Written and presented by Carole Goble (University of Manchester) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
1. The FAIRDOM Commons
for Systems Biology
Prof Carole Goble
FAIRDOM Consortium
The University of Manchester, UK
carole.goble@manchester.ac.uk
EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015
6. Project Centric: Programmes, Projects,
Groups, Individuals
Is there any group generating
kinetic data?
Is this data available?
What methods are been used to
determine enzyme activity?
What SOP was used for
this sample?
Where is the validation data for
this model?
7. Find
Yellow pages: projects, people
Catalogue of assets. Linked assets.
Structured studies
Manage and store assets
Controlled access
Versioning
Access gateway to other
repositories
Access/Archive
Interoperate
Standards
Curation support
Tool plug-ins and API
Export to other platforms
Reuse/Reproduce
Consistent reporting
Simulate models with exp’mtl data
Publisher/Funder Commons with DOIs
Download, package and export
FAIRDOM Platform
www.seek4science.org
8. SEEK:
Catalogue and Commons for many projects
Web-based Cataloguing for describing, finding, linking and promoting ongoing
research and outcomes. Supports auto and manual upload.
Small files, aggregates across public archives and project repositories.
Scaled local LIMS and analytics Lab Platform
Extract,Transform and Load tooling direct from the
instrumentation, data analysis pipelines.Automatic
archiving.
Handles large data.
FAIRDOM Platform
20. Informed Use of Accessed Assets
Structured studies, standards
Common elements
and relationships
between things
produced and used in
experiments.
Common elements
Specific elements for
specific data types.
Just Enough
Results Model
http://seek4science.org/JERMOntologyhttp://isatab.sourceforge.net/format.html
24. 5 Ways of making
FAIRDOM assets citable
Project
Commons
Project X
Commons
Community
Commons
FAIRDOMHub.org
2
13
4
5
FAIRDOM Platform and Software Suite
25. “Research Objects”
Inside SEEK, Exporting outside
Sys Bio is
inherently
compound
Research Objects
are a framework for
bundling metadata,
links to assets or
assets themselves.
26. RO Unzip
• Reproducibility
• Versioning
• Systematic and
extensible meta-data
collection
• Cross platform exchange
• Publishing
Living Snapshot
Research Objects
snapshots and versioning
27. Discussion points
• Citing entries in public archives
– URLs, DOIs – accessing the citation
metadata
• Citation
– Resolution, semantics, granularity
• Multiple DOIs for snapshots
• Tamper-proof RO currency
– Blockchain, Ethereum
• RO trajectories
– Provenance propagation
– Derived products
• Credit trajectories
– Micro-credit tracking
• Social-political acceptance
– All research products valued
– FAIR publishing effort recognised
• Defend it (snapshot)
• Locate it (most recent)
• Reuse it (a version, a component)
• Credit it (contributory authorship)
• Cross link it (connections)
28. Carole Goble Stuart Owen
Finn Bacall
Jacky Snoep
Wolfgang
Mueller
Olga Krebs Quyen Nguyen
Natalie Stanford
KatyWolstencroft
Peter Kunzst Bernd Rinn
Donal FellowsAlanWilliams
Rostyslav
Kuzyakiv
Jakub
Straszewski
Chandrasekhar
Ramakrishnan
Caterina
Barillari
Norman Morrison