Presented at the Nov 2019 DFW hackathon

1. AgriSchemas and FAIR-ification of DFW
Data
Rothamsted Research, 11/11/2019
Marco Brandizi <marco.brandizi@rothamsted.ac.uk>
Find these slides on SlideShare

2. Linked Data
APIs
APIs + standards
Guidelines
Tabular formats
Vocabularies ’n onto services
Specific
formats
What do we have in Agrifood?

3. The DFW Needs

4. The Knetminer Needs
• Green: Ondex plug-ins
• rdf2neo is a generic, non Ondex-specific
rdf->Neo4j conversion tool
• Brandizi et al, IB-2018
(https://dx.doi.org/10.1515%2Fjib-2018-0023)
• Brandizi et al, SWAT4LS-2018
(https://doi.org/10.6084/m9.figshare.7314323.v1)

5. Towards interoperability: AgriSchemas

6. Towards interoperability: AgriSchemas

7. Towards interoperability: AgriSchemas
Experimental data (EBI
GXA)
Molecular biology
(Knetminer)
Host-pathogen interaction (PHI-
Base)

8. Towards interoperability: AgriSchemas
Molecular biology
(Knetminer)

9. Towards interoperability: AgriSchemas
Experimental data (EBI GXA)

10. Towards interoperability: AgriSchemas
Host-pathogen interaction (PHI-
Base)

11. The Knetminer SPARQL endpoint
A first prototype of Knetminer data
+ EBI’s GXA data, modelled after AgriSchemas
Try it live:
http://knetminer-data.cyverseuk.org/lodestar/sparql
More examples:
https://bit.ly/2X34rgF

12. Integration and Interoperability
Knetminer Info
GXA Info

13. What’s next?
• This hackathon:
• Review what’s done so fare with AgriSchemas
• Possibly think of new use cases
• eg, CerealsDB, AHDB, T3, GG3, DFW vocabularies, DFW datasets being
published
• eg, weather data (in particular, those linked to trials via MIAPPE)
• Start defining the AgriSchemas schema/ontology
• Possibly now or surely later:
• Convert real data sets
• Finalise the endpoint and convert to Neo4j
• Develop sample applications (eg, Python analyses, Jupyter analyses)
• Submit to some journal…