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
OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata to EOSC
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
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
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
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
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
Hinweis der Redaktion
REUSE flavour
FAIRDOM - FAIR asset management and sharing experiences in Systems Biology
Over the past 5 years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs and so forth. Don’t stop reading. Yes, data management isn’t likely to win anyone a Nobel prize. But publications should be supported and accompanied by data, methods, procedures, etc. to assure reproducibility of results. Funding agencies expect data (and increasingly software) management retention and access plans as part of the proposal process for projects to be funded. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation. The FAIRDOM (Findable, Accessible, Interoperable, Reusable Data, Operations and Models) Initiative has 8 years of experience of asset sharing and data infrastructure ranging across European programmes (SysMO and EraSysAPP ERANets), national initiatives (de.NBI, German Virtual Liver Network, UK SynBio centres) and PI's labs . It aims to support Systems Biology researchers with data and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety. This talk will use the FAIRDOM Initiative to discuss the FAIR management of data, SOPs, and models for Sys Bio, highlighting the challenges of and approaches to sharing, credit, citation and asset infrastructures in practice. I'll also highlight recent experiments in affecting sharing using behavioural interventions. http://www.fair-dom.org http://www.fairdomhub.org http://www.seek4science.org