AgriSchemas Progress Report
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This document discusses efforts to make agricultural data more interoperable using standards like AgriSchemas. It provides examples of existing agricultural data sources like experimental data from EBI GXA, molecular biology data from Knetminer, and host-pathogen interaction data from PHI-Base. It describes work to model Knetminer and GXA data according to AgriSchemas and provide public SPARQL access. The hackathon goals are to further review and develop AgriSchemas, consider additional use cases and data sources, start defining the AgriSchemas schema/ontology, and work on converting real datasets and applications.
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AgriSchemas Progress Report
- 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?
- 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)
- 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…
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