The FAIRDOM Commons for Systems Biology

1. The FAIRDOM Commons for Systems 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 Commons and Catalogue for Sys Bio Projectshttp://www.seek4science.org

3. Data Samples SOPs Models Publications

4. For results to be citable, they have to be… • Findable • Available (Shared) • Interoperable • Reusable/Reproducible

5. SingleType-specific structured archives General cloud 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 Commons for 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, Investigation Centric Mixed types, Mixed Resources

10. Project Centric, Investigation Centric Mixed types, Mixed Resources

11. FAIRDOM Commons FAIRDOM Platform and Software Suite Project Commons Project X Commons Community Commons FAIRDOMHub.org

12. FAIRDOMHub Commons

13. Importance and Accessibility of citable assets https://doi.org/10.15490/seek.1.investigation.56

14. Models added value simulate and annotate in browser

15. 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

16. https://doi.org/10.15490/seek.1.investigation.56 Credit and Attribution Citing FAIRDOM Entries, SEEK itself, living and snapshot entries, Contributors Snoep et al Glucose metabolism in Plasmodium falciparum trophoziotes, FAIRDOMHub, March 2015, https://doi.org/10.15 490/seek.1.investigati on.56, version ??

17. From Restricted to Citable

18. Informed Use of Accessed 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

19. Templates Informed Use of Accessed Assets Structured studies, standards In browser

20. Consumers Producers Local Project Repositories harvesting link Standards organise validate FAIRDOM Repositories FAIRDOM Platform: Catalogue, Commons, Collections, Project-centric Data Management COMMONS

21. Local Research Environment Public Publication Environment Peer Review Selective Sharing Scientist Lab Collaborators Private Publicly available Retained Archived Exchanged Selectively Project

22. 5 Ways of making FAIRDOM assets citable Project Commons Project X Commons Community Commons FAIRDOMHub.org 2 13 4 5 FAIRDOM Platform and Software Suite

23. “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.

24. RO Unzip • Reproducibility • Versioning • Systematic and extensible meta-data collection • Cross platform exchange • Publishing Living Snapshot Research Objects snapshots and versioning

25. 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)

26. Carole Goble Stuart Owen 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