RO-Crate and repositories

Stian Soiland-Reyes

eScience lab, The University of Manchester

INDElab, University of Amsterdam

BY-COVID WP1

2023-12-07

This work is licensed under a
Creative Commons Attribution 4.0 International License.

scholar.social/@soilandreyes

https://orcid.org/0000-0001-9842-9718
https://slides.com/soilandreyes/

Aims of FAIR Research Objects

Describe and package data collections, datasets, software etc. with their metadata

Platform-independent object exchange between repositories and services

Support reproducibility and analysis: link data with codes and workflows

Transfer of sensitive/large distributed datasets with persistent identifiers

Aggregate citations and persistent identifiers

Propagate provenance and existing metadata

Publish and archive mixed objects and references

Reuse existing standards, but hide their complexity

https://covid19.workflowhub.eu/

https://workflowhub.eu/

https://workflowhub.eu/workflows/237

{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      },
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/crate/1.1"
        },
        {
          "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/"
        }
      ]
    },
    {
      "@id": "ro-crate-preview.html",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      }
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "mainEntity": {
        "@id": "Galaxy-Workflow-Purge_duplicates_from_hifiasm_assembly_v1.0.ga"
      },
      "hasPart": [
        {
          "@id": "Galaxy-Workflow-Purge_duplicates_from_hifiasm_assembly_v1.0.ga"
        },
        {
          "@id": "purge_image.png"
        }
      ],
      "identifier": "https://workflowhub.eu/workflows/237?version=1",
      "url": "https://workflowhub.eu/workflows/237/ro_crate?version=1",
      "name": "Research Object Crate for Purge duplicates from hifiasm assembly v1.0 (HiFi genome assembly stage 3)",
      "description": "Optional workflow to purge duplicates from the contig assembly.\r\n\r\nInfrastructure_deployment_metadata: Galaxy Australia (Galaxy)",
      "sdDatePublished": "2021-11-23 10:44:32 +0000",
      "creativeWorkStatus": "Stable"
    },
    {
      "@id": "Galaxy-Workflow-Purge_duplicates_from_hifiasm_assembly_v1.0.ga",
      "@type": [
        "File",
        "SoftwareSourceCode",
        "ComputationalWorkflow"
      ],
      "programmingLanguage": {
        "@id": "#galaxy"
      },
      "image": {
        "@id": "purge_image.png"
      },
      "contentSize": 115723,
      "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
      "description": "Optional workflow to purge duplicates from the contig assembly.\r\n\r\nInfrastructure_deployment_metadata: Galaxy Australia (Galaxy)",
      "name": "Purge duplicates from hifiasm assembly v1.0 (HiFi genome assembly stage 3)",
      "url": "https://workflowhub.eu/workflows/237?version=1",
      "keywords": "Assembly, purge_dups, HiFi",
      "version": 1,
      "license": "https://opensource.org/licenses/GPL-3.0",
      "creator": {
        "@id": "https://workflowhub.eu/people/139"
      },
      "producer": [
        {
          "@id": "https://workflowhub.eu/projects/54"
        },
        {
          "@id": "https://workflowhub.eu/projects/30"
        }
      ],
      "dateCreated": "2021-11-15T01:39:22Z",
      "dateModified": "2021-11-15T01:40:24Z",
      "isPartOf": [

      ],
      "input": [
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-inputs-HiFiASM 1o assembly"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-inputs-HiFi reads as FASTQ"
        }
      ],
      "output": [
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-split_fasta"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-alignment_output"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-stat_file"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-pbcstat_cov"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-pbcstat_wig"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-hist"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-calcuts_log"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-calcuts_tab"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-purge_dups_log"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-purge_dups_bed"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-get_seqs_hap"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-get_seqs_purged"
        },
        {
          "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-stats"
        }
      ],
      "sdPublisher": {
        "@id": "http://about.workflowhub.eu"
      }
    },
    {
      "@id": "purge_image.png",
      "@type": [
        "File",
        "ImageObject",
        "WorkflowSketch"
      ],
      "contentSize": 118673
    },
    {
      "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
      "@type": "CreativeWork",
      "name": "Workflow RO-Crate Profile",
      "version": "0.2.0"
    },
    {
      "@id": "https://workflowhub.eu/people/139",
      "@type": "Person",
      "name": "Gareth Price"
    },
    {
      "@id": "https://workflowhub.eu/projects/54",
      "@type": [
        "Project",
        "Organization"
      ],
      "name": "Galaxy Australia"
    },
    {
      "@id": "https://workflowhub.eu/projects/30",
      "@type": [
        "Project",
        "Organization"
      ],
      "name": "Australian BioCommons"
    },
    {
      "@id": "#galaxy",
      "@type": "ComputerLanguage",
      "name": "Galaxy",
      "identifier": {
        "@id": "https://galaxyproject.org/"
      },
      "url": {
        "@id": "https://galaxyproject.org/"
      }
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-inputs-HiFiASM%201o%20assembly",
      "@type": "FormalParameter",
      "name": "HiFiASM 1o assembly",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-inputs-HiFi%20reads%20as%20FASTQ",
      "@type": "FormalParameter",
      "name": "HiFi reads as FASTQ",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-split_fasta",
      "@type": "FormalParameter",
      "name": "split_fasta",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-alignment_output",
      "@type": "FormalParameter",
      "name": "alignment_output",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-stat_file",
      "@type": "FormalParameter",
      "name": "stat_file",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-pbcstat_cov",
      "@type": "FormalParameter",
      "name": "pbcstat_cov",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-pbcstat_wig",
      "@type": "FormalParameter",
      "name": "pbcstat_wig",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-hist",
      "@type": "FormalParameter",
      "name": "hist",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-calcuts_log",
      "@type": "FormalParameter",
      "name": "calcuts_log",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-calcuts_tab",
      "@type": "FormalParameter",
      "name": "calcuts_tab",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-purge_dups_log",
      "@type": "FormalParameter",
      "name": "purge_dups_log",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-purge_dups_bed",
      "@type": "FormalParameter",
      "name": "purge_dups_bed",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-get_seqs_hap",
      "@type": "FormalParameter",
      "name": "get_seqs_hap",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-get_seqs_purged",
      "@type": "FormalParameter",
      "name": "get_seqs_purged",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "#purge_duplicates_from_hifiasm_assembly_v1_0__hifi_genome_assembly_stage_3_-outputs-stats",
      "@type": "FormalParameter",
      "name": "stats",
      "dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
    },
    {
      "@id": "http://about.workflowhub.eu",
      "@type": "Organization",
      "name": "WorkflowHub",
      "url": "http://about.workflowhub.eu"
    }
  ]
}

ro-crate-metadata.json

Text

(ro-crate) stain@xena:~/Downloads$ ls workflow-237-1.crate.zip (ro-crate) stain@xena:~/Downloads$ mkdir workflow-237-1 ; cd workflow-237-1 (ro-crate) stain@xena:~/Downloads/workflow-237-1$ unzip ../workflow*zip Archive: ../workflow-237-1.crate.zip inflating: purge_image.png inflating: ro-crate-metadata.json inflating: Galaxy-Workflow-Purge_duplicates_from_hifiasm_assembly_v1.0.ga inflating: ro-crate-preview.html (ro-crate) stain@xena:~/Downloads/workflow-237-1$ rochtml ro-crate-metadata.json (ro-crate) stain@xena:~/Downloads/workflow-237-1$ ls Galaxy-Workflow-Purge_duplicates_from_hifiasm_assembly_v1.0.ga purge_image.png ro-crate-metadata.json ro-crate-preview.html (ro-crate) stain@xena:~/Downloads/workflow-237-1$

https://www.npmjs.com/package/ro-crate-html-js

Generate a HTML preview from JSON-LD

https://w3id.org/ro/doi/10.5281/zenodo.6913045

https://w3id.org/5s-crate/

Techie deep-dive!

Warning: JSON ahead

https://schema.org/

https://bioschemas.org/

https://w3id.org/ro/crate/1.1

https://www.researchobject.org/ro-crate/specification.html

RO-Crate tutorials

https://www.researchobject.org/ro-crate/tutorials

https://www.researchobject.org/packaging_data_with_ro-crate/

https://pypi.org/project/rocrate/

https://www.researchobject.org/ro-crate/tools/

Making your own RO-Crate with Crate-O

https://github.com/Language-Research-Technology/crate-o

https://language-research-technology.github.io/crate-o/

Provenance of computational processes

https://www.researchobject.org/workflow-run-crate/

https://trefx.uk/5s-crate/0.4/

Workflow definition is optional,
but recommended

    {
        "@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47",
        "@type": "CreateAction",
        "name": "Galaxy workflow run 5a5970ab-4375-444d-9a87-a764a66e3a47",
        "endTime": "2018-09-19T17:01:07+10:00",
        "instrument": {"@id": "Galaxy-Workflow-Hello_World.ga"},
        "subjectOf": {"@id": "https://usegalaxy.eu/u/5dbf7f05329e49c98b31243b5f35045c/p/invocation-report-a3a1d27edb703e5c"},
        "object": [
            {"@id": "inputs/abcdef.txt"},
            {"@id": "#verbose-pv"}
        ],
        "result": [
            {"@id": "outputs/Select_first_on_data_1_2.txt"},
            {"@id": "outputs/tac_on_data_360_1.txt"}
        ]
    },
    {
        "@id": "Galaxy-Workflow-Hello_World.ga",
        "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
        "name": "Hello World (Galaxy Workflow)",
        "author": {"@id": "https://orcid.org/0000-0001-9842-9718"},
        "creator": {"@id": "https://orcid.org/0000-0001-9842-9718"},
        "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"},
        "input": [
            {"@id": "#simple_input"},
            {"@id": "#verbose-param"}
        ],
        "output": [
            {"@id": "#reversed"},
            {"@id": "#last_lines"}
        ]
    },

Choice of layered profiles:
Process Run Crate – some tool was executed
Workflow Run Crate – the tool was a workflow
Provenance Run Crate – we know which tools the workflow ran

RO-Crate in repositories

https://www.researchobject.org/ro-crate/in-use/

https://www.rohub.org/

{
  "@context": [
    "https://w3id.org/ro/crate/1.1/context",
    "https://w3id.org/ro/terms/earth-science#",
    {
      "description": "http://purl.org/dc/terms/description",
      "title": "http://purl.org/dc/terms/title",
      "creation_mode": "http://w3id.org/ro-id/rohub/model#creation_mode"
    }
  ],
  "@graph": [
    {
      "@type": "CreativeWork",
      "@id": "ro-crate-metadata.json",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.1"
      },
      "about": {
        "@id": "./"
      }
    },
    {
      "@id": "./",
      "identifier": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3",
      "hasPart": [
        {
          "@id": "biblio%2F"
        },
        {
          "@id": "workflows%2Fcomponents%2F"
        },
        {
          "@id": "config%2F"
        },
        {
          "@id": "datasets%2F"
        },
        {
          "@id": "datasets%2Finputs%2F"
        },
        {
          "@id": "workflows%2Fmain%2F"
        },
        {
          "@id": "workflows%2Fnested%2F"
        },
        {
          "@id": "datasets%2Fresults%2F"
        },
        {
          "@id": "workflows%2F"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/2ca9dde1-bb6c-4a17-8a9c-121bbf83ac7b"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/b6d2647a-6efd-4454-b3dd-474a778a1566"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/e156ca6a-9f4e-4b66-93f8-829dff666379"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/515fd558-2e2e-41e6-a613-71146ba0866c"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/fc64e1c2-a7de-41db-a2b2-372b81cda150"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/ce7f4ce9-0a6e-41a1-b1ec-f95d1f883c5a"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/0373a7b7-ab54-4a09-9bfe-325fc5cff786"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/9e8046f8-d307-4a10-963d-4ab8b8ac534a"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/51d98bb1-2fc4-4468-8f17-c9c05edb7b57"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/45f46903-cdf3-4d38-be14-56ace30fe13c"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/7ed4fd74-68ee-4956-9a4f-a93e268b30a9"
        },
        {
          "@id": "https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3/resources/df584059-663d-4da3-8eec-d01467544383"
        }
      ],
      "@type": [
        "Dataset"
      ],
      "creator": [
        "antonio.petrizzo@ve.ismar.cnr.it",
        "fantina.madricardo@ve.ismar.cnr.it",
        "vanessa.moschino@ve.ismar.cnr.it"
      ],
      "author": [
        "antonio.petrizzo@ve.ismar.cnr.it",
        "fantina.madricardo@ve.ismar.cnr.it",
        "vanessa.moschino@ve.ismar.cnr.it"
      ],
      "studySubject": [
        "http://eurovoc.europa.eu/3949"
      ],
      "citeAs": "Petrizzo, Antonio, Fantina Madricardo, Vanessa Moschino, and Valentina Grande. \"Automatic detection of MLs targets from the bathymetry.\" ROHub. Sep 19 ,2023. https://w3id.org/ro-id/058215c9-d7d3-4e78-8f49-5655f899d5e3.",
      "datePublished": "2023-09-19 20:25:33.253021+00:00",
      "dateCreated": "2023-09-19 20:25:33.253021+00:00",
      "dateModified": "2023-10-12 09:56:30.663064+00:00",
      "contributors": [
        "valentina.grande@bo.ismar.cnr.it"
      ],
      "name": "Automatic detection of MLs targets from the bathymetry",
      "contentSize": 11789848,
      "encodingFormat": "application/ld+json",
      "contentUrl": "https://api.rohub.org/api/ros/058215c9-d7d3-4e78-8f49-5655f899d5e3/crate/download/",
      "http://purl.org/pav/contributedBy": "https://w3id.org/ro-id/users/valentina.grande%40bo.ismar.cnr.it",
      "publisher": "https://w3id.org/ro-id/users/direttore%40ismar.cnr.it",
      "http://w3id.org/ro-id/rohub/model#community": "f04bc8e9-07b9-46db-a96a-81848a939de4",
      "https://schema.org/contributor": [
        "Valentina Grande (CNR-ISMAR)",
        "Valentina Grande (CNR-ISMAR)"
      ],
      "https://schema.org/keywords": [
        "marine pollution",
        "geophysics"
      ],
      "http://w3id.org/ro-id/rohub/model#creation_mode": "MANUAL",
      "keywords": [
        "marine litter",
        "detection",
        "bathymetry",
        "adriatic sea",
        "jupyter notebook",
        "venice lagoon"
      ],
      "description": "A dedicated workflow in ArcGIS (shared as Jupyter notebook) was developed to identify targets from the bathymetry within the MAELSTROM Project - Smart technology for MArinE Litter SusTainable RemOval and Management. In that framework, the workflow identified marine litter on the seafloor starting from a bathymetric surface collected in Sacca Fisola (Venice Lagoon) on 2021.",
      "mainEntity": "Workflow",
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RO-Crate in Dataverse

First prototype: Use the COPO data brokering platform to support the processing, validation, and ingestion of standardised sample, barcode and sequencing metadata into the biodiversity genomics data ecosystem

Next:

Consuming as part of larger pipeline
RO-Crate as submission format

Debby Ku, Aaliyah Providence, Seanna McTaggart, Felix Shaw (Earlham Institute), ++

BGE mini-hackathons

ATAP: RO-Crate in backend

https://data.atap.edu.au

Attached vs Detached RO-Crate

Attached RO-Crate are used when there is some kind of folder-structure, typically archived as a ZIP file,

or on a traditional website.

Absolute URLs may still be listed as parts, but typically the parts are "files" and "directories" using relative paths.

https://www.researchobject.org/ro-crate/1.2-DRAFT/structure.html

{ "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context",
  "@graph": [
    {
      "@type": "CreativeWork",
      "@id": "ro-crate-metadata.json",
      "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"},
      "about": {"@id": "./"}
    },  
    {
      "@id": "./",
      "@type": [
        "Dataset"
      ],
      "hasPart": [
        {
          "@id": "cp7glop.ai"
        },
        {
          "@id": "lots_of_little_files/"
        }
      ]
    },
    {
      "@id": "cp7glop.ai",
      "@type": "File",
      "name": "Diagram showing trend to increase",
      "contentSize": "383766",
      "description": "Illustrator file for Glop Pot",
      "encodingFormat": "application/pdf"
    },
    {
      "@id": "lots_of_little_files/",
      "@type": "Dataset",
      "name": "Too many files",
      "description": "This directory contains many small files, that we're not going to describe in detail."
    }
  ]
}

Detached RO-Crate has a standalone JSON-LD metadata file, e.g. returned by an API.

All the resources have absolute URIs

This style may also be suitable for a repository exposing the metadata from an RO-Crate ZIP file without exposing its individual files.

{ "@context": "https://w3id.org/ro/crate/1.2-DRAFT/context",
  "@graph": [
    {
      "@type": "CreativeWork",
      "@id": "ro-crate-metadata.json",
      "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2-DRAFT"},
      "about": {"@id": "https://example.com/item/15?crate"}
    },  
    {
      "@id": "https://example.com/item/15?crate",
      "@type": [
        "Dataset"
      ],
      "hasPart": [
        {
          "@id": "https://example.com/data/12312/cp7glop.ai"
        }
      ]
    },
    {
      "@id": "http://example.com/data/12312/cp7glop.ai",
      "@type": "File",
      "name": "Diagram showing trend to increase",
      "contentSize": "383766",
      "description": "Illustrator file for Glop Pot",
      "encodingFormat": "application/pdf"
    }
  ]
}

Thank you!

Considerations for WP1:

Upload computational workflows, notebooks etc. to WorkflowHub.eu!
Datahub to accept WorkflowHub crates
RO-Crate as a submission format?
RO-Crate as a publication/archive format?
RO-Crate as exchange/internal format?
Computational vs. data-centric vs. real world
Use existing specific formats (WP3) and/or lift to general metadata in crate
Making RO-Crate profile for DataHub