akikuno/TSUMUGI-dev: 0.4.0

v0.4.0 (2025-11-12)

💥 Breaking

• Adopted the Phenodigm/Resnik similarity pipeline so phenotype matching now respects the hierarchical structure of MPO instead of relying on plain Jaccard overlap.
  Issue: #71
  [Commit Detail]

• Surface common ancestor MP terms on KO mouse edges, filtering out low-information matches to highlight meaningful shared phenotypes.
  Issue: #118
  [Commit Detail]

• Pre-compute degree and betweenness centrality for every node and expose slider-based filters to spotlight highly connected genes.
  Issue: #108
  [Commit Detail]

🌟 New Features

• Expanded the phenotype similarity and severity scales from 0–10 to 1–100 so users get Phenodigm-level precision when scoring networks.
  Issue: #119
  [Commit Detail]

• Added a JPEG export mode alongside the existing PNG and SVG download options for Cytoscape.js views.
  Issue: #117
  [Commit Detail]

• Normalized degree and betweenness scores by phenotype count and introduced an optional log-scale transform to curb hub bias.
  Issue: #113
  [Commit Detail]

• Delivered Cytoscape Desktop–compatible GraphML exports (nodes and edges) for seamless round-tripping between the web app and local analyses.
  Issue: #92
  [Commit Detail]

🐛 Bug Fixes

• Recompute centrality metrics whenever filters change so node sizes and values stay in sync with the visible subnetwork.
  Issue: #112
  [Commit Detail]

• Fix gene search bug for single character input
  Issue: #86
  [Commit Detail]

🖼️ User Interface

• Add Phenotype Severity and Similarity Scores to Network Tooltips
  Issue: #107
  [Commit Detail]

• Improve Network Visualization for Gene Symbol Pages
  Issue: #105
  [Commit Detail]

• Provide in-product tooltips and an info icon that explain phenotype metrics directly within the interface.
  Issue: #100

• Allow tooltips to be repositioned via touch interactions so tablet users can keep data in view.
  Issue: #97