GIDE search input ro-crate profile

January 2026

ro-crate-metadata structure overview

As input, we expect a detached RO-Crate consisiting solely of an ro-crate-metadata.json. This file MUST:

Generally abide by the requirements of a detatched ro-crate. At a high level this includes:
- 1.1 Contain a self-describing RO-Crate Metadata Descriptor, with an @id of ro-crate-metadata.json.
- 1.2 Have a root dataset entity which the ro-crate-madatada.json describes (via the 'about' property).
The root dataset entity has an @id that is an absolute url to a page where the more information can be found about the entry and the data can be obtained.
Use the context term definitions in gide-search-context.jsonld. Additional terms MAY be added, however, terms that are defined in this context MUST NOT be changed to point at new IRIs.

Note that this profile is designed for detached ro-crates, and so depends on https://w3id.org/ro/crate/X where X equal to or greater than 1.2 (the version which defined detached ro-crates).

The schema described below is considered 'open', in that additional relevant connections can be added to the document, though there is no guarentee that these will be used in indexing for search.

Expected objects

The @graph of the ro-crate-metadata MUST include:

Exactly one self-describing RO-Crate Metadata Descriptor.
Exactly one root dataset entity of type Dataset, linked from the self-describing RO-Crate Metadata Descriptor via the about property.
One or more Taxon objects, of type Taxon, at least linked to the root dataset entity via the about property.
One or more Imaging Method objects, of type DefinedTerm, at least linked to the root dataset entity via the measurementMethod property.
One or more Authors, of type Person, linked to the root dataset entity via the author property.
Exactly one Publisher object, of type Organisation, linked to the root dataset entity via the publisher property.

We RECOMMEND including additional objects:

Objects of type Organisation to describe Author affiliation
Further descriptions of the biological content that was captured in the images, with objects of type BioSample, and DefinedTerm.
Further descriptions of the methods used to capture the images, with objects of type LabProtocol and DefinedTerm.
Descriptions of the methods used to analyse or annotation images
Publications, of type Publication, which the dataset supported, or which provide additional detail on the methods used to create the dataset.

Overview of graph between objects

Where a property can connect to a list of objects of different types, these have been grouped into a box. As an example, we require all relevant biological subjects of imaging to be referenced by the 'about' property of the dataset, but this does not preclude additional links between these objects (such as a BioSample's taxonomicRange also connecting to a Taxon listed in the 'about' of the dataset).

          graph LR;
            rocMetadata["ro-crate-metadata.json"] -- about --> RootDataset["[root] Dataset"];
            RootDataset -- author --> Authors ;
            subgraph Authors["Person, Organisation"]
                Person
                Organisation
            end
            Person -- affiliation --> Organisation ;

            RootDataset -- about --> BiologicalMetadata;
            subgraph BiologicalMetadata["Subject of imaging"]
                BioSample
                DefinedTerm1["DefinedTerm"]
                Taxon
            end

            BioSample -- taxonomicRange --> Taxon;
            BioSample -- other properties --> DefinedTerm1;

            RootDataset --  measurementMethod --> ImagingMetadata;

            subgraph ImagingMetadata["Methods of imaging"]
                LabProtocol
                DefinedTerm2["DefinedTerm"]
            end

            LabProtocol -- measurementTechnique --> DefinedTerm2;

            RootDataset -- publisher --> Organisation1["Organisation"];
            RootDataset -- size --> QuantitativeValue;
            RootDataset -- funder --> Grant
            RootDataset -- seeAlso --> ScholarlyArticle

Detailed Object schema

Property prefixes:

rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
schema: http://schema.org/
dwc: http://rs.tdwg.org/dwc/terms/
dwciri: http://rs.tdwg.org/dwc/iri/
bao: http://www.bioassayontology.org/bao#

Note that the requirements requirements below apply to both the json field names as well as the RDF graph that would be produced by a conversion to RDF using the context of the json-ld document.

Dataset

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	URL of the entry in its original database
@type	rdf:type	REQUIRED	1+	MUST include Dataset, but may include other types.
name	schema:name	REQUIRED	1	SHOULD identify the dataset to humans
description	schema:description	REQUIRED	1	SHOULD provide an overview of the dataset to summarising the context in which the dataset is important.
datePublished	schema:datePublished	REQUIRED	1	MUST be single string value in ISO 8601 date format. SHOULD be specified to the day.
license	schema:license	REQUIRED	1	SHOULD be a URL to a licence description, e.g.
author	schema:author	REQUIRED	1+	MUST be Persons or Organsiations who contributed to the creation the dataset
publisher	schema:publisher	REQUIRED	1	MUST be a a single Organisation that provides the data at URL of the @id of this entry.
about	schema:about	REQUIRED	1+	MUST contain all the information of on the biological matter relevant to this dataset. These MAY be BioSamples, Taxons, or DefinedTerms.
measurementMethod	dwciri:measurementMethod	REQUIRED	1+	MUST contain all the information of on the imaging techniques relevant to this dataset. These may be LabProtocols, or DefinedTerms.
thumbnailUrl	schema:thumbnailUrl	Recommended	0+	MUST be a list of URLs from which a thumbnail of an example image for the dataset can be obtained, for use in displaying example of the images.
identifier	schema:identifier	Recommended	1	MUST be a unique identifier used by the publisher of the dataset to refer to this dataset.
keywords	schema:keywords	optional	0+	Relevant keywords or tags used to describe the subject, methods, or contents of dataset.
funder	schema:funder	optional	0+	The Grants which funded the contributors or creation of this dataset.
seeAlso	rdfs:seeAlso	optional	0+	The ScholarlyArticles that were published alongside, or supported by, this Dataset.
size	schema:size	optional	0+	QuantitativeValues defining dimensions of the Dataset. Some dimensions are recommended (see the QuantitativeValue section below)

Person

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD be an ORCID id, otherwise a local identifier to the document
@type	rdf:type	REQUIRED	1+	MUST include Person, but may include other types.
name	schema:name	REQUIRED	1	SHOULD be the person's name for use in crediting authorship of the Dataset
affiliation	schema:affiliation	Recommended	0+	SHOULD be the Organisations a person was a member of at the time of creating or publishing this dataset, that are related to the creation of this dataset.
email	email	optional	1	SHOULD be the email address to use to contact the Person about this Dataset

Organisation

Can appear through the property chains:

Dataset - publisher -> Organisation
Dataset - author -> Organisation
Dataset - author -> Person - affiliation -> Organisation

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD be an RORID id, a URI, or otherwise a local identifier to the document.
@type	rdf:type	REQUIRED	1+	MUST include Organisation, but may include other types.
name	schema:name	REQUIRED	1	SHOULD be a an identifying name (or acryonym, if that is more commonly used) of the organisation.
url	schema:url	optional	1	SHOULD be a url to the main landing page of the organisation
address	schema:address	optional	1	MUST be the organisation's address.

DefinedTerm

Can found through the property chains:

Dataset - about -> DefinedTerm
Dataset - about -> BioSample - x -> DefinedTerm
Dataset - measurementMethod -> DefinedTerm
Dataset - measurementMethod -> LabProtocol - measurementTechnique -> DefinedTerm

where X can be a number of different relations (e.g. hasCellLine). If the connetion obj - X -> DefinedTerm is present, and Dataset - about | measurementMethod -> obj, then Dataset - about | measurementMethod -> DefinedTerm MUST also be included explicitly.

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	MUST be an absolute URI to documentation about the term
@type	rdf:type	REQUIRED	1+	MUST include DefinedTerm, but may include other types.
name	schema:name	REQUIRED	1	SHOULD identify the term to humans, similar to an rdfs:label.

Taxon

Can be found through the property chains:

Dataset - about -> Taxon
Dataset - about -> BioSample - taxonomicRange -> Taxon

If the connetion BioSample - X -> Taxon is present, and Dataset - about -> BioSample, then Dataset - about -> Taxon MUST also be included explicitly.

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD be an NCBI taxonomy ID
@type	rdf:type	REQUIRED	1+	MUST include Taxon, but may include other types.
scientificName	dwc:scientificName	REQUIRED	1	MUST be the scientific name of the Taxon, following the relevant nomenclature code for the taxon. SHOULD be as complete as possible.
vernacularName	dwc:vernacularName	optional	1	SHOULD be a common or vernacular name of the Taxon.

BioSample

Please note that the BioSample type is a draft proposal to be added to schema.org, and thus http://schema.org/BioSample does not resolve. Details of the specification can be found at https://bioschemas.org/types/BioSample/0.2-DRAFT.

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	CAN be a resolvable URL if one is available, but more likely it will be a local identifer within the document.
@type	rdf:type	REQUIRED	1+	MUST include BioSample, but may include other types.
name	schema:name	REQUIRED	1	SHOULD identify the main features of this biosample that distinguish it from others relevant to this dataset.
description	schema:description	REQUIRED	1	SHOULD provide details of the biosample, such as variables that were modified on a case-by-case basis.
taxonomicRange	schema:taxonomicRange	Recommended	0+	The Taxons representing a classification of the BioSample.
hasCellLine	bao:hasCellLine	optional	0+	The DefinedTerm representing a classification of the BioSample.

LabProtocol

Please note that the LabProtocol type and labEquipment property are draft proposal to be added to schema.org, and thus http://schema.org/LabProtocol and http://schema.org/labEquipment do not resolve. Details of the specification can instead be found at https://bioschemas.org/profiles/LabProtocol/0.8-DRAFT.

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	CAN be a resolvable URL if one is available, but more likely it will be a local identifer within the document.
@type	rdf:type	REQUIRED	1+	MUST include LabProtocol, but may include other types.
name	schema:name	REQUIRED	1	SHOULD identify the protocol and distinguish it from others relevant to this dataset.
description	schema:description	REQUIRED	1	SHOULD provide details of the steps or settings involved in the protocol.
labEquipment	schema:labEquipment	Recommended	0+	SHOULD be a description of the equipment used in the capture of the image.
measurementTechnique	schema:description	Recommended	0+	SHOULD be a DefinedTerm from the FBBI ontology if possible.

Grant

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD a resolvable id, such as a DOI, otherwise a local identifier to the document
@type	rdf:type	REQUIRED	1+	MUST include Organisation, but may include other types.
name	schema:name	REQUIRED	1	SHOULD be the name or title of the grant.
identifier	schema:identifier	optional	1	SHOULD be included if @id is only a local indentifier.
url	schema:url	optional	1	SHOULD be a link to a website where more information can be found about the grant.

ScholarlyArticle

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD be a resolvable id, such as a DOI, otherwise a local identifier to the document
@type	rdf:type	REQUIRED	1+	MUST include Organisation, but may include other types.
name	schema:name	REQUIRED	1	MUST be the title of the article as published.
datePublished	schema:datePublished	Recommended	1	MUST be single string value in ISO 8601 date format.

QuantitativeValue

We recommend providing two QuantitativeValues for a dataset to give an estimate of the quantity of data associated that can be retrieved from the publisher

The number of files/images etc, stored by the publisher of the dataset. This MUST use the unitCode http://purl.obolibrary.org/obo/UO_0000189 (count) and the unitText "file count".
The quantity of bytes of the total dataset, as recorded by the publisher (whether compressed or otherwise). This MUST use the unitCode http://purl.obolibrary.org/obo/UO_0000233 (bytes) and the unitText "bytes".

Additional QuantitativeValue may be included.

Field	Property	Requirement	Cardinality	Description
@id		REQUIRED	1	SHOULD be a local identifier for the QuantitativeValue.
@type	rdf:type	REQUIRED	1+	MUST include QuantitativeValue, but may include other types.
value	schema:value	REQUIRED	1	SHOULD be number, using '.' to indicate a decimal point (rather than ','), and SHOULD avoid using either symbol as readability separators.
unitCode	schema:unitCode	REQUIRED	1
unitText	schema:UnitText	REQUIRED	1