Stian Soiland-Reyes, Michael Crusoe
eScience lab, University of Manchester
http://orcid.org/0000-0001-9842-9718
http://slides.com/soilandreyes/
2016-12-19
This work is licensed under a
Creative Commons Attribution 4.0 International License.
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"
},
]