Workflow DRAFT Profile

Version: 0.3-DRAFT-2020_03_03 (03 March 2020)

Bioschemas specification for describing a workflow 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 > SoftwareSourceCode

Description

A workflow consists of an orchestrated and repeatable pattern of activity enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms. (source Wikipedia.org)

Latest profiles

Latest release: none

Previous profiles

Previous version: 0.2-DRAFT-2019_11_29

Contributors

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

Group Leader(s)

Alan Williams

Stuart Owen

Bert Droesbeke

Other team members

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

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: contributor
"contributor" : "Stefan Helfrich"

//Property: creator
"creator" : "Thomas Duigou"

//Property: dateCreated
"dateCreated" ; "2019-04-30"

//Property: dateModified
"dateModified" : "2019-11-05"

//Property: description
"description": "RetroPath2.0 builds a reaction network from a set of source compounds to a set of sink compounds. When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively link a source to a subset of sink compounds. This sub-network is considered as a scope and is output in dedicated files."

//Property: identifier
"identifier": "72782bbecfeff6f3e43e2278ee3353adf4515207"

//Property: license
"license" : "https://spdx.org/licenses/CC-BY-4.0.html"

//Property: name
"name": "RetroPath2.0 IBISBA workflow node"

//Property: sdPublisher
"sdPublisher" : "IBISBA Admin"

//Property: version
"version" : 1

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": "SoftwareSourceCode" }`
@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/ComputationalWorkflow/0.3-DRAFT-2020_03_03", "@type": "CreativeWork" } }`
creator	Organization Person	Schema: The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.	MANY		Property ≪creator≫ example `"creator" : "Thomas Duigou"`
dateCreated	Date DateTime	Schema: The date on which the CreativeWork was created or the item was added to a DataFeed.	ONE		Property ≪dateCreated≫ example `"dateCreated" ; "2019-04-30"`
input	Thing	Schema: the input required to use the workflow (eg. xl spreadsheet, xml file, …)	MANY
name	Text	Schema: The name of the item. Bioschemas: The name of the item as input	ONE		Property ≪name≫ example `"name": "RetroPath2.0 IBISBA workflow node"`
output	Thing	Schema: the output produced by the workflow	MANY
programmingLanguage	ComputerLanguage Text	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.	ONE		Property ≪sdPublisher≫ example `"sdPublisher" : "IBISBA Admin"`
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		Property ≪version≫ example `"version" : 1`
Marginality: Recommended.
contributor	Organization Person	Schema: A secondary contributor to the CreativeWork or Event.	MANY		Property ≪contributor≫ example `"contributor" : "Stefan Helfrich"`
description	Text	Schema: A description of the item.	ONE		Property ≪description≫ example "description": "RetroPath2.0 builds a reaction network from a set of source compounds to a set of sink compounds. When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively link a source to a subset of sink compounds. This sub-network is considered as a scope and is output in dedicated files."
hasPart	CreativeWork	Schema: Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense). Inverse property: isPartOf.	MANY
keywords	Text	Schema: Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.	ONE
license	CreativeWork URL	Schema: A license document that applies to this content, typically indicated by URL.	ONE		Property ≪license≫ example `"license" : "https://spdx.org/licenses/CC-BY-4.0.html"`
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
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		Property ≪dateModified≫ example `"dateModified" : "2019-11-05"`
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		Property ≪identifier≫ example `"identifier": "72782bbecfeff6f3e43e2278ee3353adf4515207"`
image	ImageObject URL	Schema: An image of the item. This can be a URL or a fully described ImageObject.	MANY