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ARC RO-Crate Profile

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

ARC Datamap RO-Crate profile

Version: 0.1
Authors: ARC RO-Crate community
License: MIT License
Example conforming crate: ro-crate-metadata.json
Profile Crate: ro-crate-metadata.jsonld
Extends:
- RO-Crate 1.2 specification
JSON-LD context: https://www.researchobject.org/ro-terms/arc/context.jsonld
Vocabulary terms: https://w3id.org/ro/terms/arc#
Table of contents

Overview

This profile shows the intended representation of the ARC datamap in the RO-Crate. The datamap contains contextual information for fragments within data files. Data files are already referenced in their respective datasets through hasPart. We extend this by splitting data files into data fragments (using the same type MediaObject for the fragments and connecting them through hasPart).

Data Fragment Selector

Furthermore, we add the contextual information per entry in the datamap to the Dataset objects. The fragments and their information then reference each other.

Datamap

See our peer-reviewed publication for more information on the datamap and its usage: Fragment-level FAIRness

Detailed Description

We use MediaObject for data fragments and annotate them through the variableMeasured property in the Dataset object. Specifically, we plan the following:

Each entry in the datamap becomes one entry in variableMeasured of type PropertyValue.
Each data fragment becomes an object of type MediaObject, referenced from its file object through hasPart.
The data fragments from the data map point to descriptions in form of a PropertyValue through the about property.
The PropertyValue objects point back through subjectOf.

flowchart TD

dataset[Datamap=Dataset]

DataFile[Data=File]
DataFragment[DataFragment=MediaObject]

prop[DataContext=PropertyValue]

DataFile --hasPart--> DataFragment
dataset --hasPart--> DataFile

DataFragment --about--> prop
prop --subjectOf--> DataFragment

dataset --variableMeasured--> prop

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

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": "http://purl.obolibrary.org/obo/NCIT_C45253",
      "@type": "DefinedTerm",
      "name": "string",
      "termCode": "http://purl.obolibrary.org/obo/NCIT_C45253"
    },
    {
      "@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",
      "pattern": {
        "@id": "http://purl.obolibrary.org/obo/NCIT_C45253"
      },
      "about": {
        "@id": "#Descriptor_processed_data.csv#col=1"
      }
    },
    {
      "@id": "http://purl.obolibrary.org/obo/NCIT_C48150",
      "@type": "DefinedTerm",
      "name": "float",
      "termCode": "http://purl.obolibrary.org/obo/NCIT_C48150"
    },
    {
      "@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",
      "pattern": {
        "@id": "http://purl.obolibrary.org/obo/NCIT_C48150"
      },
      "about": {
        "@id": "#Descriptor_processed_data.csv#col=2"
      }
    },
    {
      "@id": "processed_data.csv#col=3",
      "@type": "File",
      "name": "processed_data.csv#col=3",
      "encodingFormat": "text/csv",
      "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111",
      "pattern": {
        "@id": "http://purl.obolibrary.org/obo/NCIT_C48150"
      },
      "about": {
        "@id": "#Descriptor_processed_data.csv#col=3"
      }
    },
    {
      "@id": "processed_data.csv",
      "@type": "File",
      "name": "processed_data.csv",
      "encodingFormat": "text/csv",
      "hasPart": [
        {
          "@id": "processed_data.csv#col=1"
        },
        {
          "@id": "processed_data.csv#col=2"
        },
        {
          "@id": "processed_data.csv#col=3"
        }
      ]
    },
    {
      "@id": "#Descriptor_processed_data.csv#col=1",
      "@type": "PropertyValue",
      "name": "FragmentDescriptor",
      "value": "Protein identifier",
      "propertyID": "https://github.com/nfdi4plants/ARC-specification/blob/dev/ISA-XLSX.md#datamap-table-sheets",
      "valueReference": "http://purl.obolibrary.org/obo/NCIT_C165059",
      "alternateName": "protID",
      "subjectOf": {
        "@id": "processed_data.csv#col=1"
      }
    },
    {
      "@id": "#Descriptor_processed_data.csv#col=2",
      "@type": "PropertyValue",
      "name": "FragmentDescriptor",
      "value": "molecule count",
      "propertyID": "https://github.com/nfdi4plants/ARC-specification/blob/dev/ISA-XLSX.md#datamap-table-sheets",
      "unitCode": "http://purl.obolibrary.org/obo/NCIT_C68892",
      "unitText": "Millimole per Kilogram",
      "valueReference": "http://purl.obolibrary.org/obo/UO_0000192",
      "alternateName": "quant1",
      "subjectOf": {
        "@id": "processed_data.csv#col=2"
      }
    },
    {
      "@id": "#Descriptor_processed_data.csv#col=3",
      "@type": "PropertyValue",
      "name": "FragmentDescriptor",
      "value": "molecule count",
      "propertyID": "https://github.com/nfdi4plants/ARC-specification/blob/dev/ISA-XLSX.md#datamap-table-sheets",
      "unitCode": "http://purl.obolibrary.org/obo/NCIT_C68892",
      "unitText": "Millimole per Kilogram",
      "valueReference": "http://purl.obolibrary.org/obo/UO_0000192",
      "alternateName": "quant2",
      "subjectOf": {
        "@id": "processed_data.csv#col=3"
      }
    },
    {
      "@id": "LICENSE",
      "@type": "CreativeWork",
      "text": "ALL RIGHTS RESERVED BY THE AUTHORS"
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "description": "An example of a ROCrate with a datamap, including annotation of a tabular data file.",
      "name": "ARC Datamap Crate Example",
      "hasPart": {
        "@id": "processed_data.csv"
      },
      "variableMeasured": [
        {
          "@id": "#Descriptor_processed_data.csv#col=1"
        },
        {
          "@id": "#Descriptor_processed_data.csv#col=2"
        },
        {
          "@id": "#Descriptor_processed_data.csv#col=3"
        }
      ],
      "dateCreated": "2026-06-25T22:58:40.2416018",
      "license": {
        "@id": "LICENSE"
      }
    },
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.2"
      },
      "about": {
        "@id": "./"
      }
    }
  ]
}

Requirements

Dataset

Object containing and annotating data files and fragments. In the context of this profile, this object is used to represent the datamap and its entries.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be ‘schema.org/Dataset’
@id	MUST	Text or URL	Should be a subdirectory corresponding to this dataset.
hasPart	SHOULD	File	The data files resulting from the processes performed in this dataset.
variableMeasured	COULD	Text or schema.org/PropertyValue	A fragment description entry from the datamap as a PropertyValue following the fragment description profile.

Data (File)

Describes and points to a Data file.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be ‘File’ or ‘MediaObject’
@id	MUST	Text or URL	Should be the path pointing to the file./
name	MUST	Text or URL	The name of the file.
comment	COULD	schema.org/Comment	Comment
encodingFormat	COULD	Text of URL	Media format as a MIME type
hasPart	COULD	File	The data fragments within this file. They must follow the Data Fragment profile.

Data Fragment

Describes and points to a Fragment of a Data file. In addition to the filepath, the @id property must contain a fragment selector(separated by a #) to point to the specific fragment within the file. The specifcation describing the fragment selector should be provided in the usageInfo property.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be ‘File’ or ‘MediaObject’
@id	MUST	Text or URL	Should be the path pointing to the file with a fragment selector attached.
usageInfo	MUST	Text of URL	(Formal) Description of the fragment selector.
about	SHOULD	schema.org/PropertyValue	The fragment description for this fragment. It must follow the fragment description profile.
pattern	SHOULD	DefinedTerm	Defines the shape or format of entries in this fragment.
name	COULD	Text or URL	The name of the file.
comment	COULD	schema.org/Comment	Comment
encodingFormat	COULD	Text of URL	Media format as a MIME type

Fragment Description

Adds further annotation to a Fragment of a Data file.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be ‘schema.org/PropertyValue’
@id	MUST	Text or URL
name	MUST	Text	Must be “FragmentDescriptor”
propertyID	MUST	URL	TO-DO?
subjectOf	MUST	schema.org/MediaObject	The described data fragement using a fragment selector, following the data fragment profile.
value	SHOULD	Text	Explication of the data fragment contents
valueReference	SHOULD	URL	Value ontology reference
unitText	SHOULD	Text	Unit of the data fragment
unitCode	SHOULD	URL	Unit ontology reference
alternateName	SHOULD	Text	The label of the fragment, e.g. a column header.
measurementMethod	SHOULD	Text	Name of the tool used to create the data.
description	SHOULD	Text	Can be used to describe further details of the fragment