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FAIRDOM – FAIR Asset
management and sharing
experiences in Systems and
Synthetic Biology
Prof Carole Goble
The FAIRDOM Consortium
carole.goble@manchester.ac.uk
http://fair-dom.org, http://fairdomhub.org
COMBINE 2016, Newcastle, UK 19 September 2016
FAIR
Findable
Accessible
Interoperable
Reusable
https://www.force11.org/group/fairgroup/fairprinciples
Intelligible
Reproducible
Citable
Track & Countable
Findable
Accessible
Interoperable
Reusable
Data
Operations
Models
Systems and Synthetic
Biology Projects
Sys Bio Projects ....
52006
11 projects
2015
12 projects
Stakeholders Stress…
Sponsored to Support Projects: National level and ERANets
Funders / Institutions
• Capitalising on investments
• Skills
• Justification, Audit,
Compliance
• Showcase access
Publishers
• Reproducibility
• New publishable assets
• New services
• Showcase access
Projects….
Researchers’ Productivity Rhetoric
Multi-partner
Distributed
Dynamic membership
Overlaps
Sensitivities
Collaboration
Publication
Showcasing
Compliance
Retention
Home-grown resources
Public resources
Mixed Skills
Projects’ “PAP-PA”
People, Assets, Processes -> Publishing,Analysis
People
Assets
Processes
Projects’ People, Assets, Processes
Organisation, Communication, Dissemination
Simulation
SOPs
Data Models
StandardsAnalytics
Pipelines
Samples
Tracking
Versioning
Validation
Articles
Strains
Upstream, downstream assets discovery
Organisation Communication Dissemination
Helps
navigation Reuse
later
Enable team
to reuse/
reproduce
Help others
find out
Reuse with
new partners
Tell more and
take credit
Collecting and tracking data/models
Choosing what to keep
Preparing what to share and when
Most data/models won’t be shared
• Wrong experimental method
• Hidden parameter discovered
• Faulty experiment
Promote standardised metadata practices
FAIR Projects & Programmes
What methods are been used to determine enzyme activity?
What SOP was used for this
sample?
Where is the validation data for this model?
Is there any group generating kinetic data?
Is this data available?
Track versions of my model
Whats the relationship between the data and
model
Which data belong to
which publications?
FAIR Projects and Programmes
Findable Exchange & find
assets and
people
Citation
Credit
Accessible
Share, disseminate and publish
assets sensitively
Gateway to third party tools,
archives
Store assets
Package assets
Track collection of data and metadata
Consistent reporting for interpretation,
interop & comparison
Promote and support standardised metadata
practices.
Support reproducible publications
Organise and link assets
Maintain the experimental context
Retain results beyond a project
Reuse results, tools, archives
Respect local solutions
Standards! Standards!
FAIRDOM Initiative
Project Support
Community Actions
Platforms,Tools
Public Project Commons
FAIRDOM Community, Knowledge Hub
http://www.fair-dom.org
Know-how, Guides,Templates, Workshops,Training,
Webinars, Standards and Policy Forums
Policy and International Initiatives
Surveys
Stanford et alThe evolution of standards and data management practices in systems
biology, Molecular Systems Biology (2015) 11: 851 DOI 10.15252/msb.20156053
Community Clubs
http://www.fair-dom.org
Samples Club with ELIXIR, BBMRI-ERIC, EBI…
Rework and harmonise
sample metadata
framework
bioschemas.org
Developers Foundry
Support developers of Systems Biology
tools and platforms
3rd Foundry meeting
Dec 1-2 2016, Frankfurt
FAIRDOM Platforms andTools
FAIR Sharing
Metadata Catalogue
Project Commons
Cross-repository gateway
Tool gateway
Results repository
Web-based
Local Storage
Analytics
Tracking
LIMS, Auto-archiving
In flight repositoryLocal-based
FAIRDOM Platform Installations
*Troup, E.; Clark, I; Swain, P; Millar, AJ; Zielinski,T (2015) Practical evaluation of SEEK and
openBIS for biological data management in SynthSys http://hdl.handle.net/1842/12236
Local retention and In flight management,
Private sharing
Centres, large or national projects
Local skills
One stop showcase
Programmes
Post-project retention
Supplementary materials
People and Project Commons
FAIRDOMHub.org
self-managed workspaces
Sharing sensitivity
Investigation
Study Analysis
Data
Model
SOP(Assay)
Linking, “Packaging” & Citing
Codes, Data, Models, SOPs,
Samples, Strains, Articles,
People, Projects….
Packaging
25
Jon Olav Vik,
Norwegian
University of
Life Science
26
Programme
Overarching research theme (The Digital Salmon)
Project
Research grant (DigiSal, GenoSysFat)
Investigation
A particular biological process, phenomenon or thing
(typically corresponds to [plans for] one or more closely
related papers)
Study
Experiment whose design reflects a specific biological
research question
Assay
Standardized measurement or diagnostic experiment
using a specific protocol
(applied to material from a study)
Jon Olav Vik,
Norwegian
University of
Life Science
Visible, but details maybe
inaccessible
Visibility controls
STUDY ASSAYINVESTIGATION
Experimental
assay
Modeling assay
Publication
Maksim
Zakhartsev
Glucose
Glycerol
Ethanol
Glycolysis
PPP
TCA
CO2
Lactate
Carbohydrates
Nucleotides
Kinases
Pyrophosphotase
RNA
Electron transport
Maintenance
C1 metabolism
Proteines
NH4 transportSulfur metabolism
Biomass
Lipids
Stoichiometric model
3
0
Stoichiometric model of
Saccaromyces cerevisiae
growing anaerobically at
D=0.1 h¯¹
Compartments 1
Pathways 35
Transformers: 254
reactions 214
transports 33
polymerizati
on
7
Compounds 253
balanced
comp.
234
Supplementary information
Annotation
file
SEEK
Stoichiometric
matrix
SEEK
SBML
SEEK
Stationary
fluxes
SEEK
ODE-based model
3
2
example =
glc-permease
 variables: Cex
glc, Cglc, Cg6p
parameters: Rmax, Kglc, KI-g6p, KII-g6p
0 500 1000 1500
0
2
4
6
glc-ex
C
i
[mmol/L]
0 500 1000 1500
0
0.05
0.1
glc-in
C
i
[mmol/L]
0 500 1000 1500
0
2
4
6
g6p
C
i
[mmol/L]
0 500 1000 1500
0
1
2
3
f6p
time [sec]
C
i
[mmol/L]
  0
ex
glc pulseex pulsex
glc glc Perm glc
r
dC FC
D C C t r a C
dt V
   
max
.1
.1 6 6
.1 .1 6 .1 .1 6 .1
.1
max
.1
.1
.1
1
1 1
1
1
1
1
perm influx efflux
ex
glc
perm
glc
influx ex
glc
ex
glc glc glc g p glc g p
glcglc glc I g p glc II g p
glc
glc
perm
glc
efflux
glc
glc glc
glc
r r r
C
R
K
r
C
C K C C C C
CK K K K K
K
C
R
K
r
C
C K
K
 
 


 
     
  


 

6 6
.1 6 .1 .1 6 .1
.1
1
ex
glc g p glc g p
ex
glc glc I g p glc II g p
glc
C C C C
C K K K K
K
 
 
   
  
[Rizzi et al., 1997]
DATA file
Equations
Simulations
https://dx.doi.org/10.11
11/febs.13237
https://doi.org/10.15490/seek.1.inves
tigation.56
Model Publication
Publishing and data citation
reviewer
Institutional
Repository
FAIRDOM Catalogue, a web of resources
drawing together across resources; reusing tools and repositories
respect local project solutions, tool plugins
Standards
Personal Data
Local Stores
External
Databases
Publishing services
Modelling
tools
SOPs
BiVes
Data
tools
Specialist Public Repositories
General archives
Repository Repertoire
Stanford et alThe evolution of standards and data management practices in systems
biology, Molecular Systems Biology (2015) 11: 851 DOI 10.15252/msb.20156053
Local Data Stores
Laissez-Faire
openBIS
metadata extraction
data relationship/linking
data processing
minimal user input
*Troup, E.; Clark, I; Swain, P; Millar, AJ; Zielinski,T (2015) Practical evaluation of SEEK and openBIS for
biological data management in SynthSys http://hdl.handle.net/1842/12236
Modelling standards based
in browser validation and simulation
Model comparison and versioning
SBML Model simulation
[Stellenbosch,
Rostock]
http://seekdb.bionet.nsc.ru/
Alexey Kolodkin
Siberian Branch
RussianAcademy of Sciences
Reproducible model simulations in
papers using COMBINE Archive & SED-ML
[Jacky Snoep, DagmarWaltemath, Martin Peters ]
Three tiered
service
store DOI citable
supplementary files
on FAIRDOMHub
model and
data curation
reproducible
clickable figures in
papers using SED-
ML
COMBINEArchives support
Martin PetersTalkWednesday Morning
COMBINEArchives support
Martin PetersTalkWednesday Morning
COMBINEArchives support
Martin PetersTalkWednesday Morning
Standards-based Structured Description
templates, register, harvest, index, search
Metadata Catalogue
Storage
Registermetadata
Uploaddata
Registerlink
Registeraccessmethod
Closed
Storage
Hooking together
templates, register, harvest, index, search
Just Enough
Results Model
Sample
Spread
sheets!!
JBEI-ICE
LabCollector
LabArchives
Jupyter
Galaxy / Refinery in the works….
SPARQL endpoint release
Focus – joining stuff up!
- JSON read/write API
- ISA-TAB output
Spreadsheet tooling for metadata
templates and metadata harvesting
Data annotation with standards
Embed ontologies into Excel templates
Excel spreadsheets enriched
with ontology annotations
Upload, extract metadata
and register
in browser viewing +
annotations
Model annotation – in schema
Model annotation – semanticSBML
Samples Club samples framework
Sample type
defines a sharable
standard
Spotlight: Synthetic Biology
SynBioChem Centre, UK
FAIRDOMWorkflows and Pathways
Project Support – Understanding Process
Planning, Setups, Curation, Advice, Support
Community support
Specialprojectsupport
Specialprojectsupport
model technical curation
with our JWS Online partners
PALs project
ambassadors
co-design, tailoring,
communication,
requirements, review
standard, best practices
More Projects and Centres
User Meeting, Barcelona@ICSB 2016
Processes and People
• 80% process, 20% tech
• Structuring the ISA
• PIs
• Sticking to conventions and
policies
• Tension with standards
take-up vs laissez faire
• Time and resource
• Local responsibility
• Recognition
• Institutional Repositories
• Automagic
• Licenses
• Negotiated access
• Embargos
• Permission controls
• Staged sharing
• Private walled gardens
FAIR Play
Using FAIRDOM my own
lab colleagues saw what I
was doing and called to
collaborate!
Jurgen Hannstra
Vrije Universiteit Amsterdam,
Netherlands
FAIR Play
• Drivers
– External dominate
– Personal productivity
• Trading behaviours
– Tribal based
– Modellers vs
Experimentalists
• “enclave” sharing
– Rather than public
donation
• Reciprocity & credit
– Citation
affecting behavioural change
through libertarian paternalism*
*Garza et al Framing the Community Data System Interface, https://dx.doi.org/10.6084/m9.figshare.1300051.v5
Stanford et al The evolution of
standards and data
management practices in
systems biology, Molecular
Systems Biology (2015) 11: 851
DOI 10.15252/msb.20156053
FAIRDOMAssociation e.V.
Jon OlavVik,
Norwegian University
of Life Science
Maksim Zakhartsev
Plant Systems Biology
University Hohenheim
Stuttgart, Germany
Alexey Kolodkin
Siberian Branch
Russian Academy of Sciences
Tomasz Zieliński,
SynthSys Centre
University Edinburgh

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