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v0.8.0 - Biological Knowledge Graph Architecture

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@engkinandatama engkinandatama released this 10 Oct 03:11
· 4 commits to main since this release
v0.8.0
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What's Changed

  • Knowledge Graph Core (PRD-21): Implemented ontological biological Knowledge Graph models, in-memory store, and subgraph builder pipeline.
  • Multi-layer Entity Connections: Seamlessly traverses and builds subgraphs across Genes (HGNC), Proteins (UniProt), Transcripts (Ensembl), Pathways (Reactome), GO terms (QuickGO), Diseases (Open Targets), and Publications (Europe PMC).
  • FastMCP Tool: Added build_entity_subgraph tool to server.py for LLM agents.
  • CLI Command: Added biocontext graph <query> to CLI with selective layer inclusion flags.
  • Testing: Added unit and integration tests with 100% passing rate.
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