KnetMiner 5.6: Leaping into Multispecies

KnetMiner 5.6: Leaping into Multispecies

KnetMiner 5.6 introduces multispecies functionality, performance improvements, bug fixes, UI enhancements, website updates, a new tutorial, additional species, and updated datasets.

Key New Features

Multispecies Functionality

KnetMiner now supports multiple species in a single knowledge graph. Users can:

• Select a species from the new species selector in the header.

• See species-specific search results in Gene View.

• View all species data in Evidence View for broader context.

• Automatically load the chromosome map for the selected species.

• Explore Network View with cross-species relationships.

YAML-Based Configuration

A new YAML configuration system makes it easier to customize KnetMiner instances with advanced features like rules, property interpolation, and overrides. More details are available on GitHub.

Gene Names and Synonyms

• Gene View now displays all names and synonyms for a gene.

• Improved selection of default gene names for consistency.

• Species initials are now prefixed to gene labels in Network View.

Network Data Exporter

Users can now export networks in:

• Tabular format for reports.

• Cytoscape JSON format for further analytics.

A guide pops up after download, explaining how to import JSON data into Cytoscape Desktop.

Gene Ranking via KnetScore

Gene View now includes KnetScore, a ranking system to prioritize candidate genes based on evidence and significance.

Evidence View Enhancements

• Users can quickly view all genes linked to specific evidence nodes.

• A popup tool allows users to download gene accessions for recursive searches.

KnetGraph Programmatic Endpoints

The KnetMiner API homepage has been modernized with:

• Updated links and improved UI.

• Academic use only (contact for commercial licensing).

• Access programmatic endpoints here.

New Tutorial

The updated tutorial page features:

• Improved design and functionality.

• Google indexing for easier discovery.

• Access the tutorial here.

Improved Evidence Filtering

The evidence type filter now:

• Displays evidence type names next to symbols.

• Supports multi-type filtering.

Expanding KnetMiner

• Check out the latest updates on our release notes.

• Developers can explore the Revision History.

Upgrade to Pro

• Pro users get larger networks, more gene queries, and extra storage.

• Explore Paid KnetMiner Bundles for Poaceae, Solanaceae, and Brassicaceae.

• Bespoke multi-species knowledge graphs available—contact us for a quote.

Happy KnetMining!

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