This organisation holds older versions of KnetMiner software, from before the launch of Nova KnetMiner. Most of it is no longer maintained, no longer supported, and should not be used for new work.
Go to knetminer.com. That is the live application, and the only place to get the current version.
Current KnetMiner development happens in the KnetMiner organisation. The main application is closed-source, so most of those repositories are private and you will not be able to browse them. A few supporting tools are public.
If you need access, a licence, or an on-premise deployment, get in touch through knetminer.com rather than opening issues here.
The code is kept public for reference and reproducibility, not for reuse:
- published papers cite these repositories, and those citations should not break
- earlier KnetMiner and Ondex releases remain part of the scientific record
- some of this work is still useful to read, even where it no longer runs
Expect old dependencies, dead links, stale documentation, and build instructions that no longer work. Issues and pull requests here are generally not monitored.
| KnetMiner (pre-Nova) | The earlier web application, its backend, and supporting services. Superseded. |
| Ondex / KnetBuilder | The data-integration platform used to build the knowledge graphs. knetbuilder was previously known as Ondex; the older ondex-* repositories are archived. |
| Visualisation components | knetmaps.js and genomaps.js. Both have successors — genomaps.js is continued in the KnetMiner org. |
| Knowledge graphs and datasets | Graph-building scripts and use cases from past projects. |
| Infrastructure and internal tooling | Build, CI, deployment and lab scripts of historical interest only. |
A few general-purpose tools live in this organisation because they were built alongside KnetMiner, but they are not KnetMiner-specific and are still worked on. Judge these by their own commit history rather than by this notice:
rdf2pg— converting and loading RDF into Neo4jagri-schemas— schemas and ontologies for agrifood
If you are citing the software or the method, cite the paper rather than a repository:
Hassani-Pak, K. et al. (2021) KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. Plant Biotechnology Journal 19(8), 1670–1678. doi:10.1111/pbi.13583
KnetMiner was developed at Rothamsted Research and is now developed by KnetMiner Ltd. Rothamsted's own research software is at github.com/Rothamsted.
