What is it?

These are the KnetGraph endpoints for the knowledge graphs which power KnetMiner. KnetMiner is an application to explore knowledge graphs for candidate gene discovery. Our team uses KnetGraphs in KnetMiner to provide access to information in plant biology.

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:

• Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach
• Our introductions on the KnetMiner Blog and on the DFW blog.
• A tool we have developed to keep RDF data and Neo4j aligned under the same model: rdf2pg.
• A student project, which uses our SPARQL endpoint to find significant traits associated to genes of interest, by means of a gene set enrichment analysis approach (GSEA), which leverage the flexibility and power of standardised knowledge graphs.

Acknowledgements

• Our data endpoints run on Cyverse UK resources, kindly supported by the Earlham institute.
• The hereby SPARQL browser is based on the EBI's LODEStar tool, which runs on top of Virtuoso.
• This work is funded by the UK BBSRC Designing Future Wheat (DFW) project.

License Terms

This work and data is licensed under the Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license, which allows for non-commercial use and requires attribution to the original author. Contact us on hello@knetminer.com to learn more.