RO-Crate, workflows and
FAIR Digital Objects

Stian Soiland-Reyes

eScience lab, The University of Manchester

INDElab, University of Amsterdam

FAIR Digital Object Forum
CWFR & FDO SEM meeting
2021-07-02

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

@soilandreyes

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

1 0.5281/zenodo.5076043

H2020-INFRAEOSC-2018-2 824087

H2020-INFRAEDI-2018-1 823830

H2020-INFRAIA-2017-1 730976

H2020-INFRADEV-2019-2 871118

H2020-INFRAIA-2018-1 823827

https://doi.org/10.1038/sdata.2016.18

Findable

Accessible

Interoperable

Reusable

https://doi.org/10.1038/sdata.2016.18

To be Findable:

F1. (meta)data are assigned a globally unique and persistent identifier

F2. data are described with rich metadata (defined by R1 below)

F3. metadata clearly and explicitly include the identifier of the data it describes

F4. (meta)data are registered or indexed in a searchable resource

https://doi.org/10.1038/sdata.2016.18

To be Findable:

F1. (meta)data are assigned a globally unique and persistent identifier

F2. data are described with rich metadata (defined by R1 below)

F3. metadata clearly and explicitly include the identifier of the data it describes

F4. (meta)data are registered or indexed in a searchable resource

To be Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol

A1.1 the protocol is open, free, and universally implementable

A1.2 the protocol allows for an authentication and authorization procedure, where necessary

A2. metadata are accessible, even when the data are no longer available

https://doi.org/10.1038/sdata.2016.18

To be Findable:

F1. (meta)data are assigned a globally unique and persistent identifier

F2. data are described with rich metadata (defined by R1 below)

F3. metadata clearly and explicitly include the identifier of the data it describes

F4. (meta)data are registered or indexed in a searchable resource

To be Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol

A1.1 the protocol is open, free, and universally implementable

A1.2 the protocol allows for an authentication and authorization procedure, where necessary

A2. metadata are accessible, even when the data are no longer available

To be Interoperable:

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

I2. (meta)data use vocabularies that follow FAIR principles

I3. (meta)data include qualified references to other (meta)data

https://doi.org/10.1038/sdata.2016.18

To be Findable:

F1. (meta)data are assigned a globally unique and persistent identifier

F2. data are described with rich metadata (defined by R1 below)

F3. metadata clearly and explicitly include the identifier of the data it describes

F4. (meta)data are registered or indexed in a searchable resource

To be Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol

A1.1 the protocol is open, free, and universally implementable

A1.2 the protocol allows for an authentication and authorization procedure, where necessary

A2. metadata are accessible, even when the data are no longer available

To be Interoperable:

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

I2. (meta)data use vocabularies that follow FAIR principles

I3. (meta)data include qualified references to other (meta)data

To be Reusable:

R1. meta(data) are richly described with a plurality of accurate and relevant attributes

R1.1. (meta)data are released with a clear and accessible data usage license

R1.2. (meta)data are associated with detailed provenance

R1.3. (meta)data meet domain-relevant community standards

https://doi.org/10.1038/sdata.2016.18

To be Findable:

F1. (meta)data are assigned a globally unique and persistent identifier

F2. data are described with rich metadata (defined by R1 below)

F3. metadata clearly and explicitly include the identifier of the data it describes

F4. (meta)data are registered or indexed in a searchable resource

To be Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol

A1.1 the protocol is open, free, and universally implementable

A1.2 the protocol allows for an authentication and authorization procedure, where necessary

A2. metadata are accessible, even when the data are no longer available

To be Interoperable:

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

I2. (meta)data use vocabularies that follow FAIR principles

I3. (meta)data include qualified references to other (meta)data

To be Reusable:

R1. meta(data) are richly described with a plurality of accurate and relevant attributes

R1.1. (meta)data are released with a clear and accessible data usage license

R1.2. (meta)data are associated with detailed provenance

R1.3. (meta)data meet domain-relevant community standards

https://doi.org/10.1038/d41586-019-01307-2

They ride with what I refer to as the four horsemen of the reproducibility apocalypse:

Publication bias
Low statistical power
P-value hacking
HARKing (hypothesizing after results are known)

Reproducibility?

https://doi.org/10.1038/s41586-019-0965-1

https://github.com/Finn-Lab/MGS-gut

Workflows

You can download our code from the URL supplied. Good luck downloading the only postdoc who can get it to run, though #overlyhonestmethods
— Ian Holmes (@ianholmes) January 8, 2013

https://twitter.com/ianholmes/status/288689712636493824

Automation

– Automate computational aspects
– Repetitive pipelines, sweep campaigns

Scaling—compute cycles

– Make use of computational infrastructure
– Handle large data

Abstraction⁠—people cycles

– Shield complexity and incompatibilities
– Report, re-usue, evolve, share, compare
– Repeat—Tweak—Repeat
– First-class commodities

Provenance—reporting

– Capture, report and utilize log and data lineage
– Auto-documentation
– Tracable evolution, audit, transparency
– Reproducible science

Findable

Accessible

Interoperable

Reusable

(Reproducible)

Why use workflows?

Adapted from Bertram Ludäscher (2015)
https://www.slideshare.net/ludaesch/works-2015provenancemileage
https://doi.org/10.1007/s13222-012-0100-z

https://s.apache.org/existing-workflow-systems

http://www.commonwl.org/

cwlVersion: v1.0
class: Workflow
inputs:
  inp: File
  ex: string

outputs:
  classout:
    type: File
    outputSource: compile/classfile

steps:
  untar:
    run: tar-param.cwl
    in:
      tarfile: inp
      extractfile: ex
    out: [example_out]

  compile:
    run: arguments.cwl
    in:
      src: untar/example_out
    out: [classfile]

Nature 573, 149-150 (2019)
https://doi.org/10.1038/d41586-019-02619-z

cwlVersion: v1.0
class: Workflow

inputs:
  toConvert: File


outputs:
  converted: 
    type: File
    outputSource: convertMethylation/converted
  combined: 
    type: File
    outputSource: mergeSymmetric/combined


steps:
  convertMethylation:
    run: interconverter.cwl
    in:
      toConvert: toConvert
    out: [converted]
  mergeSymmetric:
    run: symmetriccpgs.cwl
    in:
      toCombine: convertMethylation/converted
    out: [combined]

https://github.com/NCBI-Hackathons/Epigenomics_CWL/blob/master/cwl/tools/preprocess.cwl

cwlVersion: v1.0
class: CommandLineTool
inputs:
  toConvert:
    type: File
    inputBinding:
      prefix: -i
outputs:
  converted:
    type: File
    outputBinding:
      glob: "*.meth"
baseCommand: interconverter.sh
arguments: ["-d", $(runtime.outdir)]

hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"

cwlVersion: v1.0
class: CommandLineTool
inputs:
  toCombine:
    type: File
    inputBinding:
      prefix: -i
outputs:
  combined:
    type: File
    outputBinding:
      glob: "*.sym"

baseCommand: symmetriccpgs.sh
arguments: ["-d", $(runtime.outdir)]

hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"

https://view.commonwl.org/

Permalink:

https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl

Digital Objects for CWL workflows

https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl


<https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/symmetriccpgs.cwl>
        a                cwl:CommandLineTool ;
        cwl:arguments    ( "-d" "$(runtime.outdir)" ) ;
        cwl:baseCommand  ( "symmetriccpgs.sh" ) ;
        cwl:cwlVersion   cwl:v1.0 ;
        cwl:hints        [ a                             cwl:DockerRequirement ;
                           DockerRequirement:dockerPull  "quay.io/neksa/screw-tool"
                         ] ;
        cwl:inputs       <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/symmetriccpgs.cwl#toCombine> ;
        cwl:outputs      <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/symmetriccpgs.cwl#combined> .

<https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl>
        a               cwl:Workflow ;
        Workflow:steps  <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl#convertMethylation> , <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl#mergeSymmetric> ;
        cwl:cwlVersion  cwl:v1.0 ;
        cwl:inputs      <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl#toConvert> ;
        cwl:outputs     <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl#combined> , <https://w3id.org/cwl/view/git/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl#converted> .

cwlVersion: v1.0
class: Workflow

inputs:
  toConvert: File


outputs:
  converted: 
    type: File
    outputSource: convertMethylation/converted
  combined: 
    type: File
    outputSource: mergeSymmetric/combined


steps:
  convertMethylation:
    run: interconverter.cwl
    in:
      toConvert: toConvert
    out: [converted]
  mergeSymmetric:
    run: symmetriccpgs.cwl
    in:
      toCombine: convertMethylation/converted
    out: [combined]

https://github.com/NCBI-Hackathons/Epigenomics_CWL/blob/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: interconverter.sh
hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"
arguments: ["-d", $(runtime.outdir)]
inputs:
  toConvert:
    type: File
    inputBinding:
      prefix: -i
outputs:
  converted:
    type: File
    outputBinding:
      glob: "*.meth"

cwlVersion: v1.0
class: CommandLineTool
baseCommand: symmetriccpgs.sh
arguments: ["-d", $(runtime.outdir)]
hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"

inputs:
  toCombine:
    type: File
    inputBinding:
      prefix: -i
outputs:
  combined:
    type: File
    outputBinding:
      glob: "*.sym"

https://quay.io/repository/neksa/screw-tool

…/tools/interconverter.cwl

…/tools/symmetriccpgs.cwl

https://raw.githubusercontent.com/NCBI-Hackathons/Epigenomics_CWL/934baaadf133eda785426079d98489307d02f3d7/cwl/tools/preprocess.cwl

https://doi.org/10.1016/j.future.2011.08.004

What is RO-Crate?

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

RO-Crate is method for self-decribed datasets as a digital object using a single Linked Data metadata document

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

The dataset may contain any kind of
resource, about anything, in any format
as a file, URL or PID

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

Each resource have a machine readable description in JSON-LD format

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

A human-readable description/preview in an HTML file that lives alongside the metadata

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

Provenance and workflow information can be included
– to assist in re-use of data and research processes

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

RO-Crate Digital Objects may be packaged for distribution eg via Zip, Bagit and OCFL
– or simply be published on the Web

Credit: Peter Sefton
Adapted from https://arkisto-platform.github.io/standards/ro-crate/

Techie deep-dive!

Warning: JSON ahead

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

https://www.w3.org/TR/json-ld/

https://json-ld.org/

https://schema.org/

https://bioschemas.org/

RO-Crate for data scientists

Credit: Marco La Rosa, Peter Sefton

https://arkisto-platform.github.io/describo/

https://arkisto-platform.github.io/tools/description/describo-online/

Making your own RO-Crate with Describo

https://doi.org/10.4225/59/5a4d9b76d79f4
https://data.research.uts.edu.au/examples/ro-crate/0.2/Victoria_Arch_pub/

FAIR is not just machine-readable!

RO-Crate for digital humanities

https://arkisto-platform.github.io/case-studies/paradisec/

Capturing cultural heritage records
as RO-Crates

http://mod.paradisec.org.au/view/NT1/98007

RO-Crate for repositories

RO-Crate as a
metadata archival format

Metadata held alongside hetereogeneous data

Exchange mechanism (import/export)

Avoid vendor lock-in

RO-Crate for
workflow descriptions

https://workflowhub.eu/

https://workflowhub.eu/workflows/68

https://about.workflowhub.eu/Workflow-RO-Crate/

https://pypi.org/project/galaxy2cwl/

Describing workflows with RO-Crate

https://about.workflowhub.eu/Workflow-RO-Crate/

https://pypi.org/project/galaxy2cwl/

Describing workflows
with RO-Crate

Containers

Describe workflow

Tests

Registry

Workflows

Authors and contributors

Credit: Thanasis Vergoulis

https://doi.org/10.5281/zenodo.4671709

https://github.com/athenarc/schema

Executing Workflow RO-Crates

RO-Crate for
workflow test specifications

Credit: Simone Leo

https://lifemonitor.eu/workflow_testing_ro_crate

Workflow Testing RO-Crate

Workflow definition (e.g. Galaxy, Snakemake)
Test suite: Instances of Test definitions
Binds to particular test engines, e.g. Planemo, Jenkins

RO-Crate for
computational tools

https://www.researchobject.org/ro-crate/1.1/provenance.html#software-used-to-create-files

https://bioschemas.org/profiles/ComputationalTool/

https://mmb.irbbarcelona.org/biobb/

https://doi.org/10.5281/zenodo.4602855

Making Canonical Workflow Building Blocks interoperable across workflow languages

RO-Crate for
workflow run provenance

RO-Crate minimal provenance: Some software was used

https://www.researchobject.org/ro-crate/1.1/provenance.html

Credit: José Mª Fernández, ELIXIR All Hands, 2021-06-11

https://github.com/inab/WfExS-backend/

What is needed for a Workflow Run RO-Crate?

Workflow language & version
Workflow engine & version (e.g. Toil)
Workflow definition
Input data (or pointers to such)
Parameters? What can be implicit and explicit? (see BCO?)
Tool Dependencies to install (mostly implied by CWL/Nextflow/Galaxy, but might need versions/repos)
Container platform requirement [e.g. Docker, Conda]
Operating system requirement
Hardware requirements (memory, CPU, GPU)
- Equivalent of AWS cloud instance type sufficient?
Where to run/submit (e.g. usegalaxy.eu)
Explicit/resolved container IDs
Archive containers from Docker Hub (protect against image expiration)
...

Join discussion in the
Workflow Hub Club community!
https://about.workflowhub.eu/

--> Separation of concern

RO-Crate for
regulatory sciences

https://www.biocomputeobject.org/

https://doi.org/10.1371/journal.pbio.3000099

IEEE2791-2020

Alternate metadata views

Domain-specific explanation: BCO

General index: RO-Crate

ro-crate-metadata.json

https://biocompute-objects.github.io/bco-ro-crate/

{
  "@context": [
    "https://w3id.org/ro/crate/1.0/context",
    {
      "@vocab": "https://schema.org/"
    }
  ],
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      },
      "identifier": "ro-crate-metadata.json",
      "conformsTo": {
        "@id": "https://w3id.org/ro/crate/1.0"
      },
      "license": {
        "@id": "https://creativecommons.org/licenses/by-sa/3.0"
      },
      "description": "Made with Describo: https://uts-eresearch.github.io/describo/"
    },
    {
      "@type": "Dataset",
      "author": {
        "@id": "https://orcid.org/0000-0001-9842-9718"
      },
      "citation": {
        "@id": "https://doi.org/10.5281/zenodo.3966161"
      },
      "contactPoint": {
        "@id": "https://github.com/biocompute-objects/bco-ro-example-chipseq/issues"
      },
      "datePublished": "2020-09-09T23:00:00.000Z",
      "description": "Workflow run of a ChIP-seq peak-calling, QC and differential analysis pipeline",
      "distribution": {
        "@id": "https://github.com/biocompute-objects/bco-ro-example-chipseq/archive/main.zip"
      },
      "hasPart": [
        {
          "@id": "https://raw.githubusercontent.com/nf-core/chipseq/1.2.1/main.nf"
        },
        {
          "@id": "chipseq_20200910.json"
        },
        {
          "@id": "results/"
        },
        {
          "@id": "nextflow.log"
        },
        {
          "@id": ".nextflow.log"
        }
      ],
      "license": {
        "@id": "https://spdx.org/licenses/CC0-1.0"
      },
      "name": "Workflow run of nf-core/chipseq",
      "publisher": {
        "@id": "https://biocomputeobject.org/"
      },
      "@id": "./"
    },
    {
      "@type": "File",
      "dateModified": "2020-09-10T13:10:50.246Z",
      "name": ".nextflow.log",
      "@reverse": {
        "hasPart": [
          {
            "@id": "./"
          }
        ]
      },
      "@id": ".nextflow.log"
    },
    {
      "@type": "File",
      "conformsTo": {
        "@id": "https://w3id.org/ieee/ieee-2791-schema/"
      },
      "dateModified": "2020-09-10T13:50:02.378Z",
      "identifier": {
        "@id": "urn:uuid:dc308d7c-7949-446a-9c39-511b8ab40caf"
      },
      "license": {
        "@id": "https://spdx.org/licenses/CC0-1.0"
      },
      "name": "chipseq_20200910.json",
      "description": "IEEE 2791 description",
      "@reverse": {
        "hasPart": [
          {
            "@id": "./"
          }
        ]
      },
      "@id": "chipseq_20200910.json"
    },
    {
      "@type": "Organization",
      "description": " Two non-overlapping entities work in parallel to help drive BioCompute, the IEEE 2791-2020 Standard, and a Public Private Partnership. Leadership for the Public Private Partnership consists of an Executive Steering Committee and a Technical Steering Committee. The schema that is referenced by the current draft of the IEEE standard is maintained by an IEEE GitLab repository. ",
      "name": "BioCompute Objects",
      "@reverse": {
        "publisher": [
          {
            "@id": "./"
          }
        ]
      },
      "@id": "https://biocomputeobject.org/"
    },
    {
      "@type": "ScholarlyArticle",
      "name": "nf-core/chipseq: nf-core/chipseq v1.2.1 - Platinum Mole",
      "@reverse": {
        "citation": [
          {
            "@id": "./"
          },
          {
            "@id": "https://raw.githubusercontent.com/nf-core/chipseq/1.2.1/main.nf"
          }
        ]
      },
      "@id": "https://doi.org/10.5281/zenodo.3966161"
    },
    {
      "@type": "CreativeWork",
      "identifier": "https://spdx.org/licenses/MIT",
      "name": "MIT License",
      "@reverse": {
        "license": [
          {
            "@id": "https://raw.githubusercontent.com/nf-core/chipseq/1.2.1/main.nf"
          }
        ]
      },
      "@id": "https://github.com/nf-core/chipseq/blob/1.2.1/LICENSE"
    },
    {
      "@type": "CreativeWork",
      "description": "\nMIT License\n\nCopyright (c) 2018 nf-core\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.",
      "name": "MIT License",
      "@reverse": {
        "license": [
          {
            "@id": "results/"
          }
        ]
      },
      "@id": "https://github.com/nf-core/test-datasets/blob/atacseq/LICENSE"
    },
    {
      "@type": "DataDownload",
      "path": "https://github.com/biocompute-objects/bco-ro-example-chipseq/archive/main.zip",
      "license": {
        "@id": "https://spdx.org/licenses/CC0-1.0"
      },
      "name": "GitHub download of biocompute-objects/bco-ro-example-chipseq",
      "@reverse": {
        "distribution": [
          {
            "@id": "./"
          }
        ]
      },
      "@id": "https://github.com/biocompute-objects/bco-ro-example-chipseq/archive/main.zip"
    },
    {
      "@type": "ContactPoint",
      "name": " bco-ro-example-chipseq GitHub issue tracker",
      "url": "https://github.com/biocompute-objects/bco-ro-example-chipseq/issues",
      "@reverse": {
        "contactPoint": [
          {
            "@id": "./"
          }
        ]
      },
      "@id": "https://github.com/biocompute-objects/bco-ro-example-chipseq/issues"
    },
    {
      "@type": "Person",
      "name": "Stian Soiland-Reyes",
      "@reverse": {
        "author": [
          {
            "@id": "./"
          },
          {
            "@id": "results/"
          }
        ]
      },
      "@id": "https://orcid.org/0000-0001-9842-9718"
    },
    {
      "@type": [
        "ComputationalWorkflow",
        "File"
      ],
      "author": [
        {
          "@id": "#714de175-aa77-47f1-9f99-6a4fba65530a"
        },
        {
          "@id": "#bfb876e7-e767-4209-ad66-e1e1379c249f"
        },
        {
          "@id": "#0164006f-bd58-4ebc-9a50-b8bd4ac3025c"
        },
        {
          "@id": "#556c747c-376a-4a85-82a1-9b99520d24fd"
        },
        {
          "@id": "#93c23523-03b5-41dc-be4c-6a9a2e0e221d"
        },
        {
          "@id": "#781b9b5a-dc06-4709-8f14-65ee08b8c543"
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RO-Crate for enabling a
large number of
data citations

Credit: Paolo Manghi
AGU Data Citation Workshop
https://doi.org/10.5281/zenodo.4916734

RO-Crate as aggregation:
data citation reliquary

4-dimensional RO-Crates?

Credit: Oscar Corcho, Carole Goble
https://doi.org/10.5281/zenodo.4913285

RO-Crate profiles

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

Credit: Carole Goble
Dataverse Community Meeting 2021

https://www.slideshare.net/carolegoble/

https://about.workflowhub.eu/Workflow-RO-Crate/

FAIR Digital Objects

…with RO-Crate as metadata object

RO-Crate as FAIR Digital Object (FDO)

+ FAIR Signposting

Credit:

Herbert van de Sompel
FAIR Signposting: A KISS Approach to a Burning Issue

https://www.slideshare.net/hvdsomp/

RFC8288

https://signposting.org/FAIR/

FAIR Signposting

Credit:

Herbert van de Sompel
FAIR Signposting: A KISS Approach to a Burning Issue

https://www.slideshare.net/hvdsomp/

RFC8288

https://signposting.org/FAIR/

FAIR Signposting

https://doi.org/10.17026/dans-xdg-jtew

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Cache-Control: no-cache, max-age=0, must-revalidate
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="cite-as"
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="describedby" ; type="application/vnd.datacite.datacite+xml"
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="describedby" ; type="application/vnd.citationstyles.csl+json"
Link: <http://www.persistent-identifier.nl?identifier=urn%3Anbn%3Anl%3Aui%3A13-k7v-xhk> ; rel="cite-as"
Link: <https://easy.dans.knaw.nl/ui/resources/easy/export?sid=easy-dataset%3A32697&format=XML> ;
        rel="describedby"; type="application/xml" ; profile="https://easy.dans.knaw.nl/easy/easymetadata/",
      <https://easy.dans.knaw.nl/ui/resources/easy/export?sid=easy-dataset%3A32697&format=CSV> ;
        rel="describedby"; type="txt/csv"
Link: <http://example.com/api/datasets/export?exporter=schema.org&persistentId=doi:10.17026/dans-xdg-jtew>;
        rel="describedby"; type="application/json+ld", 
Link: <https://schema.org/AboutPage>; rel="type",
      <https://schema.org/Dataset>; rel="type", 
Link: https://creativecommons.org/licenses/cc0/;rel="license"
Link: <http://example.com/api/datasets/:persistentId/versions/1.0/linkset?persistentId=doi:10.17026/dans-xdg-jtew> ; 
        rel="linkset"; type="application/linkset+json"              
Content-Type: text/html;charset=UTF-8
Content-Language: en-US
Strict-Transport-Security: max-age=31536000; includeSubDomains

application/linkset+json

https://datatracker.ietf.org/doc/html/draft-ietf-httpapi-linkset-02

HEAD https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:32697 HTTP/1.1
Connection: close

HTTP/1.1 200 OK
Date: Tue, 29 Jun 2021 15:02:06 GMT
Cache-Control: no-cache, max-age=0, must-revalidate
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="cite-as"
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="describedby" ; type="application/vnd.datacite.datacite+xml"
Link: <https://doi.org/10.17026/dans-xdg-jtew> ; rel="describedby" ; type="application/vnd.citationstyles.csl+json"
Link: <http://www.persistent-identifier.nl?identifier=urn%3Anbn%3Anl%3Aui%3A13-k7v-xhk> ; rel="cite-as"
Link: <https://easy.dans.knaw.nl/ui/resources/easy/export?sid=easy-dataset%3A32697&format=XML> ;
        rel="describedby"; type="application/xml" ; profile="https://easy.dans.knaw.nl/easy/easymetadata/",
      <https://easy.dans.knaw.nl/ui/resources/easy/export?sid=easy-dataset%3A32697&format=CSV> ;
        rel="describedby"; type="txt/csv"
Link: <http://example.com/api/datasets/export?exporter=schema.org&persistentId=doi:10.17026/dans-xdg-jtew>;
        rel="describedby"; type="application/json+ld", 
Link: <https://schema.org/AboutPage>; rel="type",
      <https://schema.org/Dataset>; rel="type", 
Link: https://creativecommons.org/licenses/cc0/;rel="license"
Link: <http://example.com/api/datasets/:persistentId/versions/1.0/linkset?persistentId=doi:10.17026/dans-xdg-jtew> ; 
        rel="linkset"; type="application/linkset+json"              
Content-Type: text/html;charset=UTF-8
Content-Language: en-US
Strict-Transport-Security: max-age=31536000; includeSubDomains

{
  "linkset": [
    {
      "anchor": "http://localhost:8080/dataset.xhtml?persistentId=doi:10.17026/dans-xdg-jtew",
      "cite-as": [
        {
          "href": "https://doi.org/10.17026/dans-xdg-jtew"
        }
      ],
      "type": [
        {
          "href": "https://schema.org/AboutPage"
        },
        {
          "href": "https://schema.org/Dataset"
        }
      ],
      "license": {
        "href": "https://creativecommons.org/licenses/cc0/"
      },
      "describedby": [
        {
          "href": "https://doi.org/10.17026/dans-xdg-jtew",
          "type": "application/vnd.citationstyles.csl+json"
        },
        {
          "href": "http://localhost:8080/api/datasets/export?exporter=schema.org&persistentId=doi:10.17026/dans-xdg-jtew",
          "type": "application/json+ld"
        }
      ],
      "item": []
    }
  ]
}

Interpreting application/linkset+json as JSON-LD

https://tinyurl.com/yfjkefqf

… or mapped to schema.org

https://tinyurl.com/24az3rrw

FDO for Workflow RO-Crate

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

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=describedby
Link: <https://orcid.org/0000-0003-0513-0288>;rel=author
…

Resolving an RO-Crate with FAIR Signposting

rel=author

rel=type

ComputationalWorkflow

rel=license

rel=item

rel=describedby;

type="application/ld+json;profile=https://w3id.org/ro/crate"

rel=cite-as

rel=item;

type="application/zip"

More FDOs?

More workflow FDOs?

Canonical workflow (e.g. BioBB)

Workflow entry (e.g. WorkflowHub)

Workflow definition (e.g. Galaxy file)

Example run of workflow (e.g. CWLProv, BCO)

Workflow visualizations (e.g. CWL Viewer)

Tool definitions used by workflow step

Container image run from definition

(Recipe for container image)

Software package(s) installed in container

Entry in software registry (bio.tools, RRID, ASCL)

Software citations (e.g. JoSS)

Lessons learnt

Lessons Learnt

Workflows are hetereogeneous
- Need to unify core metadata and extract structure
  --> derived resources
- Workflows may have many sub-components
Workflows may already have a Web or Git presence
- … or may be uploaded from disk
- --> WorkflowHub as DOI provider
Workflows involve existing digital objects 'out of our control'
- Tools, containers, GitHub Repos
Tools and software are heterogeneous compound objects
Workflow runs show (all) the details
--> need for explanation and context

Paul Walk https://orcid.org/0000-0003-1541-5631
brandon whitehead https://orcid.org/0000-0002-0337-8610
Mark Wilkinson https://orcid.org/0000-0001-6960-357X
Paul Groth https://orcid.org/0000-0003-0183-6910
Erich Bremer https://orcid.org/0000-0003-0223-1059
LJ Garcia Castro https://orcid.org/0000-0003-3986-0510
Karl Sebby https://orcid.org/0000-0001-6022-9825
Alexander Kanitz https://orcid.org/0000-0002-3468-0652
Ana Trisovic https://orcid.org/0000-0003-1991-0533
Gavin Kennedy https://orcid.org/0000-0003-3910-0474
Mark Graves https://orcid.org/0000-0003-3486-8193
Jasper Koehorst https://orcid.org/0000-0001-8172-8981
Simone Leo https://orcid.org/0000-0001-8271-5429
Marc Portier https://orcid.org/0000-0002-9648-6484
Paul Brack https://orcid.org/0000-0002-5432-2748
Milan Ojsteršek https://orcid.org/0000-0003-1743-8300
Bert Droesbeke https://orcid.org/0000-0003-0522-5674
Chenxu Niu https://orcid.org/0000-0002-2142-1731
Kosuke Tanabe https://orcid.org/0000-0002-9986-7223
Tomasz Miksa https://orcid.org/0000-0002-4929-7875
Marco La Rosa https://orcid.org/0000-0001-5383-6993
Cedric Decruw https://github.com/cedricdcc
Andreas Czerniak https://orcid.org/0000-0003-3883-4169
Jeremy Jay https://orcid.org/0000-0002-5761-7533
Sergio Serra https://orcid.org/0000-0002-0792-8157

RO-Crate Community

Peter Sefton https://orcid.org/0000-0002-3545-944X (co-chair)
Stian Soiland-Reyes https://orcid.org/0000-0001-9842-9718 (co-chair)
Eoghan Ó Carragáin https://orcid.org/0000-0001-8131-2150 (emeritus chair)
Oscar Corcho https://orcid.org/0000-0002-9260-0753
Daniel Garijo https://orcid.org/0000-0003-0454-7145
Raul Palma https://orcid.org/0000-0003-4289-4922
Frederik Coppens https://orcid.org/0000-0001-6565-5145
Carole Goble https://orcid.org/0000-0003-1219-2137
José María Fernández https://orcid.org/0000-0002-4806-5140
Kyle Chard https://orcid.org/0000-0002-7370-4805
Jose Manuel Gomez-Perez https://orcid.org/0000-0002-5491-6431
Michael R Crusoe https://orcid.org/0000-0002-2961-9670
Ignacio Eguinoa https://orcid.org/0000-0002-6190-122X
Nick Juty https://orcid.org/0000-0002-2036-8350
Kristi Holmes https://orcid.org/0000-0001-8420-5254
Jason A. Clark https://orcid.org/0000-0002-3588-6257
Salvador Capella-Gutierrez https://orcid.org/0000-0002-0309-604X
Alasdair J. G. Gray https://orcid.org/0000-0002-5711-4872
Stuart Owen https://orcid.org/0000-0003-2130-0865
Alan R Williams https://orcid.org/0000-0003-3156-2105
Giacomo Tartari https://orcid.org/0000-0003-1130-2154
Finn Bacall https://orcid.org/0000-0002-0048-3300
Thomas Thelen https://orcid.org/0000-0002-1756-2128
Hervé Ménager https://orcid.org/0000-0002-7552-1009
Laura Rodríguez-Navas https://orcid.org/0000-0003-4929-1219

The RO-Crate Community is open for anyone to join us!

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

2021-07-02 Introduction to RO-Crate, FAIR workflows and a FAIR Digital Object profile

By Stian Soiland-Reyes

2021-07-02 Introduction to RO-Crate, FAIR workflows and a FAIR Digital Object profile

Presented 2021-07-02 at joint meeting of The Canonical Workflow Frameworks for Research (CWFR) and Semantics (SEM) working groups of the FAIR Digital Object Forum initiative.

2,238

Technical architect at eScience Lab, Dept of Computer Science, The University of Manchester. Open Source research software engineer. Interest: Linked Data, Web, provenance, annotations, Open Science, reproducible research results.

RO-Crate, workflows and FAIR Digital Objects

Stian Soiland-Reyes

Workflows

Why use workflows?

Digital Objects for CWL workflows

What is RO-Crate?

Techie deep-dive!

RO-Crate for data scientists

Making your own RO-Crate with Describo

FAIR is not just machine-readable!

RO-Crate for digital humanities

Capturing cultural heritage records as RO-Crates

RO-Crate for repositories

RO-Crate as a metadata archival format

RO-Crate for workflow descriptions

Describing workflows with RO-Crate

Describing workflows with RO-Crate

Executing Workflow RO-Crates

RO-Crate for workflow test specifications

Workflow Testing RO-Crate

RO-Crate for computational tools

Making Canonical Workflow Building Blocks interoperable across workflow languages

RO-Crate for workflow run provenance

What is needed for a Workflow Run RO-Crate?

RO-Crate for regulatory sciences

RO-Crate for enabling a large number of data citations

RO-Crate as aggregation: data citation reliquary

4-dimensional RO-Crates?

RO-Crate profiles

FAIR Digital Objects

RO-Crate as FAIR Digital Object (FDO)

+ FAIR Signposting

FDO for Workflow RO-Crate

Resolving an RO-Crate with content-negotiation

Resolving an RO-Crate with content-negotiation

Resolving an RO-Crate with content-negotiation

Downside: Indirection to find core metadata

Resolving an RO-Crate with FAIR Signposting

More FDOs?

More workflow FDOs?

Lessons learnt

Lessons Learnt

RO-Crate Community

2021-07-02 Introduction to RO-Crate, FAIR workflows and a FAIR Digital Object profile

More from Stian Soiland-Reyes

RO-Crate, workflows and
FAIR Digital Objects

Capturing cultural heritage records
as RO-Crates

RO-Crate as a
metadata archival format

RO-Crate for
workflow descriptions

Describing workflows
with RO-Crate

RO-Crate for
workflow test specifications

RO-Crate for
computational tools

RO-Crate for
workflow run provenance

RO-Crate for
regulatory sciences

RO-Crate for enabling a
large number of
data citations

RO-Crate as aggregation:
data citation reliquary