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Research Shared
BOSC July 11th 2015, Dublin Norman Morrison, The University of Manchester
researchobject.org
Framework desiderata
Technology Independent.
The least possible The simplest feasible
Graceful degradation
Standard tooling
How?
The Container Packaging: Zip files, Docker images, BagIt, Web, … Catalogues & Commons: FAIRDOM SEEK, Farr Commons CKAN, myExperiment, Zenodo, Figshare, …
Manifest Describes the aggregated resources, their annotations and provenance
Manifest
Manifest
Manifest Construction • Identification – id, title, creator, status…. • Aggregates – list of ids/links to resources • Annotations – list of annotations about
resources
Manifest
Manifest Description • Checklists – what should be there • Provenance – where it came from • Versioning – its evolution • Dependencies – what else is needed
Manifest
Manifest id: doi:10.000/zenodo.123 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 oa:motivatedBy oa:questioning
RO Principles
Use unique identifiers as names for things.
Use some mechanism of aggregation to group things together.
Provide metadata about those things & how they relate to each other.
Real world examples
• Reviewed to Reproduced • Workflow run (CWL) • Farr Commons • Capturing and describing Docker images
for CERN Atlas analyses • FAIR-DOM http://fair-dom.org/
– SEEK http://seek4science.org/ • FAIR Publishing - RO to Figshare
Reviewed to Reproduced
From González-Beltrán et al. doi:10.1371/journal.pone.0127612
Reproducibility Same data Same code
Systematic and extensible meta-data collection ✔
✔
Workflow Run
workflowrun.prov.ttl (RDF)
outputA.txt
outputC.jpg
outputB/
intermediates/
1.txt 2.txt
3.txt
de/def2e58b-50e2-4949-9980-fd310166621a.txt
inputA.txt workflow attribution
execution environment
Aggregating in Research Object
ZIP folder structure (RO Bundle)
mimetype application/vnd.wf4ever.robundle+zip
.ro/manifest.json
URI reference
s
Exchange Reproducibility Same data Same code Systematic and extensible meta-data collection Uses RO Model WF Extension - basis of CWL
✔
✔
✔
✔
Use case: ATLAS Collider Data Analytics
Portable, lightweight application runtime and packaging tool.
Image
ATLAS and CMS detector data
Charles Vardeman, Da Huo
All data and files of the execution + Instructions
convert
bundle
manifest
Relate files and layers
Add provenance and annotations Link in other
content
run
Exchange Reproducibility Same data Same code Same run time environment Systematic and extensible meta-data collection
✔
✔
✔
Research Objects
• Reproducibility – Same data, same code, same run time
environment • Versioning • Exchange • Systematic and extensible meta-data
collection
Research Objects
Publish a digital record of your entire scientific
enterprise
You can give it to someone
else You can get credit for it
People think you are a good
person You get a promotion
• Why does this matter to Biologists?
Conclusion
• Simple solution, addressing needs towards transparent FAIR principles – Findable, Accessible, Interoperable, Reproducible
• Adoption – Training
• Online tutorials • Face to face
– Need more tools that take advantage of the RO Framework and lower the cost (technological debt) of reproducibility
• Work together
Acknowledgements Carole Goble Stian Soiland-‐Reyes Matt Gamble Rob Haines Sean Bechhofer Phil Crouch Finn Bacall Stuart Owen Carole Goble Khalid Belhajjame Graham Klyne Jun Zhao Daniel Garijo, Oscar Corcho Esteban García Cuesta
University of Manchester
University of Oxford Lancaster University
UPM
http://researchobject.org http://fair-‐dom.org http://www.seek4science.org http://www.farrinstitute.org http://www.wf4ever-‐project.org http://myexperiment.org
Raul Palma
iSOCO
PSNC
Paris 6