FAIR Data, Operations and Model management for Systems Biology and Systems Medicine Projects

FAIR Data, Operations and Model management for Systems Biology and Systems Medicine Projects

Prof Carole GobleThe FAIRDOM [email protected]://fair-dom.org, http://fairdomhub.org

1st Conference of the European Association of Systems Medicine, 26-28 October 2016, Berlin

mailto:[email protected]

http://fair-dom.org/

http://fair-dom.org/

http://fairdomhub.org/



Asset Management and Sharing

• Access to public funded research

• Reproducible results• Value and cite all

research outcomes• Sustained data

infrastructure

Findable

Accessible

Interoperable

Reusable(Intelligible)

(Reproducible)

(Citable)

(Trackable)

https://www.force11.org/group/fairgroup/fairprinciples

Projects .... and Programmes....funder and research project legacy

P1. BaCell-SysMOThe transition from growing to non-growing Bacillus subtilis cells - A systems biology approach

P2. COSMICSystems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves

P3. SUMOSystems Understanding of Microbial Oxygen Responses Escherichia coli

P4. KOSMOBACIon and solute homeostasis in enteric bacteria Escherichia coli

P5. SysMO-LABComparative Systems Biology: Lactic Acid Bacteria: Lactococcus lactis, Enterococcus faecalis, Streptococcus pyogenes

P6. PSYSMOSystems analysis of biotech induced stresses: towards a quantum increase in process performance in the cell factory Pseudomonas putida

P7. SCaRABSystems Biology of a genetically engineered Pseudomonas fluorescens with inducible exo-polysaccharide production: analysis of the dynamics and robustness of metabolic networks

P8. MOSESMicroOrganism Systems Biology: Energy and Saccharomyces cerevisiaeP9. TRANSLUCENT

Gene interaction networks and models of cation homeostasis

in Saccharomyces cerevisiaeP10. STREAM Global metabolic switching in

Streptomyces coelicolor

P11. SulfoSYS Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature

variation

P12. SysMO-DB Data management group • Reuse • Compliance• Retention• Dissemination• Collaboration• Reproducibility• Resource &

Skills Limitations

FindableAccessibleInteroperableReusable

DataOperationsModels

Sponsors

FAIRDOM Association e.V. Partnersopen innovation, not for profit

LifeGlimmer GmBH SB-ScienceManagement GmBH New Forest Ventures Ltd

FAIRDOM Pillars

Project Support

Community Actions

Platforms, Tools

Public Project Commons

Systems Approach…people, assets, processes pragmatics

• Multiple, interrelated assets• Multiple, dispersed repositories• Multi-partner, -discipline

projects

• Team science practices• Experiment – Asset

lifecycles• Academic innovation

drivers

Multiple, interrelated assetsstructured formats, standards, ontologies context

Analytics &Pipelines

Literature

SBML, CellML, PharmMLMatlab, MathematicaFortran, R, Python

SOPS

Multiple omics:genomics, transcriptomicsproteomics, metabolomicsfluxomics, reactomics

ImagesReaction kineticsSamples, Specimens, StrainsHuman data

STANDARDSversioning,

tracking:provenance, parameters,

citation

Operations

Data

SOPs

Models

FAIR Data and Metadata Standards that help to improve understanding and exchange….

Nicolas Le Novère, Babraham Institute, UK.

…researchers do not always use them....

Format MetadataMetadata Ontologies

*top three most popular

The evolution of standards and data management practices in systems biology (2015). Stanford et al, Molecular Systems Biology, 11(12):851

… makes model reuse tricky…

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

Specialist Public Repositories

General archives

Multi Repository RepertoireAccess, Reuse

Local Data Stores


sharing/publishing assets in public archives…

Data Models

*top three most popular


Multi-partner, multi-disciplinary projectswhere sharing and metadata collection isn’t second nature

ConsortiaGrp

3Grp

1

Grp 2

Multi-partner, multi-disciplinary projectsSOPs and Yellow Pages top request…

Who is working with wh

ich organism?

What methods are been used to determine enzyme activity?

Under which experimental conditions are

my

partners working on for the measurement

of glucose

concentration?What is the provenance of the parameters for this version of the model?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?

Downstream assets discovery and sharing

Organisation Communication Dissemination

Navigate through assets

Reuse later

Enable team to reuse/

reproduceHelp

others find out

Reuse with new

partners

Tell more, take credit

Standardised metadata practices

Assets

Find… own hard disk for storage…


Samiul Hasan, GSKBiocuration need in Pharma: Drivers from a Translational Bioinformatics Perspective, Poster S16

The FAIR ProjectChallengeTrack collection of data and metadata X X

Maintain the experimental context X

Find and exchange assets X X

Retain results beyond a project X X

Share, disseminate and publish assets sensitively

X X X

Consistent reporting for interpretation, interoperability & comparison

X X

Promote standardised metadata practices. X X

Organise and link assets X X

Reuse tools and community archives X

Respect local and legacy solutions X X

Support reproducible publications X X X X

Credit owners X X

FAIRDOM Pillars

Project Support

Community Actions

Platforms, Tools

Public Project Commons

Community, Knowledge Hubhttp://www.fair-dom.org

Know-how, Guides, Templates, Workshops, Training, Webinars, Standards and Policy Forums

Project Support Processes, Practices, People…take time and persuasion

Community support Special project

support Special project

support

PALs project ambassadors

best practices, forums, trainingcuration handholdingSBML model technical curation

Asset Management Platformsan ecosystem of resources

Front endWeb based rich interfaceCatalogue and CommonsAll about the metadataResults repositoryhttp://seek4science.org

Back end Scaled LIMS and analyticsAuto-archivingInstruments data repositoryhttps://sis.id.ethz.ch/software/openbis.html

A community Commons….self managed workspaces

Controlled sharing and publishing

• Licenses• Negotiated access• Embargos• Permission controls• Staged sharing• Private walled gardens

FAIR Play Practices

Using FAIRDOM my own lab colleagues saw what I was doing and called to collaborate!

Jurgen HannstraVrije Universiteit Amsterdam, Netherlands

Investigation

Study Analysis

Data

Model

SOP(Assay)

….organised in an ISA (Investigation, Study, Assay/Analysis) format.

Linking, “Packaging” & Citing Codes, Data, Models, SOPs, Samples, Strains, Articles, People, Projects….

PackagingRetaining ContextSupporting Decision making

STUDY ASSAYINVESTIGATION

Experimental assay

Modeling assay

Publication

[Maksim Zakhartsev]

... a “Research Object” Cataloguemetadata aggregated across repositoriesretaining context to support decision making and reuse

Local Stores

ExternalDatabases

Publishing services

Secure Stores

Model Resources

… with integrated toolingmetadata annotation against standardsmodel validation, comparison and simulation

SBML Model simulation

Model comparison

Model versioning

Reproducing simulations

[Jacky Snoep, Dagmar Waltemate, Martin Peters, Martin Scharm]

Retaining context, supporting decision makingTowards data harmonisation and indexing

[Susanna Sansone]

Stealthy Ramps for helping with Metadata Standards Tooling for annotations and templates for different types of assay datatowards data harmonisation. Incentive by side effect.

Embed ontologies into Excel templates

Excel spreadsheets enriched with ontology annotations

Upload, extract metadata and register

http://www.rightfield.org.uk

Exchange and PublishingSupplementary information

Annotation file

Stoichiometric matrix

SBML Stationary fluxes

[Maxim Zakhartsev]

https://doi.org/10.15490/seek.1.investigation.56

Penkler et al (2015) FEBSJ 282:1481-1511.

Reproducible Exchange and Publishingand better credit

reviewer

Author List: Joe Bloggs; Jane DoeTitle: My Investigation Date: September 2016DOI: https://doi.org/10.15490/seek##

information travels with the data and models

https://doi.org/10.15490/seek#%23



FAIRDOM-SEEK local or public commons

*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

FAIRDOMHub.org

Vrije Universiteit

Yellow Pages

http://hdl.handle.net/1842/12236

http://hdl.handle.net/1842/12236

IMOMESIC pathwayIntegrating Modelling of Metabolism and Signalling towards an Application in Liver Cancerhttps://fairdomhub.org/projects/24

[Ursula Klingmüller, Martin Böhm]

What about FAIR Systems Medicine?Olaf Wolkenhauer et al, Enabling multiscale modeling in systems medicine, Genome Medicine 2014 6:21*

1. Samples

2. Access to sensitive data

3. Multi-models

*DOI: 10.1186/gm538, http://genomemedicine.com/content/6/3/21

Samples metadata frameworkBBMRI, ELIXIR, Biosamples, FAIRDOM, UKCRC Tissue Directory, UK Synthetic Biology Centres

User defined sample models

Interlinking between sample typesSample type defines a sharable standard

Template toolingAuto extraction

Tied to assay processes

FAIR Sensitive Data, certified repositorieswalled gardens and registration flags for Cataloguelegal restrictions for sharing anonymised and non-anonymized data

Open Data

Register metadataUpload dataRegister link

Register access methodRegister metadata

Register access methodLocal AAI service

Register metadata

Closed Data

Closed Data

Model Laissez-Faire

• Navigation between• Single standards at 1

scale• Multi-model hosting

Linking models….• connecting (experimental/simulation) data to

models• connecting the single standards?• interfacing between the different scales?

In summary…Pragmatic FAIR support for projects people, assets, processes

• Multiple, interrelated assets• Multiple, dispersed repositories• Multi-partner, -discipline

projects• Multiple community tools

• Team science practices• Experiment – Asset

lifecycles• Academic innovation

drivers

ISA structured

“Research Objects”

Repository spanning catalogue

metadata

Standards-based tools

Challenges to FAIR Asset Management

Free Puppies

FAIR Play microscopes -> data scopes, sharing citizenship, incentives by side effects

PI leadershipSticking to conventionsLocal responsibilityTime and resourceCuration recognition

Trust• Tribal trading behaviours• Enclave sharing • Not public donation• Reciprocity & credit

Drivers … • External dominate• Personal productivity

affecting behavioural change through libertarian paternalism

[Kristian Garza]

Jon Olav Vik, Norwegian University of Life ScienceMaksim ZakhartsevUniversity Hohenheim, Stuttgart, Germany

Alexey KolodkinSiberian BranchRussian Academy of Sciences

Tomasz Zieliński,SynthSys CentreUniversity Edinburgh, UK

Martin Peters, Martin Scharm Systems Biology BioinformaticsUniversity of Rostock, Germany

3rd Foundry meeting, Dec 1-2 2016

Frankfurt

Developers FoundrySupport developers of Systems Biology tools and platforms