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ARC RO-Crate Profile

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

ARC Process Core Crate

This profile uses terminology from the RO-Crate 1.2 specification, and extends it with additional terms from the ARC ro-terms and Bioschemas namespace.

Overview

The aim of the profile is to be able to fully represent ISA-JSON as RO-Crate, fully capturing the metadata and files in a non-lossy form such that it should be possible to convert between one to the other, in either direction, without loss of information.

The profile relies on types from Bioschemas types:

LabProtocol - A child of HowTo to make it clearer that it is intended to specifically describe the planned instructions for upcoming lab processes.

LabProcess - A child of Action, to specifically describe the details and outcomes of an executed LabProtocol. Thereby separating the “what was planned” and “what happened” between LabProtocol and LabProcess respectively. A working group is working on the new type and adaptations of existing types.

The following graph summarizes the Process Core model in terms of Bioschemas/Schema.org vocabulary:

flowchart TD

dataset[Dataset]

Process[LabProcess]

Protocol[LabProtocol]

Sample[Sample]

DataFile[File]


prop[PropertyValue]

dataset --hasPart----> DataFile
dataset --processSequence--> Process

Process --"result"---> DataFile
Process --"result"--> Sample
Process --"object"--> Sample
Process --executesLabProtocol--> Protocol
Process --parameterValue---> prop

Sample --additionalProperty--> prop

Protocol --labEquipment---> prop
Protocol --reagent---> prop

Example Metadata File (ro-crate-metadata.json)

{
  "@context": [
    "https://w3id.org/ro/crate/1.2/context",
    {
      "Sample": "https://bioschemas.org/Sample",
      "LabProtocol": "https://bioschemas.org/LabProtocol",
      "LabProcess": "https://bioschemas.org/LabProcess",
      "computationalTool": "https://bioschemas.org/properties/computationalTool",
      "labEquipment": "https://bioschemas.org/properties/labEquipment",
      "reagent": "https://bioschemas.org/properties/reagent",
      "intendedUse": "https://bioschemas.org/properties/intendedUse",
      "executesLabProtocol": "https://bioschemas.org/properties/executesLabProtocol",
      "parameterValue": "https://bioschemas.org/properties/parameterValue",
      "columnIndex": "https://w3id.org/ro/terms/arc#columnIndex"
    }
  ],
  "@graph": [
    {
      "@id": "datafile.wiff",
      "@type": "File",
      "name": "datafile.wiff"
    },
    {
      "@id": "#CharacteristicValue_organism_Arabidopsis_thaliana",
      "@type": "PropertyValue",
      "additionalType": "CharacteristicValue",
      "name": "organism",
      "value": "Arabidopsis thaliana",
      "propertyID": "https://bioregistry.io/OBI:0100026",
      "valueReference": "http://purl.obolibrary.org/obo/NCBITAXON_3702"
    },
    {
      "@id": "#Material_MyObservable",
      "@type": "Sample",
      "additionalType": "Material",
      "name": "MyObservable",
      "additionalProperty": {
        "@id": "#CharacteristicValue_organism_Arabidopsis_thaliana"
      }
    },
    {
      "@id": "#Sample_MySample",
      "@type": "Sample",
      "additionalType": "Sample",
      "name": "MySample"
    },
    {
      "@id": "#CharacteristicValue_Temperature_25",
      "@type": "PropertyValue",
      "additionalType": "CharacteristicValue",
      "name": "Temperature",
      "value": "25",
      "propertyID": "https://bioregistry.io/NCIT:C25206",
      "unitCode": "http://purl.obolibrary.org/obo/UO_0000027",
      "unitText": "degree Celsius"
    },
    {
      "@id": "#Process_Preparation",
      "@type": "LabProcess",
      "name": "Preparation",
      "object": {
        "@id": "#Material_MyObservable"
      },
      "result": {
        "@id": "#Sample_MySample"
      },
      "parameterValue": {
        "@id": "#CharacteristicValue_Temperature_25"
      }
    },
    {
      "@id": "#Process_Measurement",
      "@type": "LabProcess",
      "name": "Measurement",
      "object": {
        "@id": "#Sample_MySample"
      },
      "result": {
        "@id": "datafile.wiff"
      }
    },
    {
      "@id": "LICENSE",
      "@type": "CreativeWork",
      "text": "ALL RIGHTS RESERVED BY THE AUTHORS"
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "description": "An example of a ROCrate with a core process model, including preparation and measurement processes.",
      "name": "Experimental ARC Process Core Crate Example",
      "hasPart": {
        "@id": "datafile.wiff"
      },
      "about": [
        {
          "@id": "#Process_Preparation"
        },
        {
          "@id": "#Process_Measurement"
        }
      ],
      "dateCreated": "2026-06-24T23:04:48.2431278",
      "license": {
        "@id": "LICENSE"
      }
    },
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.2"
      },
      "about": {
        "@id": "./"
      }
    }
  ]
}

Requirements

Dataset

schema.org/Dataset containing and contexualizing the processes.

Property Required Expected Type Description
@id MUST Text or URL According to ROCrate specification.
@type MUST Text MUST be ‘schema.org/Dataset’
about SHOULD bioschemas.org/LabProcess The processes described here and possibly leading up to the files grouped in this dataset.
hasPart COULD File Data files resulting from the process sequence.

LabProcess

Has the new Bioschemas DRAFT bioschemas.org/LabProcess type and maps to the ISA-JSON Process

Property Required Expected Type Description
@id MUST Text or URL Could identify the process using the isa metadata filename and the protocol reference or process name.
@type MUST Text MUST be ‘bioschemas.org/LabProcess’
name MUST Text -
object SHOULD bioschemas.org/Sample or File The input of the process. If there are multiple inputs, they SHOULD be stored as a sorted list to establish correspondence with outputs. (Both lists need the same length in that case.)
result SHOULD bioschemas.org/Sample or File The output of the process. If there are multiple outputs, they SHOULD be stored as a sorted list to establish correspondence with inputs. (Both lists need the same length in that case.)
executesLabProtocol SHOULD bioschemas.org/LabProtocol The protocol executed
parameterValue SHOULD schema.org/PropertyValue (Parameter) A parameter value of the experimental process, usually a key-value pair using ontology terms

LabProtocol

Is based on the Bioschemas bioschemas.org/LabProtocol type and maps to the ISA-JSON Protocol

Property Required Expected Type Description
@id MUST Text or URL Could be the url pointing to the protocol resource.
@type MUST Text MUST be ‘bioschemas.org/LabProtocol’
description SHOULD Text A short description of the protocol (e.g. an abstract)
intendedUse SHOULD schema.org/DefinedTerm or Text or URL The protocol type as an ontology term
name SHOULD Text Main title of the LabProtocol.
computationalTool COULD schema.org/DefinedTerm or schema.org/PropertyValue (Component) or schema.org/SoftwareApplication Software or tool used as part of the lab protocol to complete a part of it.
labEquipment COULD schema.org/DefinedTerm or schema.org/PropertyValue (Component) or Text or URL For LabProtocols it would be a laboratory equipment use by a person to follow one or more steps described in this LabProtocol.
reagent COULD schema.org/BioChemEntity or schema.org/DefinedTerm or schema.org/PropertyValue (Component) or Text or URL Reagents used in the protocol.
url COULD URL Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource Identifier (URI).
version COULD Number or Text An identifier for the version to ensure protocol tracking.

Sample

Is based on the Bioschemas bioschemas.org/Sample type, and represents the ISA-JSON Sample, Source and Material

Property Required Expected Type Description
@id MUST Text or URL Could be the unique sample name.
@type MUST Text MUST be ‘bioschemas.org/Sample’
name MUST Text A name identifying the sample.
additionalProperty SHOULD schema.org/PropertyValue (Characteristic or Factor) characteristics or factors

Data

Describes and points to a Data file or a segment of a Data file (via data fragment selectors), and maps to the ISA-JSON Data

Property Required Expected Type Description
@id MUST Text or URL Should be the path pointing to the file
@type MUST Text MUST be ‘File’ or ‘MediaObject’
name MUST Text or URL The name of the file.
comment COULD schema.org/Comment Comment
disambiguatingDescription COULD Text The type of the data file (“Raw Data File”, “Derived Data File” or “Image File”).
encodingFormat COULD Text of URL Media format as a MIME type
hasPart COULD Text of URL Data fragments of this Data object, described by data fragment selectors. SHOULD not be used on data fragments.
usageInfo COULD Text of URL Description/specification of the data fragment selector, if the object describes a data fragment and a selector is present in the path/@id. SHOULD only be used on data fragments.

Entities referenced by an processes’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.

Data entities involved in an application’s input and output SHOULD have an @id that reflects the original file or directory name as processed by the application, but MAY be renamed to avoid clashes with other entities in the crate. In this case, they SHOULD refer to the original name via alternateName. This is particularly important to support reproducibility in cases where an application expects to find input in specific locations and with specific names (see the MIRAX example in Representing multi-file objects).

Processes as graph edges

Data Fragment-level annotation

Data Fragment-level annotation diagram

[
  {
    "@id": "raw_data1.wiff",
    "@type": "File",
    "name": "raw_data1.wiff"
  },
  {
    "@id": "raw_data2.wiff",
    "@type": "File",
    "name": "raw_data2.wiff"
  },
  {
    "@id": "processed_data.csv#col=1",
    "@type": "File",
    "name": "processed_data.csv#col=1",
    "encodingFormat": "text/csv",
    "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111"
  },
  {
    "@id": "processed_data.csv#col=2",
    "@type": "File",
    "name": "processed_data.csv#col=2",
    "encodingFormat": "text/csv",
    "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111"
  },
  {
    "@id": "#Process_DataProcessing_1",
    "@type": "LabProcess",
    "name": "DataProcessing_1",
    "object": {
      "@id": "raw_data1.wiff"
    },
    "result": {
      "@id": "processed_data.csv#col=1"
    }
  },
  {
    "@id": "#Process_DataProcessing_2",
    "@type": "LabProcess",
    "name": "DataProcessing_2",
    "object": {
      "@id": "raw_data2.wiff"
    },
    "result": {
      "@id": "processed_data.csv#col=2"
    }
  }
]

Experimental process

Computational process

PropertyValue Annotations