Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

Stian Soiland-Reyes

eScience lab, The University of Manchester

INDElab, University of Amsterdam

WoSSS21: Workshop on
Sustainable Software Sustainability
2021-10-07

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/

https://doi.org/10.5281/zenodo.5554684

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/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

Reproducibility?

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

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

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://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 model

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

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

Enabling large number of
data citations:
AGU Data Citation Reliquary

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

RO-Crate for
workflow descriptions

https://workflowhub.eu/workflows/68

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

RO-Crate for
workflow run provenane

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

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

Preserving a Workflow Run as 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?
Tool Dependencies to install (mostly implied by workflow?)
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/

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": {
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      },
      "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"
          }
        ]
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      "@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": {
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      },
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      "@reverse": {
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        ],
        "about": [
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    },
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      "dateModified": "2020-09-10T12:04:26.336Z",
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bco-ieee2791.json

RO-Crate for
computational tools

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

Use case:
HPC simulation Workflow
using building blocks

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

https://doi.org/10.5281/zenodo.5542553

Making Canonical Workflow Building Blocks interoperable across workflow languages

Accepted

https://stain.github.io/ro-crate-paper/

https://doi.org/10.5281/zenodo.5146228
arXiv:2108.06503

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
Ronald Siebes https://orcid.org/0000-0001-8772-7904
Shaun de Witt https://orcid.org/0000-0003-4196-3658
Shady El Damaty https://orcid.org/0000-0002-2318-4477
Douglas Lowe https://orcid.org/0000-0002-1248-3594
Sergio Serra https://orcid.org/0000-0002-0792-8157
Xuanqi Li https://orcid.org/0000-0003-1498-6205

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
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

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

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

RO-Crate next steps

Future directions

2021-10-07 Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

By Stian Soiland-Reyes

2021-10-07 Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

Presented 2021-10-07 at Workshop on Sustainable Software Sustainability (WoSSS21)

1,575

Stian Soiland-Reyes PRO

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.

Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

Stian Soiland-Reyes

Why use workflows?

What is RO-Crate?

Techie deep-dive!

RO-Crate model

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

Enabling large number of data citations: AGU Data Citation Reliquary

RO-Crate for workflow descriptions

Describing workflows with RO-Crate

RO-Crate for workflow run provenane

Preserving a Workflow Run as RO-Crate?

RO-Crate for regulatory sciences

RO-Crate for computational tools

Use case: HPC simulation Workflow using building blocks

Making Canonical Workflow Building Blocks interoperable across workflow languages

RO-Crate next steps

More documentation

Future directions

2021-10-07 Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

More from Stian Soiland-Reyes

Capturing cultural heritage records
as RO-Crates

RO-Crate as a
metadata archival format

Enabling large number of
data citations:
AGU Data Citation Reliquary

RO-Crate for
workflow descriptions

Describing workflows
with RO-Crate

RO-Crate for
workflow run provenane

RO-Crate for
regulatory sciences

RO-Crate for
computational tools

Use case:
HPC simulation Workflow
using building blocks