KnetMiner 4.0 released with user workspaces for gene networks

by Keywan Hassani-Pak

KnetMiner sees a major makeover and introduces user workspaces and cypher graph queries

Save and share your interactive gene networks

KnetMiner is often used to study complex relationships between genes and traits. Scientists perform a series of searches and explore interactive knowledge networks for their genes of interest. Sharing such a network or returning to it the next day or few months later was impossible without repeating all steps that had led to a network. Even then the underlying database release might have changed and therefore the gene networks could have looked very different.

With KnetMiner 4.0, users can now save gene networks and their layout with a single click and return to it anytime! They can share an interactive network with students, colleagues and collaborators and get notified when someone shares a network with them. Scientists can work together now to review the evidence, find interesting links, or produce publication ready network images. It is now possible to organise many saved networks, add descriptions and search across content and metadata of networks. Last but not least, scientists can publish gene networks via Twitter or embed interactive networks in their own websites.

Hello KnetSpace!

All this is now possible with our new bio-discovery platform KnetSpace, developed from scratch using Django and React. Sign-up to KnetSpace is free and quick. After sign-in, go to any knetminer.org resource such as wheat, Arabidopsis or COVID-19, do a search and click the new Save Knetwork button. Ajit Singh and Joe Hearnshaw advanced KnetMiner to upload the visible network, its layout and metadata information such as name, owner, date, version, source, genes etc via a new KnetSpace API. Searching in KnetSpace searches through actual network objects including all their nodes, edges and properties. KnetSpace is still in early Beta phase and subject to many changes. Our exciting roadmap contains a number of great features such as creating gene networks directly from KnetSpace, Pro and Team plan subscriptions and KnetMiner resource subscriptions. 

The Free plan allows users to store a limited number of public knetworks to KnetSpace. The Pro plan provides unlimited storage and allows users to make their saved networks private. Private networks can not be cloned and can not be discovered by others. Choose a plan that’s right for you.

Cypher graph query language (beta)

The second highlight of the KnetMiner 4.0 release are major enhancements to the backend. The intelligence of KnetMiner lies in finding interesting gene subgraphs in a large genome-scale knowledge graph. Previously, KnetMiner developers defined such subgraphs using semantic motif based graph searches. Marco Brandizi completely re-engineered the graph traversal code to add support for Cypher graph queries. Cypher is a very expressive and popular graph query language which will make it easier for bioinformaticians and data scientists to customise and extend the graph query portfolio. This feature is still experimental and requires a separate Neo4j graph database installation; check out our RDF2NEO tool for more details. For the time being, the default option in KnetMiner 4.0 will remain the old semantic motif technology. More documentation will be released soon.

For a full list of all new features and bug fixes, checkout the release notes.

We hope you enjoy the new KnetMiner!