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AgriSchemas Progress Report

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Presented at the Nov 2019 DFW hackathon

Published in: Science
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AgriSchemas Progress Report

  1. 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. 2. Linked Data APIs APIs + standards Guidelines Tabular formats Vocabularies ’n onto services Specific formats What do we have in Agrifood?
  3. 3. The DFW Needs
  4. 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. 5. Towards interoperability: AgriSchemas
  6. 6. Towards interoperability: AgriSchemas
  7. 7. Towards interoperability: AgriSchemas Experimental data (EBI GXA) Molecular biology (Knetminer) Host-pathogen interaction (PHI- Base)
  8. 8. Towards interoperability: AgriSchemas Molecular biology (Knetminer)
  9. 9. Towards interoperability: AgriSchemas Experimental data (EBI GXA)
  10. 10. Towards interoperability: AgriSchemas Host-pathogen interaction (PHI- Base)
  11. 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. 12. Integration and Interoperability Knetminer Info GXA Info
  13. 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…

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