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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 is an instantiation of the Semantic Designation profile, intended to represent the ARC datamap in the RO-Crate. The datamap contains contextual information for fragments within data files. Hence, these contextual information is represented as interpretations for the corresponding data entities.

To model data fragments, this profile extends the existing hierarchy at the bottom using the same mechanisms as in the normal RO-Crate data model: Data files are already referenced in their respective datasets through hasPart. Fragments are of type MediaObject (equivalent to File) and referenced by their parent file or fragment through hasPart.

Data Fragment Selector

We add the contextual information per entry in the datamap to the Dataset objects, conforming with the Semantic Designation Profile. Accordingly, 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 descriptor objects for external metadata as described in the Semantic Designation Profile. Both objects reference each other. The Dataset object lists all datamap entries. Specifically, we plan the following:

Each entry in the datamap becomes one entry in mentions of type PropertyValue.
Each data fragment becomes an object of type MediaObject, referenced from its file object through hasPart.
Each entry of the datamap becomes a semantic descriptor of type ItemList and Statement with an assertion in the form of a PropertyValue object.
The data fragments and their descriptors referennce each other through the about and subjectOf properties.

flowchart TD

dataset[Datamap=Dataset]

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

desc[DataContext=Statement/ItemList]
prop[Interpretation=PropertyValue]

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

DataFragment --subjectOf--> desc
desc --about--> DataFragment

dataset --mentions--> desc

desc --itemListElement--> 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"
      },
      "subjectOf": {
        "@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"
      },
      "subjectOf": {
        "@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"
      },
      "subjectOf": {
        "@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": [ "Statement", "ItemList" ],
      "about": {
        "@id": "processed_data.csv#col=1"
      },
      "itemListElement": [
        { "@id": "#Explication_processed_data.csv#col=1" }
      ]
    },
    {
      "@id": "#Descriptor_processed_data.csv#col=2",
      "@type": [ "Statement", "ItemList" ],
      "about": {
        "@id": "processed_data.csv#col=2"
      },
      "itemListElement": [
        { "@id": "#Explication_processed_data.csv#col=2" }
      ]
    },
    {
      "@id": "#Descriptor_processed_data.csv#col=3",
      "@type": [ "Statement", "ItemList" ],
      "about": {
        "@id": "processed_data.csv#col=3"
      },
      "itemListElement": [
        { "@id": "#Explication_processed_data.csv#col=3" }
      ]
    },
    {
      "@id": "#Explication_processed_data.csv#col=1",
      "@type": "PropertyValue",
      "name": "Explication",
      "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"
    },
    {
      "@id": "#Explication_processed_data.csv#col=2",
      "@type": "PropertyValue",
      "name": "Explication",
      "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"
    },
    {
      "@id": "#Explication_processed_data.csv#col=3",
      "@type": "PropertyValue",
      "name": "Explication",
      "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"
    },
    {
      "@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"
      },
      "mentions": [
        {
          "@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.
mentions	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 or 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 or 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	schema.org/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 or URL	Media format as a MIME type

Fragment Descriptor

Adds further annotation to a Data file or a Fragment thereof.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be `[schema.org/Statement, schema.org/ItemList]`
@id	MUST	Text or URL
about	MUST	schema.org/MediaObject	The described data fragement using a fragment selector, following the data fragment profile.
itemListElement	MUST	schema.org/PropertyValue	The assertion described in the datamap entry.

Descriptor Assertion

The actual assertion of a datamap entry, describing the contents of a data fragment. It is represented as a PropertyValue object.

Property	Required	Expected Type	Description
@type	MUST	Text	Must be ‘schema.org/PropertyValue’
@id	MUST	Text or URL
name	MUST	Text	Must be `"Explication"`
propertyID	MUST	URL	MUST be `"https://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000111"`
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