RO-Crate and repositories

Stian Soiland-Reyes

eScience lab, The University of Manchester

INDElab, University of Amsterdam

BY-COVID WP1

2023-12-07

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

{
  "@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$

Generate a HTML preview from JSON-LD

(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$
(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$
(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$
(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$

Techie deep-dive!

Warning: JSON ahead

RO-Crate tutorials

Making your own RO-Crate with Crate-O

Provenance of computational processes

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

{
  "@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"
      ],
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    },
    {
      "@id": "https://w3id.org/ro-id/190db909-5fe3-4340-96b8-fe2c867395d3",
      "name": "detection",
      "@type": "https://w3id.org/ro/terms/earth-science#Concept"
    },
    {
      "@id": "https://w3id.org/ro-id/9144be7a-ce37-416f-97a5-39225174a800",
      "name": "target",
      "@type": "https://w3id.org/ro/terms/earth-science#Concept"
    },
    {
      "@id": "https://w3id.org/ro-id/users/valentina.grande%40bo.ismar.cnr.it",
      "@type": "agent"
    },
    {
      "@id": "https://w3id.org/ro-id/users/service-account-enrichment",
      "@type": "agent"
    },
    {
      "@id": "https://w3id.org/ro-id/users/antonio.petrizzo%40ve.ismar.cnr.it",
      "@type": "agent"
    },
    {
      "@id": "https://w3id.org/ro-id/users/valentina.grande%40bo.ismar.cnr.it",
      "name": "Valentina Grande",
      "@type": "agent"
    },
    {
      "@id": "https://w3id.org/ro-id/users/antonio.petrizzo%40ve.ismar.cnr.it",
      "name": "Antonio Petrizzo",
      "@type": "agent"
    },
    {
      "@id": "https://w3id.org/ro-id/users/service-account-enrichment",
      "name": "service-account-enrichment",
      "@type": "agent"
    }
  ]
}

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), ++

ATAP: RO-Crate in backend

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.

{ "@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

2023-12-07 RO-Crate BY-COVID WP1

By Stian Soiland-Reyes

2023-12-07 RO-Crate BY-COVID WP1

Presented at BY-COVID WP1 call 2023-12-07

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