Scholarly HTML, 
Research Objects

Stian Soiland-Reyes

eScience lab, University of Manchester

@soilandreyes

http://orcid.org/0000-0001-9842-9718
http://slides.com/soilandreyes/2017-09-27/
 

 

eLife/stencila meeting, 2017-09-27


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

researchobject.org

http://bioexcel.eu/

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://w3c.github.io/scholarly-html/

https://w3id.org/people/essepuntato/papers/rash-peerj2016.html

https://dokie.li/

https://linkedresearch.org/

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http://www.idpf.org/epub3/latest/ocf

https://www.w3.org/TR/pwp/

Reproducible software

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

http://json-ld.org/

http://schema.org/

http://bioschemas.org/

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

 

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/

Copyright © 2017 W3C® (MIT, ERCIM, Keio, Beihang). W3C liability, trademark and document use rules apply.

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

OAI-ORE

Open Archives Initiative
Object Reuse and Exchange

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

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/

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