KnetMiner 5.0: richer, faster, smarter

KnetMiner 5.0 Brings Speed, Enhancements, and New Free/Pro Features

Powerful Search Queries

The gene list search has been significantly improved, now supporting wildcards (e.g., TPS* or PSY* to find all related genes). Matches can now include gene synonyms, leveraging Arabidopsis orthologs and UniProtKB-Swissprot best matches. The keyword search continues to support full Lucene query syntax, allowing powerful combinations such as:

“defense response” OR ((heat OR drought) AND tolerance)

New features include:

• Search feedback with linked/unlinked gene counts and query time

• Support for trait ontology node searches using syntax like:

genelist:TPS and keyword: “ConceptID:4346721”*

Gene Set Enrichment Analysis

The Evidence View now includes an enrichment analysis feature, identifying over-represented terms based on user gene lists. Users can:

• Select multiple terms and visualize combined linkages in Network View

• Extend enrichment analysis to traits, GO terms, pathways, protein domains, and transcription factors

• Download the full Evidence View table

• Perform iterative searches with improved search box functionality

Improved Network Visualisation

The KnetMaps network visualisation now includes:

• Advanced node labeling to distinguish species in multi-species graphs

• Dashed edges to indicate uncertain relationships

• Auto-filtering to manage large networks before rendering

• Export feature to download visible genes in tabular format

New and Updated Datasets

KnetMiner 5.0 integrates:

• Ensembl Genomes Plants 51 release

• Updated datasets from UniProt, PubMed, BioGrid, and others

• Arabidopsis knowledge graph integration via Ensembl Compara

• Multi-species knowledge graph bundles (Poaceae, Solanaceae) available via subscription

• Updated RDF-SPARQL datasets and endpoints

• Latest KnetMiner publication on Wiley

• COVID-19 KnetMiner data note on F1000Research

Free and Pro Features

KnetMiner resources (wheat, Arabidopsis, COVID-19) are now available in:

• Free Plan – Query up to 20 genes, visualize networks of up to 10 genes

• Pro Plan – Search with unlimited genes, create networks of up to 200 genes, and store unlimited networks

Further Improvements

• GenePage API enhancements: Real-time analysis of queries, visual word summaries

• On-premise deployment enhancements:

• Google Analytics settings

• Amazon S3 integration for anonymized queries and dashboards

• Updated wiki with more documentation for users and developers

For full details, visit the GitHub release notes.

We hope you enjoy the KnetMiner 5.0 experience!

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