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v0.6.0: MONDO Disease Ontology & Open Targets Grounding

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@engkinandatama engkinandatama released this 29 Sep 23:39
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v0.6.0
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BioContext v0.6.0 Release Notes

馃専 New Features & Grounding Capabilities

  • MONDO Disease Ontology Integration (MondoAdapter):
    • Added authoritative clinical disease normalization via EBI OLS4 API.
    • Resolves canonical MONDO:xxxxxxx identifiers, preferred names, descriptions, synonyms, and cross-references (OMIM, Orphanet, DOID, UMLS).
    • Flexible free-text disease search.
  • Open Targets Platform Integration (OpenTargetsAdapter):
    • Direct target-disease evidence mapping via Open Targets GraphQL API (api.platform.opentargets.org/api/v4/graphql).
    • Yields aggregate association confidence scores (0.0 - 1.0) with granular evidence breakdowns across genetic associations, somatic mutations, and literature.
  • Expanded MCP Server (10 Production Tools):
    • Exposes resolve_disease(query, limit) and get_target_diseases(gene, limit).
  • New CLI Commands:
    • biocontext disease <query>
    • biocontext targets <gene>
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