KnetMiner SPARQL endpoint

TL;DR

Enter the KnetMiner SPARQL endpoint!

Some of the datasets available from SPARQL are also accessible from Neo4j endpoints:

• Poaceae (ie, a set of gramineae, including wheat, plus Arabidopsis). For programmatic access: bolt://knetminer-neo4j.cyverseuk.org:7687 (no user/password needed).
• COVID-19 dataset, which we have started developing during the CoViD-19 Bio-hackathon in 2020. Details here. For programmatic access: bolt://knetminer-neo4j.cyverseuk.org:7689 (no user/password needed).

What is it?

This is the SPARQL endpoint for the knowledge graphs that powers KnetMiner. KnetMiner is an application to explore knowledge graph for candidate gene discovery. Our group uses it to provide access to plant biology information, as well as to support other organisms.

The data endpoints offer machine-readable access to the same data that we use for the KnetMiner application, this offers the opportunity for a wider use of the data, for instance, to do Excel exports or to run analyses by means of your own Python scripts.

Want to know more?

The endpoints are based on data standards and FAIR data principles. The data are modelled after our BioKNOW ontology. We are also in the process of defining a more extended AgriSchemas and some prototype examples are included here.

More details are available from:

• IB2018 paper.
• Our introductions on the KnetMiner Blog and on the DFW blog.
• rdf2pg, the tool we have developed to keep RDF data and Neo4j aligned under the same model.

Acknowledgements

• Our data endpoints runs on Cyverse UK resources, kindly provided by the Robert Davey's group at the Earlham institute.
• The hereby SPARQL browser is based on the EBI's LODEStar tool, which runs on top of Virtuoso.
• We are funded by the UK BBSRC Designing Future Wheat (DFW) project.