KnetMiner 4.0 released with user workspaces for gene networks

KnetMiner Sees a Major Makeover and Introduces User Workspaces and Cypher Graph Queries

Save and Share Your Interactive Gene Networks

KnetMiner is widely used to study complex relationships between genes and traits. Scientists perform searches and explore interactive knowledge networks for genes of interest. However, previously, it was impossible to save, share, or revisit a network without repeating all previous steps. Even then, database updates could result in different networks.

With KnetMiner 4.0, users can now:

• Save gene networks and their layout with a single click

• Share interactive networks with students, colleagues, and collaborators

• Receive notifications when someone shares a network

• Organise saved networks, add descriptions, and search within them

• Publish gene networks on Twitter or embed them in websites

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Hello KnetSpace!‍

All of this is now possible with KnetSpace, our new bio-discovery platform, built from scratch using Django and React. Signing up is free and quick. After signing in, users can visit any KnetMiner resource (wheat, Arabidopsis, COVID-19), run a search, and click the Save Knetwork button.

KnetSpace Features:

• Search across network objects, including nodes, edges, and properties

• Upload networks, layouts, and metadata via the KnetSpace API

• Organise and manage gene networks

Future Roadmap:

• Create gene networks directly from KnetSpace

• Pro and Team plan subscriptions

• KnetMiner resource subscriptions

Subscription Plans:

• Free Plan: Store a limited number of public networks

• Pro Plan: Unlimited storage with private networks that cannot be cloned or discovered

KnetSpace Beta

Cypher Graph Query Language (Beta)

The KnetMiner 4.0 release also introduces major backend enhancements. KnetMiner’s intelligence lies in identifying gene subgraphs within large genome-scale knowledge graphs. Previously, subgraphs were defined using semantic motif-based searches.

Now, thanks to Marco Brandizi, KnetMiner fully supports Cypher graph queries, a powerful and widely used graph query language. This will allow bioinformaticians and data scientists to customise and extend graph queries.

• Requires Neo4j graph database installation

• Check out RDF2NEO for more details

• Semantic motif technology remains the default option for now

More documentation will be available soon.

For the full list of features and bug fixes, check out the release notes.

We hope you enjoy the new KnetMiner!

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