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FAIR data and model management for systems biology.

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Written and presented by Carole Goble (University of Manchester) as part of Intelligent Systems for Molecular Biology (ISMB), Dublin. July 10th - 14th 2015.

Published in: Science
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FAIR data and model management for systems biology.

  1. 1. FAIR Data and Model Management for Systems Biology Projects Prof Carole Goble FAIRDOM Consortium The University of Manchester, UK carole.goble@manchester.ac.uk ISMB/ECCB 2015, Dublin, Ireland
  2. 2. Findable Accessible Interoperable Reusable Data S O Ps Models http://www.fair-dom.org http://www.fairdomhub.org Assets Aggregated Commons for Sys Bio Projects
  3. 3. Data Samples SOPs Models Publications
  4. 4. Programmes, Projects, Groups Is this data available? What SOP was used for this sample? Where is the validation data for this model?
  5. 5. 2008 Nature June 2015
  6. 6. Find Yellow pages: projects, people Trans-asset cataloguing & linking Structure studies Manage and store assets Controlled access Versioning Trans-repository gateway Deposit and download wrt specialist public archives Access/Archive Interoperate Standards compliant practices Curation support Tool plug-ins and API Leverage other platforms Analytics Reuse/Reproduce Consistent reporting Simulate models with exp’mtl data Publisher/Funder Commons with DOIs Download, package and export Asset Management and Sharing Platform for Systems Biology Projects http://www.fair-dom.org
  7. 7. Commons & Cataloguing platform Web-based cataloguing and aggregation. Find, Access, Describe, Structure, Link, Exchange project assets. Central and distributed repositories. RESTAPI LIMS & Analytics platform Extract,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
  8. 8. Consumers Producers Commons Project Repositories harvesting link Standards organise validate Native Commons Repositories
  9. 9. Aggregated Commons Infrastructure Cataloguing ++
  10. 10. FAIRDOM Metadata framework link studies and link assets Common elements and relationships between things produced and used in experiments. Structured descriptions Consistency Comparison Dealing with novel data Just Enough Results Model
  11. 11. https://doi.org/10.15490/seek.1.investigation.56 Penkler et al (2015) FEBSJ 282:1481-1511.
  12. 12. Linking platforms to the Commons Catalogue
  13. 13. FAIR Controlled Sharing & Publishing
  14. 14. RO Unzip Snapshot into Research Object bundles for exchange & publication
  15. 15. FAIRDOM Platform and Software Suite Different ways of using FAIRDOM with OpenBIS or with own project DB Self-m’ged Commons Project X Commons Public, Hosted Commons FAIRDOMHub.org Full independent self-management on FAIRDOMHub.org Sept 2015
  16. 16. Community Facilities Project Support Training and Services Curation Sustainability Knowledge Networks Forums, Workshops Summer Schools Working Groups Standards User and Developer WGs - Samples Partnerships Developer Foundry FAIRDOM developers Free Open Source Software VMs and Docker Supporting projects FAIRDOM Centres National Infrastructures “ISBE Light” Working with funders http://seek4science.github.io/seek/ de.NBI
  17. 17. https://sems.uni-rostock.de/reproducible-and-citable-data-and-models/
  18. 18. 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
  19. 19. Find Yellow pages: projects, people Trans-asset cataloguing & linking Structure studies Manage and store assets Controlled access Versioning Trans-repository gateway Deposit into specialist public archives Access/Archive Interoperate Standards compliant practices Curation support Tool plug-ins and API Leverage other platforms Analytics Reuse/Reproduce Consistent reporting Simulate models with exp’mtl data Publisher/Funder Commons with DOIs Download, package and export Asset Management and Sharing Platform for Systems Biology Projects http://www.fair-dom.org

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