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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
Findable
Accessible
Interoperable
Reusable
Data
S O Ps
Models
http://www.fair-dom.org
http://www.fairdomhub.org
Assets
Commons and
Catalogue for
Sys Bio Projectshttp://www.seek4science.org
Data
Samples
SOPs
Models
Publications
For results to be citable, they have to
be…
• Findable
• Available (Shared)
• Interoperable
• Reusable/Reproducible
SingleType-specific structured archives
General cloud
unstructured
archives
Public Archives for Asset Sharing
typically end results and usually public
Institutional Repositories
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?
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
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
Project Centric, Investigation Centric
Mixed types, Mixed Resources
Project Centric, Investigation Centric
Mixed types, Mixed Resources
FAIRDOM Commons
FAIRDOM Platform and Software Suite
Project
Commons
Project X
Commons
Community
Commons
FAIRDOMHub.org
FAIRDOMHub Commons
Importance and Accessibility
of citable assets
https://doi.org/10.15490/seek.1.investigation.56
Models
added value
simulate and
annotate in browser
Penkler et al (2015) FEBSJ 282:1481-1511
https://dx.doi.org/10.1111/febs.13237
https://doi.org/10.15490/seek.1.investigation.56
Evidence, Unique Identification,
Persistence
https://doi.org/10.15490/seek.1.investigation.56
Credit and Attribution
Citing FAIRDOM Entries, SEEK itself,
living and snapshot entries, Contributors
Snoep et al Glucose
metabolism in
Plasmodium
falciparum
trophoziotes,
FAIRDOMHub, March
2015,
https://doi.org/10.15
490/seek.1.investigati
on.56, version ??
From Restricted to Citable
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
Templates
Informed Use of Accessed Assets
Structured studies, standards
In browser
Consumers
Producers
Local Project
Repositories
harvesting
link
Standards
organise
validate
FAIRDOM
Repositories
FAIRDOM Platform: Catalogue, Commons,
Collections, Project-centric Data Management
COMMONS
Local Research
Environment
Public Publication
Environment
Peer
Review
Selective
Sharing
Scientist
Lab
Collaborators
Private
Publicly available
Retained
Archived
Exchanged
Selectively
Project
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
“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.
RO Unzip
• Reproducibility
• Versioning
• Systematic and
extensible meta-data
collection
• Cross platform exchange
• Publishing
Living Snapshot
Research Objects
snapshots and versioning
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)
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
The FAIRDOM Commons for Systems Biology

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The FAIRDOM Commons for Systems Biology