Research Objects

Stian Soiland-Reyes

eScience lab, University of Manchester

@soilandreyes

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

#BioCompute2017 FDA workshop
NIH, Bethesda, 2017-03-17

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

researchobject.org

http://bioexcel.eu/

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

Who is using Research Objects?

Versions	Provenance	Dependencies	Checklists

PROV

PAV

wfprov

ProvONE

Community-based

Any Research Object

Project/lab-specific

Research Object profiles

Open Archives Initiative Object Reuse and Exchange (OAI-ORE)

https://www.openarchives.org/ore/

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

PROV Model Primer

W3C Working Group Note 30 April 2013

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

http://json-ld.org/

http://schema.org/

http://bioschemas.org/

https://www.elixir-europe.org/
platforms/interoperability/bioschemas

https://w3id.org/ro/

doi:10.1016/j.websem.2015.01.003

https://w3id.org/bundle/

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

https://w3id.org/cwl/v1.0/

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://view.commonwl.org/

BCO + CWL + RO = 💕💕

BCO: Scientific overview
Domain-specific metadata
Parameters, taxonomies, keywords

TODO: not everything in single JSON,
point to other files for workflow/provenance

CWL: Analytical pipeline
Computational workflow and tool composition
#1: site-specific/template CWL ⇾ descriptive
#2: native CWL ⇾ executable, portable

RO: Packaging
Gather data, resources and tools ⇾ archive, transfer
Generic metadata
Deep attribution, linking, provenance

Questions?

This work has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contract H2020-EINFRA-2015-1-675728.

https://gitter.im/ResearchObject