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The FAIRDOM Commons for Systems Biology
The Fairdom Commons for Systems Biology, led by Professor Carole Goble, emphasizes the importance of findable, accessible, interoperable, and reusable data in the field. The platform provides a structured environment for managing research assets and facilitates the citation and reproducibility of models and data through various digital tools and standards. The document outlines the significance of generating and sharing kinetic data, the need for proper scientific methods, and highlights the benefits of using the Fairdom platform for documenting and accessing scientific research.
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The FAIRDOM Commons for Systems Biology
- 1. The FAIRDOM Commons forSystems Biology Prof Carole Goble FAIRDOM Consortium The University of Manchester, UK carole.goble@manchester.ac.uk EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015
- 2. Findable Accessible Interoperable Reusable Data S O Ps Models http://www.fair-dom.org http://www.fairdomhub.org Assets Commonsand Catalogue for Sys Bio Projectshttp://www.seek4science.org
- 3.
- 4. For results tobe citable, they have to be… • Findable • Available (Shared) • Interoperable • Reusable/Reproducible
- 5. SingleType-specific structured archives Generalcloud unstructured archives Public Archives for Asset Sharing typically end results and usually public Institutional Repositories
- 6. Project Centric: Programmes,Projects, Groups, Individuals Is there any group generating kinetic data? Is this data available? What methods are been used to determine enzyme activity? What SOP was used for this sample? Where is the validation data for this model?
- 7. Find Yellow pages: projects,people Catalogue of assets. Linked assets. Structured studies Manage and store assets Controlled access Versioning Access gateway to other repositories Access/Archive Interoperate Standards Curation support Tool plug-ins and API Export to other platforms Reuse/Reproduce Consistent reporting Simulate models with exp’mtl data Publisher/Funder Commons with DOIs Download, package and export FAIRDOM Platform www.seek4science.org
- 8. SEEK: Catalogue and Commonsfor many projects Web-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 Platform Extract,Transform and Load tooling direct from the instrumentation, data analysis pipelines.Automatic archiving. Handles large data. FAIRDOM Platform
- 9. Project Centric, InvestigationCentric Mixed types, Mixed Resources
- 10. Project Centric, InvestigationCentric Mixed types, Mixed Resources
- 11. FAIRDOM Commons FAIRDOM Platformand Software Suite Project Commons Project X Commons Community Commons FAIRDOMHub.org
- 12.
- 13. Importance and Accessibility ofcitable assets https://doi.org/10.15490/seek.1.investigation.56
- 14. Models added value simulate and annotatein browser
- 16. 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
- 17. https://doi.org/10.15490/seek.1.investigation.56 Credit and Attribution CitingFAIRDOM Entries, SEEK itself, living and snapshot entries, Contributors Snoep et al Glucose metabolism in Plasmodium falciparum trophoziotes, FAIRDOMHub, March 2015, https://doi.org/10.15 490/seek.1.investigati on.56, version ??
- 18. From Restricted toCitable
- 20. Informed Use ofAccessed Assets Structured 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
- 21. Templates Informed Use ofAccessed Assets Structured studies, standards In browser
- 22. Consumers Producers Local Project Repositories harvesting link Standards organise validate FAIRDOM Repositories FAIRDOM Platform:Catalogue, Commons, Collections, Project-centric Data Management COMMONS
- 23. Local Research Environment Public Publication Environment Peer Review Selective Sharing Scientist Lab Collaborators Private Publiclyavailable Retained Archived Exchanged Selectively Project
- 24. 5 Ways ofmaking FAIRDOM assets citable Project Commons Project X Commons Community Commons FAIRDOMHub.org 2 13 4 5 FAIRDOM Platform and Software Suite
- 25. “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.
- 26. RO Unzip • Reproducibility •Versioning • Systematic and extensible meta-data collection • Cross platform exchange • Publishing Living Snapshot Research Objects snapshots and versioning
- 27. Discussion points • Citingentries 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)
- 28. Carole Goble StuartOwen Finn Bacall Jacky Snoep Wolfgang Mueller Olga Krebs Quyen Nguyen Natalie Stanford KatyWolstencroft Peter Kunzst Bernd Rinn Donal FellowsAlanWilliams Rostyslav Kuzyakiv Jakub Straszewski Chandrasekhar Ramakrishnan Caterina Barillari Norman Morrison