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v0.5.0 — Phase 1 Milestone: Multi-Authority Resolution & 100 Benchmark Cases

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@engkinandatama engkinandatama released this 28 Sep 18:26
· 12 commits to main since this release
v0.5.0
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BioContext v0.5.0 — Phase 1 Milestone Release

Authoritative Biological Entity Resolution & Contextual Intelligence Framework.

Key Highlights

  • Multi-Authority Biological Resolution: 7 operational adapters (HGNC, NCBI Entrez, UniProtKB, Ensembl, MGI, QuickGO, Reactome).
  • 100 Benchmark Test Cases: Validated with 100% resolution accuracy across human cancer/signaling genes, clinical aliases (HER2, p53, Bcl-xL, p27Kip1), Entrez Gene IDs, UniProt accessions, and mouse models (Mus musculus).
  • End-to-End Multilayer Context: Deep biological context pipeline verified in tests/test_e2e_pipeline.py (Entity Resolution $\rightarrow$ QuickGO Functional Annotations $\rightarrow$ Reactome Pathways).
  • FastMCP Protocol Integration: 8 production-ready MCP tools compatible with Cursor, Antigravity IDE, Claude Desktop, Claude Code, and Goose.
  • Embedded Persistence: Zero-configuration SQLite cache with alias lookup optimizations.
  • Comprehensive Documentation: Complete guides in README.md, docs/QUICKSTART.md, and docs/ARCHITECTURE.md.
  • Roadmap Evolution: Formally established Phase 1.5 (Disease, Drug & Clinical Context) bridging Phase 1 to Phase 2 (Knowledge Graph & AI Reasoning).
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