Example RO:
Hive & CWL

Stian Soiland-Reyes, Michael Crusoe

eScience lab, University of Manchester

@soilandreyes

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

 

2016-12-19

What is in a Research Object?

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

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

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

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

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]
{
    "@context":  [
        {"biocompute": "https://hive.biochemistry.gwu.edu/biocompute/view/",
          "DO": "http://identifiers.org/TODO/DO/",
          "ICD": "http://identifiers.org/TODO/ICD/",
          "taxID": "http://identifiers.org/TODO/taxID/"
        },
        "http://schema.org/",
        "https://w3id.org/bundle/context"
    ],
    "id": "/",
    "manifest":  "manifest.json",

    "@id": "biocompute:1001",
    "retrievedFrom": "https://hive.biochemistry.gwu.edu/biocompute/TODO/1001.bundle.zip",

    "createdOn": "2016-06-09T08:12:14-0500",
    "createdBy": {
        "uri":     "https://hive.biochemistry.gwu.edu/",
        "name":    "HIVE BioCompute"
    }
    "authoredOn": "2016-06-06T13:25:21-0500",
    "authoredBy": [
      {
        "uri":     "biocompute:TODO-1",
        "orcid":   "http://orcid.org/0000-0002-1825-0097#TODO",
        "name":    "Charles Darwin",
        "affiliation": {
          "name": "HMS Beagle"
        }
      },
      {
        "uri":     "biocompute:TODO-2",
        "orcid":   "http://orcid.org/0000-0002-1825-0097#TODO",
        "name":    "Rosalind Franklin",
        "affiliation": {
          "url": "http://www.kcl.ac.uk/",
          "name": "King's College, London"
        }
      }
    ],
    "aggregates": [

        { "uri":  "/biocompute.json",
          "mediatype": "application/json",
          "conformsTo": "https://hive.biochemistry.gwu.edu/biocompute/spec-TODO"
        },
        { "uri":  "/workflow/hive-viral-mutation-detection.cwl",
          "mediatype": "application/x-yaml",
          "conformsTo": "https://w3id.org/cwl/v1.0/"
        },
        { "uri":  "/workflow/hive-hexagon.cwl",
          "mediatype": "application/x-yaml",
          "conformsTo": "https://w3id.org/cwl/v1.0/"
        },
        { "uri":  "/workflow/obj.1001.yaml",
          "mediatype": "application/json"
        },
        { "uri":      "/data/SNPProfile.csv",
          "mediatype": "text/csv"
        },
        { "uri":      "/data/SNPProfile.vcf",
          "mediatype": "text/plain",
          "conformsTo": "http://samtools.github.io/hts-specs/VCFv4.2.pdf"
        },
        { "uri":      "/data/SNPProfile.sam",
          "conformsTo": "http://samtools.github.io/hts-specs/SAMv1.pdf"
        },
        { "uri":      "/data/AACalls.csv",
          "mediatype": "text/csv"
       },
        { "uri":      "/data/AACalls.vcf",
          "mediatype": "text/plain",
          "conformsTo": "http://samtools.github.io/hts-specs/VCFv4.2.pdf"
        },
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/00123"},
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/00013"},
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/10065"},
        { "uri": "http://www.ebi.ac.uk/ena/data/view/JQ434001&display=fasta",
          "conformsTo": "http://edamontology.org/format_1929"
        }
    ],
    "aggregates": [ 
        "...",
        { "uri":      "/data/AACalls.csv",
          "mediatype": "text/csv"
        },
        { "uri":      "/data/AACalls.vcf",
          "mediatype": "text/plain",
          "conformsTo": "http://samtools.github.io/hts-specs/VCFv4.2.pdf"
        },
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/00123"},
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/00013"},
        { "uri": "https://hive.biochemistry.gwu.edu/biocompute/view/10065"},
        { "uri": "http://www.ebi.ac.uk/ena/data/view/JQ434001&display=fasta",
          "conformsTo": "http://edamontology.org/format_1929"
        }
    ],
    "annotations": [
      { "about": "/workflow/hive-viral-mutation-detection.cwl",
        "oa:motivatedBy": "oa:highlighting"
      },
      { "about":   "/workflow/hive-viral-mutation-detection.cwl",
        "content": "/workflow/obj.1001.yaml",
        "oa:motivatedBy": "oa:moderating"
      },
      { "about":  ["/workflow/hive-viral-mutation-detection.cwl",
                   "/workflow/obj.1001.yaml"],
        "content": "/biocompute.json",
        "oa:motivatedBy": "oa:describing"
      },
      ...
    "annotations": [
      ....
      { "about":   "/",
        "oa:bodyValue": "antiviral resistance",
        "oa:motivatedBy": "oa:tagging",
        "content": "http://example.com/ontology/antiviral"
      },
      { "about":   "/",
        "oa:motivatedBy": "oa:tagging",
        "oa:bodyValue": "SNP"
      },
      { "about":   "/",
        "content": ["DO:1883", "ICD:B17", "taxID:9606"],
        "oa:motivatedBy": "oa:linking"
      },
      { "about":   "http://www.ebi.ac.uk/ena/data/view/JQ434001&display=fasta",
        "content": "http://identifiers.org/insdc/JQ434001.1",
        "oa:motivatedBy": "oa:identifying"
      },
    ]

2016-12-19 Hive CWL RO example

By Stian Soiland-Reyes

2016-12-19 Hive CWL RO example

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