Research Object

Stian Soiland-Reyes

eScience lab, The University of Manchester

Approaches to Research Data Packaging
BoF at Research Data Alliance (RDA) 11th Plenary
Berlin, 2018-03-22


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

researchobject.org

@soilandreyes

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

A Research Object bundles and relates digital resources of a scientific experiment or investigation:​

 

Data used and results produced in experimental study​

Methods employed to produce and analyse that data​

Provenance and settings for the experiments​

People involved in the investigation​

Annotations about these resources, to improve understanding and interpretation

Research Object

id:        doi:10.15490/seek.1.investigation.56
createdOn: 2015-07-10T16:46:00Z
createdBy: http://orcid.org/0000-0001-9842-9718

aggregates:
 - id:         data/sequence/specimen5.bam
   conformsTo: http://gemrb.org/iesdp/file_formats/ie_formats/bam_v1.htm

 - id:         http://example.com/blog/about-specimen5
   authoredBy: http://orcid.org/0000-0001-7066-3350

 - id:         http://www.myexperiment.org/workflows/3355
   history:    provenance/workflow-evolution.ttl

annotations:
 - about:       data/sequence/specimen5.bam
   content:     annotations/specimen5-properties.jsonld
   createdBy:   http://orcid.org/0000-0001-7066-3350

 - about:       data/sequence/specimen5.bam
   content:     http://example.com/blog/about-specimen5
   motivatedBy: oa:questioning

Research Object manifest

(simplified)

Reuse standards:
OAI-ORE, BagIt, W3C JSON-LD, PROV, Web Annotation Model

metadata/manifest.json​
data/sequence/specimen5.bam
provenance/workflow-evolution.ttl
http://example.com/blog/about-specimen5
http://www.myexperiment.org/workflows/335

http://orcid.org/0000-0001-7066-3350
http://gemrb.org/iesdb/
   file_formats_ie_formats_bam_v1.html

https://w3id.org/ro/bagit
doi:10.1109/BigData.2016.7840618

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

https://json-ld.org/

http://www.openarchives.org/ore/

https://www.w3.org/TR/annotation-model/

 

Copyright © 2013 W3C® (MIT, ERCIM, Keio, Beihang), All Rights Reserved. W3C liability, trademark and document use rules apply.

PROV Model Primer

W3C Working Group Note 30 April 2013

http://www.w3.org/TR/prov-primer/

https://osf.io/h59uh/

doi:10.1101/191783

 

How can we capture the methods?

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]

https://github.com/rabix/composer

https://view.commonwl.org/

https://w3id.org/cwl/view/git/933…/workflows/hello/hello.cwl#main

{
  "@context" : [ "https://w3id.org/bundle/context" ],
  "id" : "/",
  "manifest" : [ "manifest.json" ],
  "createdOn" : "2017-08-24T10:57:46.325Z",
  "createdBy" : {
    "uri" : "https://view.commonwl.org",
    "name" : "Common Workflow Language Viewer"
  },
  "authoredBy" : [ {
    "uri" : "mailto:peter.amstutz@curoverse.com",
    "name" : "Peter Amstutz"
  }, {
    "uri" : "mailto:luka.stojanovic@sbgenomics.com",
    "name" : "Luka Stojanovic"
  }, {
    "uri" : "mailto:crusoe@ucdavis.edu",
    "name" : "Michael R. Crusoe"
  }, {
    "uri" : "mailto:porter@porter.st",
    "name" : "Andrey Kartashov"
  }, {
    "uri" : "mailto:janko.simonovic@sbgenomics.com",
    "name" : "Janko Simonovic"
  } ],
  "retrievedFrom" : "https://github.com/common-workflow-language/workflows/blob/lobstr-v1/workflows/lobSTR/",
  "retrievedOn" : "2017-08-24T10:57:46.325Z",
  "retrievedBy" : {
    "uri" : "https://view.commonwl.org",
    "name" : "Common Workflow Language Viewer"
  },
  "history" : [ "http:/git2prov.org/git2prov?giturl=https:/github.com/common-workflow-language/workflows.git&serialization=PROV-JSON" ],
  "aggregates" : [ {
    "uri" : "/workflow/tmp_2.fq",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-08-24T10:57:46.923Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/tmp_2.fq",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:61579f3e-63e6-49c2-b780-f67b2df461b7",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/lobSTR-demo.json",
    "mediatype" : "application/json",
    "createdOn" : "2017-08-24T10:57:47.216Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/lobSTR-demo.json",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:973caa0e-f3bd-45e8-8d29-70123bc8715a",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/models/illumina_v3.pcrfree.stuttermodel",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-08-24T10:57:47.239Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/models/illumina_v3.pcrfree.stuttermodel",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:62bbcbea-f34f-463f-990d-6148f8ed5e5c",
      "folder" : "/workflow/models/"
    }
  }, {
    "uri" : "/workflow/models/illumina_v3.pcrfree.stepmodel",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-08-24T10:57:47.266Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/models/illumina_v3.pcrfree.stepmodel",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:03439ae7-cd94-42a3-b5fe-40bfff6882d8",
      "folder" : "/workflow/models/"
    }
  }, {
    "uri" : "/workflow/samtools-sort.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-08-24T10:57:47.269Z",
    "authoredBy" : [ {
      "uri" : "mailto:luka.stojanovic@sbgenomics.com",
      "name" : "Luka Stojanovic"
    }, {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:porter@porter.st",
      "name" : "Andrey Kartashov"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/samtools-sort.cwl",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:2dc07859-efc2-4945-a95f-ba7815b68d07",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/lobSTR-workflow.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-08-24T10:57:47.42Z",
    "authoredBy" : [ {
      "uri" : "mailto:luka.stojanovic@sbgenomics.com",
      "name" : "Luka Stojanovic"
    }, {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:58bc1895-3460-46d6-91d7-fa1718d09631",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/lobSTR-arvados-demo.json",
    "mediatype" : "application/json",
    "createdOn" : "2017-08-24T10:57:47.453Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/lobSTR-arvados-demo.json",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:30c683bc-69fb-4d93-8dad-65b663783af5",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/samtools-index.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-08-24T10:57:47.458Z",
    "authoredBy" : [ {
      "uri" : "mailto:luka.stojanovic@sbgenomics.com",
      "name" : "Luka Stojanovic"
    }, {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:porter@porter.st",
      "name" : "Andrey Kartashov"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/samtools-index.cwl",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:8235d3f8-6927-4f73-b160-8521838a1cbb",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/lobSTR-tool.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-08-24T10:57:47.476Z",
    "authoredBy" : [ {
      "uri" : "mailto:luka.stojanovic@sbgenomics.com",
      "name" : "Luka Stojanovic"
    }, {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/lobSTR-tool.cwl",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:7fa6fbe4-1fc5-4cb5-9c1a-56b96c5f7aaf",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/allelotype.cwl",
    "mediatype" : "text/x-yaml",
    "createdOn" : "2017-08-24T10:57:47.537Z",
    "authoredBy" : [ {
      "uri" : "mailto:luka.stojanovic@sbgenomics.com",
      "name" : "Luka Stojanovic"
    }, {
      "uri" : "mailto:janko.simonovic@sbgenomics.com",
      "name" : "Janko Simonovic"
    }, {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/allelotype.cwl",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "conformsTo" : "https://w3id.org/cwl/v1.0",
    "bundledAs" : {
      "uri" : "urn:uuid:3706bd2f-e53f-431d-b32a-deb661d9b292",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/README",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-08-24T10:57:47.555Z",
    "authoredBy" : [ {
      "uri" : "mailto:crusoe@ucdavis.edu",
      "name" : "Michael R. Crusoe"
    }, {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/README",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:ed54c4d6-c585-4dc9-b7bc-0cf299e20b91",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/workflow/tmp_1.fq",
    "mediatype" : "application/octet-stream",
    "createdOn" : "2017-08-24T10:57:47.738Z",
    "authoredBy" : [ {
      "uri" : "mailto:peter.amstutz@curoverse.com",
      "name" : "Peter Amstutz"
    } ],
    "retrievedFrom" : "https://raw.githubusercontent.com/common-workflow-language/workflows/lobstr-v1/workflows/lobSTR/tmp_1.fq",
    "retrievedBy" : {
      "uri" : "https://view.commonwl.org",
      "name" : "Common Workflow Language Viewer"
    },
    "bundledAs" : {
      "uri" : "urn:uuid:5d431f81-ad0b-4acf-903a-9d5aa03b04df",
      "folder" : "/workflow/"
    }
  }, {
    "uri" : "/visualisation.png",
    "mediatype" : "image/png",
    "createdOn" : "2017-08-24T10:57:47.801Z",
    "retrievedFrom" : "https://view.commonwl.org/graph/png/github.com/common-workflow-language/workflows/blob/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl",
    "bundledAs" : {
      "uri" : "urn:uuid:ff9ace37-e76c-49f8-8d36-60f11ff6d257",
      "folder" : "/"
    }
  }, {
    "uri" : "/visualisation.svg",
    "mediatype" : "image/svg+xml",
    "createdOn" : "2017-08-24T10:57:47.821Z",
    "retrievedFrom" : "https://view.commonwl.org/graph/svg/github.com/common-workflow-language/workflows/blob/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl",
    "bundledAs" : {
      "uri" : "urn:uuid:a6cfb437-8818-4ab2-9081-efc74c5109e8",
      "folder" : "/"
    }
  } ],
  "annotations" : [ {
    "uri" : "urn:uuid:9f602fff-b280-41c5-9590-ab95a49c85ad",
    "about" : "/",
    "content" : "annotations/merged.cwl"
  }, {
    "uri" : "urn:uuid:0ce4b727-ff61-4534-9afb-e3d676d2782d",
    "about" : "/",
    "content" : "annotations/workflow.ttl"
  } ]
}

https://view.commonwl.org/

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow

label: "Hello World"
doc: "Outputs a message using echo"

inputs: []

outputs:
  response:
    outputSource: step0/response
    type: File

steps:
  step0:
    run:
      class: CommandLineTool
      inputs:
        message:
          type: string
          doc: "The message to print"
          default: "Hello World"
          inputBinding:
            position: 1
      baseCommand: echo
      stdout: response.txt
      outputs:
        response:
          type: stdout
    in: []
    out: [response]

https://w3id.org/ro/2016-01-28/wfprov/

Identifying intermediate data

Output 1B file is also Input 2C and Input 3D downstream

Simple filenames -> duplications

  ./data/step1/outputB.txt 
./data/step2/inputC.txt
./data/step3/inputD.txt

 

Content-adressable

SHA-256 hash of bytes as filename:

./data/51/51fb8af0c4ae0422fbe88340d91880ecb9d7537cf57339c1cf1256b7ca58f32d

RFC6920 URI as global identifier:

nih:sha-256;51fb8af0c4ae0422fbe88340d91880ecb9d7537cf57339c1cf1256b7ca58f32d

https://doi.org/10.7490/f1000research.1114781.1

www.ietf.org/id/draft-soilandreyes-arcp

Who is using Research Objects?

http://www.researchobject.org/ro2018/

Workshop on Research Objects (RO2018)

At IEEE eScience 2018,
Amsterdam, Netherlands

2018-07-01 Abstracts due

2018-07-15 Research articles and software/data articles due

2018-10-29 RO2018 workshop at IEEE eScience 2018

Submitted abstracts and articles can be in a range of open formats (e.g. HTML, ePub) and are particularly encouraged to be submitted in a FAIR research data packing format.

2018-03-22 Research Objects and CWL

By Farah Z Khan

Source: Stian Soiland-Reyes

2018-03-22 Research Objects and CWL

Presented at Approaches to Research Data Packaging - Research Data Alliance 11th Plenary BoF meeting, Berlin

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