RO-Crate Bioimaging profiles (detached)

RO-Crate Bioimaging profiles (detached)#

RO-Crate Bioimaging profiles are being developed as a machine-readable exchange mechanism for microscopy data.

A first iteration of experimentation with RO-Crates for bioimaging happened in the context of the OME 2024 NGFF Challenge. For that, a minimal design was proposed and used for managing contextual metadata on heterogeneous datasets.

The details of the use of RO-Crates in the context of the challenge, as well as a few other uses directly related to the Open Microscopy Environment are reported as an use case on the RO-Crate Website.

Similarly, a detached RO-Crate profile, heavily inspired by the MICrate here, is being developed as an interoperability mechanism for study-level metadata as part of the FoundingGIDE project. The GIDE project does not connect RO-Crate to entry points for the data, but to the pages for studies on data repositories, such as BioImage Archive and the Image Data Resource.

MICrate Specification#

Detached Ro-Crate

RO-Crate Metadata Descriptor#

{
    "@id": "ro-crate-metadata.json",
    "@type": "CreativeWork",
    "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"},
    "about": {"@id": <url_zarr>}
}

Root Data Entity#

  • Dataset

    • @id: URL (MUST)

    • @type: Dataset (MUST)

    • name: Text (SHOULD)
      [identify the dataset to humans well enough to disambiguate it from other RO-Crates]

    • description:Text (SHOULD)
      [further elaborate on the name to provide a summary of the context in which the dataset is important]

    • license:CreativeWork or URL or Text(SHOULD)
      [link to a Contextual Entity in the RO-Crate Metadata File with a name and description. MAY have a URI (eg for Creative Commons or Open Source licenses). MAY, if necessary be a textual description of how the RO-Crate may be used]

    • acquisition_method: DefinedTerm or URL (COULD)
      [link to Contextual Entity in the Ro-Crate Metadata File describing the method with name and linked specimen. MAY have a termCode and a inDefinedTermSet (eg if Contextual Entity is of type DefinedTerm).]

    • specimen:BioChemEntity (MUST)
      [to specify this Ro-Crate is about this particular subject]

    • hasPart:CreativeWork or subtype of this (COULD)

Contextual Entity#

Custom Context and Extended Metadata:#

Allows to define custom fields within your RO-Crate metadata document and describe how they should be interpreted.

"@context": [
    "https://w3id.org/ro/crate/1.2/context",
    {
      "organism_classification": "https://schema.org/taxonomicRange",
      "obo": "http://purl.obolibrary.org/obo/",
      "acquisiton_method": {
        "@reverse": "https://schema.org/result",
        "@type": "@id"
      },
      "biosample": "http://purl.obolibrary.org/obo/OBI_0002648",
      "specimen": "http://purl.obolibrary.org/obo/HSO_0000308"
    }
  ],

Minimal example#

See mic-ro-crate-metadata.json open in:

Contents