schema:

The computer programming language.


 MANY
sdPublisher Organization
Person
 Schema:

Indicates the party responsible for generating and publishing the current structured data markup, typically in cases where the structured data is derived automatically from existing published content but published on a different site. For example, student projects and open data initiatives often re-publish existing content with more explicitly structured metadata. The sdPublisherproperty helps make such practices more explicit.


Bioschemas:

The party that publishes the structured data should normally be the host site.

 ONE
url URL
 Schema:

URL of the item.


 ONE
version Number
Text
 Schema:

The version of the CreativeWork embodied by a specified resource.


Bioschemas:

version is a release, date modified may not warrant a release, but last date modified and access to all versions is important

 ONE
Marginality: Recommended.
citation CreativeWork
Text
 Schema:

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


 MANY
contributor Organization
Person
 Schema:

A secondary contributor to the CreativeWork or Event.


 MANY
creativeWorkStatus DefinedTerm
Text
 Schema:

The status of a creative work in terms of its stage in a lifecycle. Example terms include Incomplete, Draft, Published, Obsolete. Some organizations define a set of terms for the stages of their publication lifecycle.


 ONE
description Text
 Schema:

A description of the item.


 ONE
funding Grant
 MANY
hasPart CreativeWork
 Schema:

Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense). Inverse property: isPartOf.


 MANY
isBasedOn CreativeWork
Product
URL
 Schema:

A resource from which this work is derived or from which it is a modification or adaption. Supersedes isBasedOnUrl.


 ONE
keywords Text
 Schema:

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


 ONE
maintainer Organization
Person
 Schema:

A maintainer of a Dataset, software package (SoftwareApplication), or other Project. A maintainer is a Person or Organization that manages contributions to, and/or publication of, some (typically complex) artifact. It is common for distributions of software and data to be based on “upstream” sources. When maintainer is applied to a specific version of something e.g. a particular version or packaging of a Dataset, it is always possible that the upstream source has a different maintainer. The isBasedOn property can be used to indicate such relationships between datasets to make the different maintenance roles clear. Similarly in the case of software, a package may have dedicated maintainers working on integration into software distributions such as Ubuntu, as well as upstream maintainers of the underlying work.


 MANY
producer Organization
Person
 Schema:

The person or organization who produced the workflow


 MANY
publisher Organization
Person
 Schema:

The publisher of the creative work.


Bioschemas:

Where it came came from, e.g. Galaxy, github, or WF Hub if uploaded

 MANY
runtimePlatform Text
 Schema:

Runtime platform or script interpreter dependencies (Example - Java v1, Python2.3, .Net Framework 3.0). Supersedes runtime.


 MANY
softwareRequirements Text
URL
 Schema:

Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (Examples: DirectX, Java or .NET runtime). Supersedes requirements.


Bioschemas:

Renaming schema.org/requirements as softwareRequirements

 MANY
targetProduct SoftwareApplication
 Schema:

Target Operating System / Product to which the code applies. If applies to several versions, just the product name can be used.


 MANY
Marginality: Optional.
alternateName Text
 Schema:

An alias for the item.


 MANY
conditionsOfAccess Text
 Schema:

Conditions that affect the availability of, or method(s) of access to, an item. Typically used for real world items such as an ArchiveComponent held by an ArchiveOrganization. This property is not suitable for use as a general Web access control mechanism. It is expressed only in natural language.

For example “Available by appointment from the Reading Room” or “Accessible only from logged-in accounts “.


 ONE
dateModified Date
DateTime
 Schema:

The date on which the CreativeWork was most recently modified or when the item’s entry was modified within a DataFeed.


 ONE
datePublished Date
 Schema:

Date of first broadcast/publication.


 ONE
encodingFormat Text
URL
 Schema:

Media type typically expressed using a MIME format (see IANA siteand MDN reference) e.g. application/zip for a SoftwareApplication binary, audio/mpeg for .mp3 etc.).

In cases where a CreativeWork has several media type representations, encoding can be used to indicate each MediaObject alongside particular encodingFormat information.

Unregistered or niche encoding and file formats can be indicated instead via the most appropriate URL, e.g. defining Web page or a Wikipedia/Wikidata entry. Supersedes fileFormat.


Bioschemas:

Should be the type of the workflow

 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.


 MANY
image ImageObject
URL
 Schema:

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


 MANY