RO-Crate
A quick introduction

Stian Soiland-Reyes

eScience lab, The University of Manchester

INDElab, University of Amsterdam

FAIR-IMPACT Support Offer #2
Workshop #1
2023-09-25


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/

HORIZON-INFRA-2021-EOSC-01-05 (#101057344)

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

(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$

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

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/

How should we resolve an
RO-Crates from a DOI?

https://doi.org/10.48546/workflowhub.workflow.29.2

302 Found
Location: https://workflowhub.eu/workflows/29?version=2
Accept: text/html

Resolving an RO-Crate with content-negotiation 

ComputationalWorkflow

https://doi.org/10.48546/workflowhub.workflow.29.2

302 Found
Location: https://workflowhub.eu/workflows/29?version=2
Accept: text/html

Accept: application/zip

Resolving an RO-Crate with content-negotiation

https://doi.org/10.48546/workflowhub.workflow.29.2

302 Found
Location: https://workflowhub.eu/workflows/29?version=2
Accept: text/html

Accept: application/ld+json;
  profile=https://w3id.org/ro/crate
Accept: application/zip

Resolving an RO-Crate with content-negotiation

https://doi.org/10.48546/workflowhub.workflow.29.2

302 Found
Location: https://workflowhub.eu/workflows/29?version=2
Accept: application/ld+json;
  profile=https://w3id.org/ro/crate

Downside: Indirection to find core metadata and content

author
@type
ComputationalWorkflow
license
hasPart
isBasedOn

Parse JSON, find the right node

https://doi.org/10.48546/workflowhub.workflow.29.2

HEAD https://doi.org/10.48546/workflowhub.workflow.29.2

302 Found
Location: https://workflowhub.eu/workflows/29?version=2
HEAD https://workflowhub.eu/workflows/29?version=2

200 OK
Link: <https://doi.org/10.48546/workflowhub.workflow.29.2>;rel=cite-as
Link: <https://workflowhub.eu/workflows/29/ro_crate?version=2>;rel=item 
      type="application/zip" ; profile="https://w3id.org/ro/crate"
Link: <https://orcid.org/0000-0003-0513-0288>;rel=author
Link: <https://workflowhub.eu/workflows/29?version=2> ; rel="describedby" ;
      type="application/ld+json"
Link: <https://workflowhub.eu/workflows/29?version=2> ; rel="describedby" ;
      type="application/vnd.datacite.datacite+xml"
…


 

Resolving an RO-Crate with FAIR Signposting 

rel=item
rel=describedby;
type="application/ld+json"
rel=cite-as
rel=item;
type="application/zip"

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!