The FAIRDOM Commonsfor Systems Biology

Prof Carole GobleFAIRDOM ConsortiumThe University of Manchester, UKcarole.goble@manchester.ac.uk

EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015

FindableAccessibleInteroperableReusable

DataS O PsModels

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

Assets¿

Commons and Catalogue for Sys Bio Projects

http://www.seek4science.org

Data

Samples

SOPs

Models

Publications

For results to be citable, they have to be…

• Findable• Available (Shared)• Interoperable• Reusable/Reproducible

Single Type-specific structured archives

General cloud unstructured archives

Public Archives for Asset Sharingtypically end results and usually public

Institutional Repositories

Project Centric: Programmes, Projects, Groups, Individuals

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?

Find Yellow pages: projects, peopleCatalogue of assets. Linked assets.Structured studiesManage and store assetsControlled accessVersioning Access gateway to other repositories

Access/Archive

Interoperate Standards Curation supportTool plug-ins and APIExport to other platforms

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

FAIRDOM Platformwww.seek4science.org

SEEK:

Catalogue and Commons for many projectsWeb-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 PlatformExtract, 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 CentricMixed types, Mixed Resources

FAIRDOM Commons

FAIRDOM Platform and Software Suite

ProjectCommons

Project XCommons

CommunityCommons

FAIRDOMHub.org

Funder Info System

Publisher Companion

FAIRDOMHub Commons

Importance and Accessibility of citable assets

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

Modelsadded valuesimulate 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 AttributionCiting FAIRDOM Entries, SEEK itself,living and snapshot entries, Contributors

Snoep et al Glucose metabolism in Plasmodium falciparum trophoziotes, FAIRDOMHub, March 2015, https://doi.org/10.15490/seek.1.investigation.56, version ??

From Restricted to Citable

Informed Use of Accessed AssetsStructured 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 AssetsStructured studies, standards

In browser

submission

link

accesslink Consumers

Producers

Local Project Repositories

harvesting

link

subm

ission

link

Publishers

Standards

organisevalid

ate

FAIRDOMRepositories

linkdep

osit

Specialist

Tools

runresultsPublic S

pecialist

Repositories

link

deposit

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

RetainedArchived

ExchangedSelectively

Project

5 Ways of making FAIRDOM assets citable

ProjectCommons

Project XCommonsCommunityCommons

FAIRDOMHub.org2

1Public Specialist

Repositories

Publisher

Repositories

34

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 Objectssnapshots 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

Katy Wolstencroft

Peter Kunzst Bernd Rinn

Donal FellowsAlan Williams

Rostyslav Kuzyakiv

Jakub Straszewski

Chandrasekhar Ramakrishnan

CaterinaBarillari

Norman Morrison