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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
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