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ARC RO-Crate Profile

Profiles for representing ARCs (Annotated Research Contexts) as RO-Crate.

ARC Workflow Run RO-Crate Profiles

Version: 0.1
Permalink: coming soon
Example conforming crate: ro-crate-metadata.json
Profile Crate: ro-crate-metadata.jsonld
Authors
- Caroline Ott - https://orcid.org/0000-0003-1512-9504
- Florian Wetzels - https://orcid.org/0000-0002-5526-7138
- Lukas Weil - https://orcid.org/0000-0003-1945-6342
- Kevin Schneider - https://orcid.org/0000-0002-2198-5262
Table of Contents

Overview

The ARC Workflow Run (arc-wr) RO-Crate Profiles are a collection of profiles to describe both prospective (workflows, yet to be executed) and retrospective (runs, already executed) provenance of the orchestration of computational workflows in Annotated Research Contexts (ARCs). The profiles are designed to be re-usable in other profile collections and do not need to describe root entities of an RO-crate.

Computational and laboratory workflows share many similarities, but typically only differ in how they are executed. In an ARC, the latter are described using the ISA model, separating between a workflow description (LabProtocol) and its execution (LabProcess). These types provide properties to annotate parameterized metadata in the form of key-value pairs using ontology terms. For computational workflows, workflow descriptions are usually called workflows, and their execution is usually coined as a run of said workflow. arc-wr profiles aim to extend established workflow and run profiles to share the same process model as the ISA model, allowing for integration of computational and laboratory workflows in ARCs. Advantages in regards to provenance include uniform queries, metadata enrichment, or visualization.

arc-wr profiles combine a selection of existing profiles, mainly the Workflow Run Crate (WRC) profile collection (which itself combines Process Run Crate and Workflow RO-Crate) and extends it by providing means to annotate additional metadata and align terminology with other parts of an ARC. Therefore, the main purpose of the arc-wr profiles is to merge the workflows and runs described by the WRC with the LabProtocol and LabProcess profiles formulated in the ISA RO Crate Profile collection, creating a cohesive process model that tracks prospective and retrospective provenance of computational and laboratory workflows. To allow for the ARC’s immutable but evolving nature, arc-wr profiles are in general less strict than the underlying profiles, relaxing requirements for many mandatory fields. However, compatibility is guaranteed when following both the Mandatory and Recommended fields of the underlying profiles (see also the compatibility section).

Documentation principle

When computational analysis is performed on experimental samples or on the data resulting from an assay, this process is referred to as a run.

Documentation principle of a run

A workflow, on the other hand, is the computational protocol detailing how the data is processed, simulated, or analyzed on a computer without actually executing the computation. Since workflows offer significant value for reuse in other datasets, they are documented separately from runs.

Documentation principle of a workflow

The 4 main entities described by the arc-wr profiles are:

ARC Workflow
- A Dataset container object that describes a workflow folder inside an ARC.
- Can be used to enrich a Workflow Protocol with additional ISA metadata.
- Contains a mainEntity following the Workflow Protocol profile that describes the Main Workflow of this workflow folder, analogous to Workflow RO Crates.
- Can be a valid Workflow RO Crate, see the Compatibility section.
Workflow Protocol
- Contains prospective metadata of a workflow, e.g. descriptions of inputs and outputs.
- A Multi-type object of the types MediaObject, SoftwareSourceCode, ComputationalWorkflow, and LabProtocol. It represents the union of computational and laboratory workflow description.
- Can represent a Main Workflow (main entity) of a Workflow RO Crate following the bioschemas ComputationalWorkflow profile, extended with LabProtocol metadata (see also the Compatibility section).
ARC Run
- A Dataset container object that describes a run folder inside an ARC.
- Can be used to enrich Workflow Invocations with additional ISA metadata.
Workflow Invocation
- A Multi-type object of the types CreateAction and LabProcess. It represents the union of computational and laboratory workflow execution.
- Represents the invocation of a Workflow Protocol with actual values for the parameter slots of the executed Workflow Protocol.

They are connected via the following relations:

flowchart TD

run["<b>ARC Run</b><br>(Dataset)"]

workflow["<b>ARC Workflow</b><br>(Dataset)"]

runProcess["<b>Workflow Invocation</b><br>(CreateAction, LabProcess)"]

workflowProtocol["<b>Workflow Protocol</b><br>(File, Software, ComputationalWorkflow, LabProtocol)"]

run --mentions--> runProcess
run --about--> runProcess

runProcess --instrument--> workflowProtocol
runProcess --executesLabProtocol--> workflowProtocol
workflow --mainEntity--> workflowProtocol

Requirements

ARC Workflow

An ARC Workflow is an object that bundles ISA-compliant administrative metadata (e.g., the person that created it) and the prospective provenance of the workflow in form of Workflow Protocol(s). It is based upon schema.org/Dataset and maps to the ISA-XLSX Workflow. A dataset following this profile also follows the Administrative Crate profile. In particular, the ARC Workflow object MUST follow the Dataset profile defined in the Administrative Crate profile with the following adaptions and additions to the properties defined in that profile. In the context of an ARC, an ARC Workflow can be seen as the top-level object describing the contents and provenance of a single workflow folder inside the workflows folder.

An ARC Workflow contains a mainEntity following the Workflow Protocol profile that describes the Main Workflow of this workflow folder, analogous to Workflow RO Crates.

Property	Required	Cardinality	Expected Type	Description
<h4>Required Properties</h4>
`@id`	Required	ONE	schema.org/Text OR schema.org/URL	Used to distinguish the resource being described in JSON-LD.
`@type`	Required	ONE	schema.org/Dataset	Schema.org/Bioschemas class(es) for the resource declared using JSON-LD syntax.
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	MUST be ‘Workflow’ or ontology term to identify it as an ARC Workflow
`identifier`	Required	ONE	schema.org/Text OR schema.org/URL	A mandatory unique identifier, either a temporary identifier supplied by users or one generated by a repository or other database. For example, it could be an identifier complying with the LSID specification
`mainEntity`	Required	ONE	WorkflowProtocol	The Main Workflow Protocol described by the ARC Workflow. MUST follow the Workflow Protocol profile.
<h4>Recommended Properties</h4>
`name`	Recommended	ONE	schema.org/Text	A concise phrase used to encapsulate the purpose and goal of the ARC Workflow.
`description`	Recommended	ONE	schema.org/Text	A textual description of the ARC Workflow, with components such as objective or goals.
`hasPart`	Recommended	MANY	schema.org/MediaObject OR WorkflowProtocol	All data files that are part of the ARC Workflow. In an ARC, this SHOULD include all contents of the respective `workflow folder` represented by the ARC Workflow object. Can also be used so signify sub-workflows that are part of this workflow’s intended orchestration - if this is the case, MUST follow the Workflow Protocol profile.
<h4>Optional Properties</h4>
`url`	Optional	ONE	schema.org/URL	The filename or path of the metadata file describing the run. Optional, since in some contexts like an ARC the filename is implicit.

Workflow Protocol

A multitype object that combines ComputationalWorkflow and LabProtocol, providing prospective provenance of computational workflows that can be understood as traditional workflows as well as from a protocol perspective. A Workflow Protocol MUST follow the Protocol profile defined in the Process Core Crate profile.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@context`	Required	ONE	schema.org/URL	Used to provide the context (namespaces) for the JSON-LD file. Not needed in other serialisations.	https://bioschemas.org/profiles/ComputationalWorkflow
`@type`	Required	4	schema.org/Text AND schema.org/SoftwareSourceCode AND bioschemas.org/ComputationalWorkflow AND bioschemas.org/LabProtocol	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.	THIS PROFILE
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	MUST be ‘WorkflowProtocol’ or ontology term to identify it as a Workflow Protocol	THIS PROFILE
`@id`	Required	ONE	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	https://bioschemas.org/profiles/ComputationalWorkflow
<h4>Recommended Properties</h4>
`input`	Recommended	MANY	bioschemas.org/FormalParameter	An input required to use the computational workflow (eg. Excel spreadsheet, BAM file)	https://bioschemas.org/profiles/ComputationalWorkflow
`output`	Recommended	MANY	bioschemas.org/FormalParameter	An output produced by the workflow	https://bioschemas.org/profiles/ComputationalWorkflow
`dct:conformsTo`	Recommended	1	IRI	Used to state the profiles that the markup relates to. MUST be ‘https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE’	https://bioschemas.org/profiles/ComputationalWorkflow
`creator`	Recommended	MANY	schema.org/Organization OR schema.org/Person	The creator/author of this CreativeWork. This is the same as the Author property for CreativeWork.	https://bioschemas.org/profiles/ComputationalWorkflow
`dateCreated`	Recommended	ONE	schema.org/Date OR schema.org/DateTime	The date on which the CreativeWork was created or the item was added to a DataFeed.	https://bioschemas.org/profiles/ComputationalWorkflow
`license`	Recommended	MANY	schema.org/CreativeWork OR schema.org/URL	A license document that applies to this content, typically indicated by URL.	https://bioschemas.org/profiles/ComputationalWorkflow
`name`	Recommended	ONE	schema.org/Text	The name of the item.	https://bioschemas.org/profiles/ComputationalWorkflow
`programmingLanguage`	Recommended	MANY	schema.org/ComputerLanguage OR schema.org/Text	The computer programming language, Scripts written in a programming language, as well as workflows, generally need a runtime; in RO-Crate the runtime SHOULD be indicated using a liberal interpretation of programmingLanguage	https://bioschemas.org/profiles/ComputationalWorkflow
`sdPublisher`	Recommended	ONE	schema.org/Organization OR schema.org/Person	The host site for the ComputationalWorkflow	https://bioschemas.org/profiles/ComputationalWorkflow
`url`	Recommended	ONE	schema.org/URL	URL of the item.	https://bioschemas.org/profiles/ComputationalWorkflow
`version`	Recommended	ONE	schema.org/Text OR schema.org/Number	Version is a release. The date modified may not warrant a release, but last date modified and access to all versions is important	https://bioschemas.org/profiles/ComputationalWorkflow
<h4>Optional Properties</h4>
`description`	Optional	ONE	schema.org/Text	A description of the item.	https://bioschemas.org/profiles/ComputationalWorkflow
`hasPart`	Optional	MANY	schema.org/CreativeWork	The tools/scripts that are (potentially) used by the ComputationalWorkflow when it is executed, The parts are not ordered; they normally correspond to steps in the workflow, there is no specified mapping.	https://bioschemas.org/profiles/ComputationalWorkflow
`intendedUse`	Optional	ONE	schema.org/DefinedTerm OR schema.org/Text OR schema.org/URL	The protocol type as an ontology term	isa-ro-crate-profile/LabProtocol
`comment`	Optional	MANY	schema.org/Comment		isa-ro-crate-profile/LabProtocol
`computationalTool`	Optional	MANY	schema.org/SoftwareApplication OR schema.org/DefinedTerm OR schema.org/PropertyValue	Software or tool used as part of the lab protocol to complete a part of it.	isa-ro-crate-profile/LabProtocol

ARC Run

An ARC Run is an object that bundles ISA-compliant administrative metadata (e.g., the person that executed it) and the retrospective provenance of the run in form of Workflow Invocation(s). It is based upon schema.org/Dataset and maps to the ISA-XLSX Run. A dataset following this profile also follows the Process Core Crate profile. In particular, the ARC Run object MUST follow the Process Core Crate Dataset profile and the Administrative Crate Dataset profile with the following adaptions and additions to the properties defined in that profile. In the context of an ARC, an ARC Run can be seen as the top-level object describing the contents and provenance of a single run folder inside the runs folder.

Property	Required	Cardinality	Expected Type	Description
<h4>Required Properties</h4>
`@id`	Required	ONE	schema.org/Text OR schema.org/URL	Used to distinguish the resource being described in JSON-LD.
`@type`	Required	ONE	schema.org/Dataset	Schema.org/Bioschemas class(es) for the resource declared using JSON-LD syntax.
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	MUST be ‘Run’ or ontology term to identify it as an ARC Run
`identifier`	Required	ONE	schema.org/Text OR schema.org/URL	A mandatory unique identifier, either a temporary identifier supplied by users or one generated by a repository or other database. For example, it could be an identifier complying with the LSID specification
<h4>Recommended Properties</h4>
`name`	Recommended	ONE	schema.org/Text	A concise phrase used to encapsulate the purpose and goal of the ARC Run.
`description`	Recommended	ONE	schema.org/Text	A textual description of the ARC Run, with components such as objective or goals.
`about`	Recommended	MANY	WorkflowInvocation	The Workflow Invocation(s) described by the ARC Run. MUST follow the Workflow Invocation profile. MUST be equal to the `mentions` property
`mentions`	Recommended	MANY	WorkflowInvocation	The Workflow Invocation(s) described by the ARC Run. MUST follow the Workflow Invocation profile. MUST be equal to the `about` property
`creator`	Recommended	MANY	schema.org/Person	The performer(s) of the ARC Run.
`hasPart`	Recommended	MANY	schema.org/MediaObject OR WorkflowProtocol	All data files that are part of the ARC Run. In an ARC, this should include all contents of the respective `run folder` represented by the ARC Run object.
`measurementMethod`	Recommended	ONE	schema.org/URL OR schema.org/DefinedTerm	Term to identify the technology used to perform the computation, e.g. statistical testing. The term can be free text or from, for example, a controlled vocabulary or an ontology.
`measurementTechnique`	Recommended	ONE	schema.org/URL OR schema.org/DefinedTerm	Software Publisher/Creator and/or Software name used for the computation.
`conformsTo`	Recommended	ONE	schema.org/CreativeWork	MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, e.g. {“@id”: “https://w3id.org/ro/wfrun/process/0.4”}
<h4>Optional Properties</h4>
`url`	Optional	ONE	schema.org/URL	The filename or path of the metadata file describing the run. Optional, since in some contexts like an ARC the filename is implicit.
`variableMeasured`	Optional	ONE	schema.org/Text OR schema.org/PropertyValue	A term to qualify the endpoint, or what is being computed (e.g. gene expression profiling or protein identification). The term can be free text or from, for example, a controlled vocabulary or an ontology.

Workflow Invocation

A multitype object that combines CreateAction and LabProcess, providing retrospective provenance of computational workflow execution that can be understood as traditional workflow runs as well as from a process sequence perspective. An Workflow Invocation MUST follow the Process profile defined in the Process Core Crate profile, with the following additions to the properties defined in that profile.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	A unique identifier for the execution, e.g. “urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1”, “#f99a8e6c”. MAY be an absolute URI, e.g. http://example.com/runs/846756b228c1. The use of randomly generated UUIDs (type 4) is RECOMMENDED. SHOULD be listed under mentions of the root data entity.	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate
`@type`	Required	2	schema.org/CreateAction AND bioschemas.org/LabProcess	MUST be LabProcess and CreateAction to indicate that this tool created the result data entities	THIS PROFILE
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	MUST be ‘WorkflowInvocation’ or ontology term to identify it as a Workflow Invocation	THIS PROFILE
`instrument`	Required	MANY	WorkflowProtocol	The executed Workflow Protocol. MUST follow the Workflow Protocol profile. MUST be equal to the `executesLabProtocol` property.	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate; https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate
`executesLabProtocol`	Required	ONE	WorkflowProtocol	The executed Workflow Protocol. MUST follow the Workflow Protocol profile. MUST be equal to the `instrument` property.	https://bioschemas.org/types/LabProcess/0.1-DRAFT
`result`	Required	MANY	schema.org/MediaObject OR schema.org/Dataset OR schema.org/Collection OR schema.org/CreativeWork OR schema.org/PropertyValue	The identifier of one or more entities that were created or modified by this action, e.g. output files. Entities referenced by an action’s object or result SHOULD be of type File (an RO-Crate alias for MediaObject) for files, Dataset for directories and Collection for multi-file datasets, but MAY be a CreativeWork for other types of data (e.g. an online database); they MAY be of type PropertyValue to capture numbers/strings that are not stored as files.	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate, https://bioschemas.org/types/LabProcess/0.1-DRAFT
`object`	Required	MANY	schema.org/MediaObject OR schema.org/Dataset OR schema.org/Collection OR schema.org/CreativeWork OR schema.org/PropertyValue	The identifier of one or more entities of the RO-Crate that were consumed by this action, e.g. input files or reference datasets. Entities referenced by an action’s object or result SHOULD be of type File (an RO-Crate alias for MediaObject) for files, Dataset for directories and Collection for multi-file datasets, but MAY be a CreativeWork for other types of data (e.g. an online database); they MAY be of type PropertyValue to capture numbers/strings that are not stored as files.	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate, https://bioschemas.org/types/LabProcess/0.1-DRAFT
`name`	Required	ONE	schema.org/Text	Short human-readable description of the execution.	https://bioschemas.org/types/LabProcess/0.1-DRAFT
<h4>Recommended Properties</h4>
<h4>Optional Properties</h4>
`parameterValue`	Optional	ONE	schema.org/PropertyValue	A parameter value of the workflow invocation, usually a key-value pair using ontology terms	https://bioschemas.org/types/LabProcess/0.1-DRAFT
`description`	Optional	ONE	schema.org/Text OR schema.org/TextObject	Details of the execution, for instance command line arguments or settings. This field is for information only, no particular structure is to be assumed.	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate

FormalParameter

FormalParameters are used to describe shape and type of inputs and outputs of a Workflow Protocol. They provide prospective provenance, while their realized values are described by Workflow Inputs in Workflow Invocations.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	https://bioschemas.org/profiles/FormalParameter/1.1-DRAFT
`@type`	Required	MANY	bioschemas.org/FormalParameter	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.	https://bioschemas.org/profiles/FormalParameter/1.1-DRAFT
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	SHOULD include: File, Dataset or Collection if it maps to a file, directory or multi-file dataset, respectively; PropertyValue if it maps to a dictionary-like structured value (e.g. a CWL record); DataType or one of its subtypes (e.g. Integer) if it maps to a non-structured value.	https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate
<h4>Recommended Properties</h4>
`dct:conformsTo`	Recommended	1	IRI	Used to state the profiles that the markup relates to. MUST be ‘https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21’	https://bioschemas.org/profiles/ComputationalWorkflow
`encodingFormat`	Recommended	MANY	schema.org/Text OR schema.org/URL	Media type typically expressed using a MIME format (see IANA site and 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.	https://bioschemas.org/types/FormalParameter/1.0-RELEASE,https://www.researchobject.org/ro-crate/specification/1.1/workflows.html
`name`	Recommended	ONE	schema.org/Text	SHOULD match the name of the corresponding workflow parameter slot, e.g. n_lines.	https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate
<h4>Optional Properties</h4>
`description`	Optional	ONE	schema.org/Text	A description of the parameter’s purpose, e.g. Number of lines.	https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate
`workExample`	Optional	ONE	IRI	Identifier of the data entity or PropertyValue instance that realizes this parameter. The data entity or PropertyValue instance SHOULD refer to this parameter via exampleOfWork.	https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/
`defaultValue`	Optional	ONE	schema.org/Text OR schema.org/Thing	The default value of the input. For literals, this is a literal value. For objects, it is an ID reference.	https://bioschemas.org/types/FormalParameter/1.0-RELEASE
`valueRequired`	Optional	ONE	schema.org/Boolean	For an input, whether a value must be specified for the workflow to be run. Default is false.	https://bioschemas.org/types/FormalParameter/1.0-RELEASE
`identifier`	Optional	MANY	schema.org/PropertyValue	A description for the prefix or position of a FormalParameter as an input. MUST be PropertyValue - Prefix or PropertyValue - Position	https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate

PropertyValue

Where possible, PropertyValues representing parameterValues in process sequences of WorkflowInvocations SHOULD follow the respective (sub)profile defined in the ISA RO-Crate Profile Workflow Run PropertyValue objects, in general, MUST follow the PropertyValue profile defined in the Administrative Crate profile.

PropertyValue - Workflow Input

A PropertyValue that is used as an object in a Workflow Invocation to describe the realized value for an input of a Workflow Protocol. Distinguishes this PropertyValue from process sequence related objects by linking it to the realized input via the exampleOfWork property.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	https://schema.org/PropertyValue
`@type`	Required	MANY	schema.org/PropertyValue	Schema.org 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.	https://schema.org/PropertyValue
`additionalType`	Required	ONE	schema.org/Text OR schema.org/URL	MUST be ‘WorkflowInput’ or ontology term to identify it as a Workflow Input	THIS PROFILE
`exampleOfWork`	Required	ONE	IRI	Identifier of the FormalParameter instance realized by this entity - intended to describe realization of `input`s of Workflow Protocols in Workflow Invocations. MUST refer to a `input` of a Workflow Protocol to distinguish from inputs that are process parameters.	https://schema.org/PropertyValue
`value`	Required	ONE	schema.org/Boolean OR schema.org/Number OR schema.org/StructuredValue OR schema.org/Text	The value of a QuantitativeValue (including Observation) or property value node. For QuantitativeValue and MonetaryAmount, the recommended type for values is ‘Number’. For PropertyValue, it can be ‘Text’, ‘Number’, ‘Boolean’, or ‘StructuredValue’. Use values from 0123456789 [Add to Citavi project by ISBN] (Unicode ‘DIGIT ZERO’ (U+0030) to ‘DIGIT NINE’ (U+0039)) rather than superficially similar Unicode symbols. Use ‘.’ (Unicode ‘FULL STOP’ (U+002E)) rather than ‘,’ to indicate a decimal point. Avoid using these symbols as a readability separator.	https://schema.org/PropertyValue
<h4>Recommended Properties</h4>
`name`	Recommended	ONE	schema.org/Text	The name of the item.	https://schema.org/Thing
<h4>Optional Properties</h4>

PropertyValue - Prefix

A PropertyValue that is used to describe the prefix of an input of a Workflow Protocol described by a FormalParameter.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	https://schema.org/PropertyValue
`@type`	Required	MANY	schema.org/PropertyValue	Schema.org 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.	https://schema.org/PropertyValue
`name`	Required	ONE	schema.org/Text	MUST be ‘Prefix’	THIS PROFILE
`value`	Required	ONE	schema.org/Text	The CLI prefix of an input from a Workflow Protocol profile described by a FormalParameter	THIS PROFILE
<h4>Recommended Properties</h4>
<h4>Optional Properties</h4>

PropertyValue - Position

A PropertyValue that is used to describe the position of an input of a Workflow Protocol described by a FormalParameter.

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	https://schema.org/PropertyValue
`@type`	Required	MANY	schema.org/PropertyValue	Schema.org 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.	https://schema.org/PropertyValue
`name`	Required	ONE	schema.org/Text	MUST be ‘Position’	THIS PROFILE
`value`	Required	ONE	schema.org/Number	The position of an input from a Workflow Protocol profile described by a FormalParameter	THIS PROFILE
<h4>Recommended Properties</h4>
<h4>Optional Properties</h4>

SoftwareApplication

Property	Required	Cardinality	Expected Type	Description	Source Profile
<h4>Required Properties</h4>
`@id`	Required	ONE	IRI	SHOULD be an absolute URI, but MAY be a relative URI to a data entity in the crate (e.g. “bin/simulation4”) or a local identifier for tools that are not otherwise described on the web (e.g. “#statistical-analysis”)	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate
`@type`	Required	MANY	schema.org/SoftwareApplication OR schema.org/SoftwareSourceCode OR bioschemas.org/ComputationalWorkflow	SHOULD include SoftwareApplication, SoftwareSourceCode or ComputationalWorkflow	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate
<h4>Recommended Properties</h4>
`name`	Recommended	ONE	schema.org/Text	A human readable name for the tool in general (not just how it was used here)	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate
`url`	Recommended	ONE	schema.org/URL	Homepage, documentation or source for the tool	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate
`softwareVersion`	Recommended	ONE	schema.org/Text	Version of the software instance.	https://schema.org/SoftwareApplication
<h4>Optional Properties</h4>
`version`	Optional	ONE	schema.org/Text	The version string for the software application. In the case of a SoftwareApplication, this MAY be provided via the more specific softwareVersion. SoftwareApplication entities SHOULD NOT specify both version and softwareVersion: in this case, consumers SHOULD prioritize softwareVersion. In order to facilitate comparison attempts by consumers, it is RECOMMENDED to specify a machine-readable version string if available (see for instance Python’s PEP 440).	https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate/
`applicationCategory`	Optional	MANY	schema.org/Text OR schema.org/URL	Type of software application, e.g. ‘Game, Multimedia’.	https://schema.org/SoftwareApplication
`downloadUrl`	Optional	MANY	schema.org/URL	If the file can be downloaded, URL to download the binary.	https://schema.org/SoftwareApplication
`softwareRequirements`	Optional	MANY	schema.org/Text OR schema.org/URL	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.	https://schema.org/SoftwareApplication

Compatibility with underlying profiles

This section, detailing the compatibility guarantees towards the underlying Workflow Run Crate and bioschemas profiles, will be added in a future version of this profile.

Workflow Run Crate configuration in ARCs

As described above, workflows can be structured hierarchically. Each workflow (or sub-workflow) object in the hierarchy can have an associated run object in the RO-Crate metadata. The structure of JSON objects is visualized below. Every ARC Run consists of one or more Workflow Runs (and is therefore comparable to an Assay in ISA). To reduce complexity, it is recommended to use top level description (marked red). One workflow describes the transformation of one set of input data to result data. If a workflow consists of several steps, forwarding the resulting data to the next step without returning them as a final result, it is described as one Workflow Run Crate. In other words, runs should only be documented for top-level workflows.

flowchart TD
  classDef red fill:#f96,stroke:#333,stroke-width:2px;

  subgraph Workflows
    direction TB
    A["Workflow(ComputationalWorkflow, LabProtocol)"]:::red
    C["Subworkflow/Process A"]
    D["Subworkflow/Process B"]
    E["Subworkflow/Process AA"]
    F["Subworkflow/Process AB"]
    G["Subworkflow/Process AC"]
  end

  subgraph Runs
    direction TB
    B["Run(CreateAction, LabProcess)"]:::red
    H["Run A"]
    I["Run B"]
    J["Run AA"]
    K["Run AB"]
    L["Run AC"]
  end

  A -- "hasPart" --> C
  A -- "hasPart" --> D
  C -- "hasPart" --> E
  C -- "hasPart" --> F
  C -- "hasPart" --> G

  B -- "instrument" --> A
  H -- "instrument" --> C
  I -- "instrument" --> D
  J -- "instrument" --> E
  K -- "instrument" --> F
  L -- "instrument" --> G

Example ro-crate-metadata.json

ro-crate-metadata.json

The crate below is an additional illustration, describing a Galaxy workflow and its run inside an ARC:

{
  "@context": [
    "https://w3id.org/ro/crate/1.1/context",
    {
      "Sample": "https://bioschemas.org/Sample",
      "additionalProperty": "http://schema.org/additionalProperty",
      "intendedUse": "https://bioschemas.org/intendedUse",
      "computationalTool": "https://bioschemas.org/computationalTool",
      "labEquipment": "https://bioschemas.org/labEquipment",
      "reagent": "https://bioschemas.org/reagent",
      "LabProtocol": "https://bioschemas.org/LabProtocol",
      "executesLabProtocol": "https://bioschemas.org/executesLabProtocol",
      "parameterValue": "https://bioschemas.org/parameterValue",
      "LabProcess": "https://bioschemas.org/LabProcess",
      "measurementMethod": "http://schema.org/measurementMethod",
      "FormalParameter": "https://bioschemas.org/FormalParameter",
      "ComputationalWorkflow": "https://bioschemas.org/ComputationalWorkflow",
      "SoftwareSourceCode": "http://schema.org/SoftwareSourceCode",
      "input": "https://bioschemas.org/input",
      "output": "https://bioschemas.org/output"
    }
  ],
  "@graph": [
    {
      "@id": "studies/Yeast/",
      "@type": "Dataset",
      "additionalType": "Study",
      "identifier": "Yeast",
      "dateModified": "2025-06-24T11:48:36.3920198"
    },
    {
      "@id": "#Organization_Technische_Fakultät,_Institut_für_Informatik_(IIF)",
      "@type": "Organization",
      "name": "Technische Fakultät, Institut für Informatik (IIF)"
    },
    {
      "@id": "https://credit.niso.org/contributor-roles/formal-analysis/",
      "@type": "DefinedTerm",
      "name": "Formal analysis",
      "termCode": "https://credit.niso.org/contributor-roles/formal-analysis/"
    },
    {
      "@id": "#Person_Björn_Grüning",
      "@type": "Person",
      "givenName": "Björn",
      "affiliation": {
        "@id": "#Organization_Technische_Fakultät,_Institut_für_Informatik_(IIF)"
      },
      "email": "gruening@informatik.uni-freiburg.de",
      "familyName": "Grüning",
      "jobTitle": {
        "@id": "https://credit.niso.org/contributor-roles/formal-analysis/"
      },
      "address": "Georges-Köhler-Allee 106, 79110 Freiburg"
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy",
      "@type": "ComputerLanguage",
      "name": "Galaxy",
      "identifier": {
        "@id": "https://galaxyproject.org/"
      },
      "url": {
        "@id": "https://galaxyproject.org/"
      }
    },
    {
      "@id": "#FormalParameter_W_Shuffle_parameter1",
      "@type": "FormalParameter",
      "additionalType": "File",
      "name": "parameter1",
      "valueRequired": true
    },
    {
      "@id": "#FormalParameter_W_Shuffle_outputFile1",
      "additionalType": "File",
      "@type": "FormalParameter",
      "name": "outputFile1"
    },
    {
      "@id": "workflows/Shuffle/ShuffleSequences.ga",
      "@type": [
        "File",
        "ComputationalWorkflow",
        "SoftwareSourceCode",
        "LabProtocol"
      ],
      "conformsTo": {
        "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate/index.md#workflow-protocol"
      },
      "additionalType": "WorkflowProtocol",
      "creator": {
        "@id": "#Person_Björn_Grüning"
      },
      "programmingLanguage": {
        "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"
      },
      "name": "FASTA shuffle workflow",
      "input": {
        "@id": "#FormalParameter_W_Shuffle_parameter1"
      },
      "output": {
        "@id": "#FormalParameter_W_Shuffle_outputFile1"
      }
    },
    {
      "@id": "workflows/Shuffle/",
      "@type": "Dataset",
      "conformsTo": {
        "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate/index.md#arc-workflow"
      },
      "additionalType": "Workflow",
      "identifier": "Shuffle",
      "creator": {
        "@id": "#Person_Björn_Grüning"
      },
      "name": "FASTA shuffle workflow",
      "mainEntity": {
        "@id": "workflows/Shuffle/ShuffleSequences.ga"
      }
    },
    {
      "@id": "#Organization_Department_of_Biology,_University_of_Kaiserslautern",
      "@type": "Organization",
      "name": "Department of Biology, University of Kaiserslautern"
    },
    {
      "@id": "#Person_Caroline_Ott",
      "@type": "Person",
      "givenName": "Caroline",
      "affiliation": {
        "@id": "#Organization_Department_of_Biology,_University_of_Kaiserslautern"
      },
      "email": "caroline.ott@rptu.de",
      "familyName": "Ott",
      "additionalName": "J. V.",
      "address": "Erwin-Schrödinger-Straße 56, Kaiserslautern, DE"
    },
    {
      "@id": "studies/Yeast/resources/Yeast.fasta",
      "@type": "File",
      "name": "studies/Yeast/resources/Yeast.fasta",
      "exampleOfWork": {
        "@id": "#FormalParameter_W_Out_parameter1"
      }
    },
    {
      "@id": "#FactorValue_decoy_DB_type_shuffle_Random",
      "@type": "PropertyValue",
      "additionalType": "FactorValue",
      "name": "decoy DB type shuffle",
      "value": "Random",
      "propertyID": "https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1001452",
      "valueReference": "https://bioregistry.io/NCIT:C60702",
      "columnIndex": "0"
    },
    {
      "@id": "runs/Out/Galaxy6-[Tabular-to-FASTA on data 5].fasta",
      "@type": "File",
      "name": "runs/Out/Galaxy6-[Tabular-to-FASTA on data 5].fasta",
      "additionalProperty": {
        "@id": "#FactorValue_decoy_DB_type_shuffle_Random"
      }
    },
    {
      "@id": "#ParameterValue_data_transformation_Addition",
      "@type": "PropertyValue",
      "additionalType": "ParameterValue",
      "name": "data transformation",
      "value": "Addition",
      "propertyID": "https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000452",
      "columnIndex": "1"
    },
    {
      "@id": "#ParameterValue_data_transformation_Subtraction",
      "@type": "PropertyValue",
      "additionalType": "ParameterValue",
      "name": "data transformation",
      "value": "Subtraction",
      "propertyID": "https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000452",
      "valueReference": "https://bioregistry.io/NCIT:C70590",
      "columnIndex": "2"
    },
    {
      "@id": "#WorkflowInvocation_Out_Shuffle_0",
      "@type": [
        "https://bioschemas.org/CreateAction",
        "LabProcess"
      ],
      "conformsTo": {
        "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate/index.md#workflow-invocation"
      },
      "additionalType": "WorkflowInvocation",
      "name": "Out",
      "object": [
        {
          "@id": "studies/Yeast/resources/Yeast.fasta"
        }
      ],
      "result": {
        "@id": "runs/Out/Galaxy6-[Tabular-to-FASTA on data 5].fasta"
      },
      "instrument": {
        "@id": "workflows/Shuffle/ShuffleSequences.ga"
      },
      "executesLabProtocol": {
        "@id": "workflows/Shuffle/ShuffleSequences.ga"
      },
      "parameterValue": [
        {
          "@id": "#ParameterValue_data_transformation_Addition"
        },
        {
          "@id": "#ParameterValue_data_transformation_Subtraction"
        }
      ]
    },
    {
      "@id": "runs/Out/",
      "@type": "Dataset",
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/wfrun/process/0.5"
        },
        {
          "@id": "https://w3id.org/ro/wfrun/workflow/0.5"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
        },
        {
          "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate/index.md#arc-run"
        }
      ],
      "additionalType": "Run",
      "identifier": "Out",
      "creator": {
        "@id": "#Person_Caroline_Ott"
      },
      "description": "This run shuffles a fasta",
      "hasPart": [
        {
          "@id": "workflows/Shuffle/ShuffleSequences.ga"
        },
        {
          "@id": "studies/Yeast/resources/Yeast.fasta"
        },
        {
          "@id": "runs/Out/Galaxy6-[Tabular-to-FASTA on data 5].fasta"
        }
      ],
      "name": "FASTA Shuffle",
      "mentions": {
        "@id": "#WorkflowInvocation_Out_Shuffle_0"
      },
      "about": {
        "@id": "#WorkflowInvocation_Out_Shuffle_0"
      }
    },
    {   
      "@id": "https://w3id.org/ro/wfrun/process/0.5",
      "@type": "CreativeWork",
      "name": "Process Run Crate",
      "version": "0.5"
    },
    {   
      "@id": "https://w3id.org/ro/wfrun/workflow/0.5",
      "@type": "CreativeWork",
      "name": "Workflow Run Crate",
      "version": "0.5"
    },
    {   
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
      "@type": "CreativeWork",
      "name": "Workflow RO-Crate",
      "version": "1.0"
    },
    {   
      "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate",
      "@type": "CreativeWork",
      "name": "ARC Workflow Run RO-Crate Profile",
      "version": "0.1"
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "conformsTo": {
        "@id": "https://github.com/nfdi4plants/arc-ro-crate-profile/tree/profiles/0.1/wr_ro_crate"
      },
      "additionalType": "Investigation",
      "identifier": "ShuffleTest",
      "datePublished": "2025-06-24T11:48:36.3939304",
      "hasPart": [
        {
          "@id": "studies/Yeast/"
        },
        {
          "@id": "workflows/Shuffle/"
        },
        {
          "@id": "runs/Out/"
        }
      ],
      "name": "Shuffle",
      "license": "ALL RIGHTS RESERVED BY THE AUTHORS"
    },
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/crate/1.1"
        },
        { 
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
        }
      ],
      "about": {
        "@id": "./"
      }
    }
  ]
}