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OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata to EOSC

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Carole Goble presents the FAIRDOM | OSFair2017 Workshop

Workshop title: How FAIR friendly is your data catalogue?

Workshop overview:
This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users?

DAY 3 - PARALLEL SESSION 6 & 7

Published in: Science
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OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata to EOSC

  1. 1. How FAIR friendly is the FAIRDOMHub? Exposing metadata to EOSC Carole Goble University of Manchester, UK & FAIRDOM e.V. carole.goble@manchester.ac.uk EOSCpilot workshop How FAIR friendly is your Data Catalogue? Open Science Fair, 6-8 Sept 2017, Athens
  2. 2. FAIRDOM http://fair-dom.org Systems and Synthetic Biology Project Commons Community driven RI Since 2008
  3. 3. FAIRDOMHub Public Commons,VRE and Catalogue An installation of the SEEK Platform http://fairdomhub.org 80 Projects 30 Installations
  4. 4. Project-Centric Commons people, expertise Self managed spaces Yellow pages Multi-partner projects
  5. 5. FAIR Content, FAIR Projects What methods are been used to determine enzyme activity? What SOP was used for this sample? Where is the validation data for this model? Is there any group generating kinetic data? Is this data available? Track versions of my model Whats the relationship between the data and model? Which data belong to which publications?
  6. 6. One place Asset Catalogue federated types, federated stores, packaging Multi-results & Versions Data of many types… Primary, secondary, tertiary… Methods, Models, Scripts … Structured organisation Spans repository silos Regardless of location • In house project stores • Subject specialist public archives • General archives • Internal FAIRDOM stores
  7. 7. More than datasets: Structured Research Objects 16 datafiles (kinetic, flux inhibition, runout) 19 models (kinetics, validation) 13 SOPs 3 studies (model analysis, construction, validation) 24 assays/analyses (simulations, model characterisations) Penkler, G., du Toit, F., Adams, W., Rautenbach, M., Palm, D. C., van Niekerk, D. D. and Snoep, J. L. (2015), Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J, 282: 1481–1511. doi:10.1111/febs.13237
  8. 8. Investigation Study Analysis Data Model SOP(Assay) https://fairdomhub.org/investigations/56
  9. 9. Accessible < Open sharing sensitivities Permission controls Staged sharing Licenses Negotiated access Embargos Self managed spaces
  10. 10. Access content and applications resolution, execution, reproducibility SBML Model simulation Model comparison Model versioning Reproducing simulations [Jacky Snoep, Dagmar Waltemath, Martin Peters, Martin Scharm]
  11. 11. Metadata Framework FAIR Catalogue, FAIR Content Schema Dublin core Datacite, DCAT, Bioschemas Catalogue Level Investigation Studies Assay/Analysis Entry level Entry level Persistent Identifiers Orcid, DOI Identifiers.org Native identifier URLs Community conventions PIDs for all levels of content Record level: subject thematic standards
  12. 12. Accessibility persistent ids, versions, snapshots Author List: Joe Bloggs; Jane Doe Title: My Investigation Date: September 2016 DOI: https://doi.org/10.15490/seek## https://doi.org/10.15490/seek.1.investigation.56 Active entry evolves Version Fenner et al, A Data Citation Roadmap for Scholarly Data Repositories doi: https://doi.org/10.1101/097196
  13. 13. Catalogue Interoperability ISA based Research Object Packaging & Exchange Author List: Joe Bloggs; Jane Doe Title: My Investigation Date: September 2016 DOI: https://doi.org/10.15490/seek## information travels with the data and models https://doi.org/10.15490/seek.1.investigation.56 Active entry evolves Version
  14. 14. Research Object packaging Standards-based metadata framework for manifests and containers Metadata for bundling resources scattered across repositories
  15. 15. Catalogue Interoperability Linked Data Inside and Out Lower friction of semantic annotation Flexibly represent different types of data Extract and catalogue metadata Define relationships, cross- link, aggregate, query data standard based Excel templates
  16. 16. Finding and Accessing Modalities Lucene Search Query Linked Data SPARQL endpoint Browse Navigate ISA Structure API XML Linked Data Content negotiation Research Object Zipfile bundle + Linked Data Researchobject.org Resolve Datacite Identifiers.org
  17. 17. Catalogue Interoperability: Samples a key cross cutting issue in catalogues compliant
  18. 18. Interoperability: Catalogues & Repos. ELIXIR/GO-FAIR FAIR Datapoint DCAT description https://dtl-fair.atlassian.net/wiki/display/FDP/FAIR+Data+Point+Software+Specification output: standardized metadata as Linked Data input: URL FAIR API
  19. 19. How FAIR? Pretty good.
  20. 20. FAIR Catalogue for EOSC Discussion Points • FAIR at different levels – The Catalogue vsThe Content • Minimum information: Just enough and no more • Balance common metadata types with specific types – Divide and conquer drill down – Library view? Project view? Science view? – Commonality vs Imposing • Use Commodity infrastructure and protocols – For harvesting, indexing, validation, search

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