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. FAIRDOM http://fair-dom.org
Systems and Synthetic Biology
Project Commons
Community driven RI
Since 2008

3. FAIRDOMHub
Public Commons,VRE and Catalogue
An installation of
the SEEK Platform
http://fairdomhub.org
80 Projects
30 Installations

4. Project-Centric Commons
people, expertise
Self managed spaces
Yellow pages
Multi-partner projects

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. 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. 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. Investigation
Study Analysis
Data
Model
SOP(Assay)
https://fairdomhub.org/investigations/56

9. Accessible < Open
sharing sensitivities
Permission controls
Staged sharing
Licenses
Negotiated access
Embargos
Self managed
spaces

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. 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. 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. 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. Research Object packaging
Standards-based metadata framework for manifests and containers
Metadata for bundling resources scattered across repositories

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. 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. Catalogue Interoperability: Samples
a key cross cutting issue in catalogues
compliant

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. How FAIR? Pretty good.

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