FAIR Data and Model Managementfor Systems Biology

Projects

Prof Carole GobleFAIRDOM Consortium

The University of Manchester, UKcarole.goble@manchester.ac.uk

ISMB/ECCB 2015, Dublin, Ireland

FindableAccessibleInteroperableReusable

DataS O PsModels

http://www.fair-dom.orghttp://www.fairdomhub.org

Assets¿

Aggregated Commons for Sys Bio Projects

Data

Samples

SOPs

Models

Publications

Programmes, Projects, Groups

Is there any group generating kinetic data?

Who is working with wh

ich

organism?Is this data available?

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?

2008

Nature June 2015

FindYellow pages: projects, peopleTrans-asset cataloguing & linking Structure studies

Manage and store assetsControlled accessVersioning Trans-repository gatewayDeposit and download wrt specialist public archives

Access/Archive

InteroperateStandards compliant practicesCuration supportTool plug-ins and APILeverage other platformsAnalytics

Reuse/ReproduceConsistent reportingSimulate models with exp’mtl dataPublisher/Funder Commons with DOIsDownload, package and export

Asset Management and Sharing Platform for Systems Biology Projects

http://www.fair-dom.org

Commons & Cataloguing platformWeb-based cataloguing and aggregation.Find, Access, Describe, Structure, Link, Exchange project assets.Central and distributed repositories.REST API

LIMS & Analytics platformExtract, Transform and Load tooling direct from the instrumentation.Data analysis pipelines, automatic archiving.Large data.

Funding to 2019

http://www.seek4science.org

http://www.cisd.ethz.ch/software/openBIS

submission

link

accesslink Consumers

Producers

CommonsProject Repositories

harvesting

link

subm

ission

link

Publishers

Standards

organisevalid

ate

Native CommonsRepositories

linkdep

osit

Specialist

Tools

runresults

Public Specialist

Repositories

linkdeposit

Aggregated Commons InfrastructureCataloguing ++

FAIRDOM Metadata framework link studies and link assets

Common elements and relationships between things produced and used in experiments.

Structured descriptions

Consistency ComparisonDealing with novel data

Just Enough Results Model

Metadata Tooling

Smart spreadsheets, Curation Support

Standards Engagement

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

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

Linking platforms to the Commons Catalogue

FAIR Controlled Sharing & Publishing

RO Unzip

Snapshot into Research Object bundles for exchange & publication

FAIRDOM Platform and Software Suite

Different ways of using FAIRDOMwith OpenBIS or with own project DB

Self-m’gedCommons

Project XCommons

Public, HostedCommons

FAIRDOMHub.org

Full independent self-management on FAIRDOMHub.orgSept 2015

Funder

CRIS

Publisher Companion

Hosted

manag

ement

Community

FacilitiesProject Support

Training and ServicesCuration

Sustainability

Knowledge NetworksForums, Workshops

Summer SchoolsWorking Groups

StandardsUser and Developer

WGs - SamplesPartnershipsDeveloper FoundryFAIRDOM developersFree Open Source SoftwareVMs and Docker

Supporting projectsFAIRDOM CentresNational Infrastructures“ISBE Light”Working with funders

http://seek4science.github.io/seek/

de.NBI

https://sems.uni-rostock.de/reproducible-and-citable-data-and-models/

Carole Goble Stuart Owen

Finn Bacall

Jacky Snoep

Wolfgang Mueller

Olga Krebs Quyen Nguyen

Natalie Stanford

Katy Wolstencroft

Peter Kunzst Bernd Rinn

Donal FellowsAlan Williams

Rostyslav Kuzyakiv

Jakub Straszewski

Chandrasekhar Ramakrishnan

CaterinaBarillari

Norman Morrison

FindYellow pages: projects, peopleTrans-asset cataloguing & linking Structure studies

Manage and store assetsControlled accessVersioning Trans-repository gatewayDeposit into specialist public archives

Access/Archive

InteroperateStandards compliant practicesCuration supportTool plug-ins and APILeverage other platformsAnalytics

Reuse/ReproduceConsistent reportingSimulate models with exp’mtl dataPublisher/Funder Commons with DOIsDownload, package and export

Asset Management and Sharing Platform for Systems Biology Projects

http://www.fair-dom.org