New KnetMaps

KnetMaps, our in-house built Knowledge Graph explorer tool, has been dramatically upgraded. Now full screen, colourful, and more interactive, it features a structured info box for quick node data interpretation, a superior image exporter for publications, and node groupings to place compound nodes around nodes of the same species. We've also added a semantic path feature, a table view for quick node filtering, and various power features like multi-select, lasso tool, and node/edge name highlighting.

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Unlocking New Potential: Faster, Smarter KnetMaps
KnetMaps has undergone a major transformation, evolving from its legacy version into a full-screen, vibrant, and highly interactive experience. We reimagined the most common graph operations from the ground up, working closely with our UI/UX experts to ensure key functions are exactly where you need them.
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Everything has been redesigned—from a structured Info Box for quick node data interpretation to an enhanced image exporter for publication-ready visuals. Node groupings now intelligently arrange compound nodes around those of the same species, improving clarity and readability.
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Users can now perform operations directly on nodes and edges, and for the first time, re-search the full graph database directly from the Network view.
All New Semantic Path Highlighting
Another standout feature is the all-new Semantic Path Highlighting. This new feature automatically highlights the nodes and edges from any node in the graph connecting back to the seed gene that generated it. This removes any guesswork, making it clear how a particular node fits into the subgraph and relates to your gene of interest. The new table view allows for quick viewing, filtering and downloading of specific node types within the graph. We’ve also added a network-wide search straight into KnetMaps - which will search across all node properties in the graph. Power features such as multi-select, lasso tool, and options to remove disconnected nodes or highlight node/edge names have also been added, to give more control over graphs generated.

Improved Layout Algorithms

We've also improved our layout algorithms, leveraging ‘fCoSE’1  for fast and reliable layouts and ‘avsdf’2 (circular) layout for more efficient organisation (with reduced edge overlaps compared to a conventional circular layout). Another significant upgrade is the prioritisation of evidence during subgraph creation: we now use key metrics derived from search results to deliver a subgraph with relevant, recent, and high-quality nodes, resulting in more compact and user-friendly graphs instead of overwhelming hairballs.We’ve worked on these updates alongside the experts who use them most and believe they make KnetMaps a more powerful, user-friendly tool, tailored for those who need results fast.

‍1. H. Balci and U. Dogrusoz, "fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support," in IEEE Transactions on Visualization and Computer Graphics, vol. 28, no. 12, pp. 4582-4593, 1 Dec. 2022, doi: 10.1109/TVCG.2021.3095303.
2. A. Okka, D. Cakmakci, and U. Dogrusoz, "cytoscape.js-avsdf: A Cytoscape.js extension for AVSDF layout," i-Vis at Bilkent University. Available: https://github.com/iVis-at-Bilkent/cytoscape.js-avsdf

We’ve worked on these updates alongside the experts who use them most and believe they make KnetMaps a more powerful, user-friendly tool, tailored for those who need results fast.
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‍We welcome any and all positive feedback as we begin rolling out the all New KnetMiner.

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