genomoncology/biomcp

0.8.22 — 2026-04-30

New features

• Extended WHO Prequalification drug coverage to include active pharmaceutical
  ingredients (APIs) alongside finished pharmaceutical products;
  search drug --region who --product-type api filters explicit WHO searches
  to API rows. (232)
• Added the CDC CVX/MVX vaccine identity bridge for default and EU/all
  vaccine-brand drug search, backed by local CDC bundle downloads and explicit
  refresh via biomcp cvx sync. (233)
• Added CDC WONDER VAERS as the aggregate vaccine adverse-event source for
  search adverse-event --source <faers|vaers|all>, including combined
  vaccine search, health visibility, and source inventory/docs surfaces. (235)
• Added the local GTR-backed diagnostic entity with search/get diagnostic,
  first-use bundle refresh, explicit biomcp gtr sync, and the supporting
  health/docs/spec contract. (236)
• Expanded diagnostic into a local multi-source surface with WHO Prequalified IVD
  infectious-disease products, source-aware search/get behavior, and explicit
  biomcp who-ivd sync. (237)
• Added FDA 510(k) and PMA regulatory overlays to
  get diagnostic <id> regulatory, rendering source-aware FDA device status
  when records match and a truthful empty regulatory section when they do not.
  (238)
• Added opt-in diagnostic pivots to gene and disease cards with
  get gene <symbol> diagnostics and get disease <name_or_id> diagnostics,
  backed by local GTR and WHO IVD diagnostic search. (239)
• Extended article search follow-up guidance with cross-entity keyword hints:
  JSON _meta.next_commands now includes gene and drug pivots for recognizable
  keyword patterns, while markdown See also: adds discover and
  get disease recovery paths for short disease-like phrases. (242)
• Added opt-in clinical_features disease output backed by MedlinePlus
  clinical summaries, reviewed HPO phenotype mapping, source-native evidence
  URLs, and unsupported-disease empty states via
  get disease <name> clinical_features. (252, 253, 254)
• Added offline routing via biomcp suggest <question> so worked-example
  prompts can resolve to structured _meta.workflow guidance without requiring
  a live tool call. (279)
• Added workflow-ladder sidecars and schema-backed _meta.ladder[] payloads
  so routed workflows can carry explicit ladder steps across the CLI/MCP
  contract. (282)
• Added richer CLI help examples for batch/variant-limit usage and preserved
  the parser-level skill uninstall contract through current help and MCP guard
  surfaces. (217, 224)
• Added opt-in article fulltext source-boundary coverage and PDF fallback so
  article retrieval can truthfully report source limits while recovering PDF
  text when structured fulltext is unavailable. (255, 256)
• Added DDInter-backed drug-drug interaction workflows with
  biomcp drug interactions <name>, get drug <name> interactions, local
  bundle health, source-scoped empty wording, and biomcp ddinter sync.
  (303)

Docs

• Added BioASQ-oriented how-to routing rows to skills/SKILL.md for
  gene-disease association, gene localization/protein-function, drug regulatory
  date, and variant clinical-significance workflows, steering agents to
  structured-data shortcuts before article search. (240)
• Refreshed architecture, source-integration, and current-state docs so the
  shipped architecture and CLI guidance match the post-decomposition repo
  surface. (272, 273, 274, 275)
• Repaired backtick quoting in the mustmatch study/spec contract, published
  BioASQ benchmark guidance, and made the canonical SKILL.md render/install
  contract explicit for agents and operators. (276, 280, 281)
• Aligned the public landing-copy contract with the shipped suggest and
  workflow landing bullets so make test-contracts accepts the current README
  and docs homepage feature counts. (286)
• Refreshed source, licensing, versioning, CLI decomposition, diagnostic,
  clinical-features, API-key, quality-bar, and staging-demo docs to match the
  shipped v0.8.22 surface and current local-runtime key expectations. (222,
  272, 292, 304, 306, 314, 318, 329, 332, 341, 358, 362)

Fixes

• Changed custom CLI validation failures (BioMcpError::InvalidArgument) to exit
  2, matching clap parser failures and separating bad usage from runtime
  failures. (353)
• Fixed suggest so resistance-to-drug mechanism questions anchor starter
  commands on the drug instead of filler text. (291)
• Patched rustls-webpki to the safe release line and made make check enforce
  the cargo-deny advisory gate alongside the existing license gate. (290)
• Fixed cargo-install compatibility, deterministic EMA freshness checks, OLS4
  smoke routing, WHO drug JSON envelopes, and WHO API cache-limit wording so
  install, health, and explicit WHO/API drug searches stay stable. (218, 220,
  226, 232)
• Added compact diagnostic rows and capped disease diagnostic pivots so
  gene/disease diagnostic follow-ups stay scannable and bounded. (266, 267)
• Replaced the stale GTR sample with a live-valid GTR example and added
  zero-result recovery for the local diagnostic surface. (268, 269)
• Tightened entity-aware article follow-ups with a same-session loop-breaker
  for overlapping suggestions and PubMed ESearch cleanup for bounded
  question-format filler words. (277, 278, 283)
• Improved sparse drug research-code recovery, relational discover filtering,
  trial help example/flag consistency, and CTGov intervention alias preservation
  so generated follow-up commands stay useful and shell-safe for degraded or
  ambiguous inputs. (302, 310, 313, 338, 339, 340, 342, 351, 357)
• Repaired the targeted SPEC_SMOKE_ARGS lane so it stores stable smoke
  section IDs and resolves them to current mustmatch pytest item IDs at runtime;
  the quality ratchet now checks collectability before stale line-qualified
  selectors can reach make spec-smoke. (288)
• Hardened update and machine-readable CLI contracts: biomcp update fails
  closed when checksum sidecars are missing, biomcp --json version documents
  its plain-text exception, biomcp --json list remains parseable, and
  short-literal update ratchets were replaced with structural behavior checks.
  (331, 333, 352, 355)
• Stabilized MCP stdio no-input guidance, cBioPortal study download idle/stall
  handling, disease clinical-feature specs, OLS4 disease/discover fallback IDs,
  WikiPathways parallel tests, and protein ComplexPortal specs with regression
  coverage. (326, 336, 345, 346, 350, 354, 358)
• Surfaced Semantic Scholar authentication/degradation status in article search
  and honored Retry-After during authenticated retries so throttled searches
  disclose source health and back off correctly. (364, 365, 366)

Internal

• Completed release/docs contract cleanup for the 0.8.22 line so the latest
  release notes, ticket inventory, and release metadata stay aligned. (264, 265)
• Made make check include the public Python/docs contract lane and added
  make release-gate as the named local release-blocking command, so
  release-readiness docs and validation profiles share one contract. (287)
• Reworked SPEC_SMOKE_ARGS handling around stable smoke inventory and current
  mustmatch pytest item IDs, and cleaned up .march artifact handling for
  repo submission paths. (270, 271)
• Migrated the release gate to the spec-v2 corpus, made spec-pr self-contained
  for March kickoff, restored release-gate reliability, and kept stable smoke,
  canary, cache-warm, and test-contract lanes aligned with the current shipped
  docs/spec surface. (294, 297, 298, 299, 300, 301, 307, 308, 344)
• Decomposed oversized CLI modules, absorbed residual line-cap allowlists,
  clarified the benchmark harness as internal, and added runtime-wiring/line-cap
  ratchets so structural cleanup cannot reintroduce public-surface drift. (309,
  319, 320, 321, 322, 323, 324, 325, 334, 335, 343, 347)
• Strengthened release readiness with gene-all warm-budget coverage, local gate
  uv-build fixes, leaked-artifact cleanup, binary asset attributes, CI wrapper
  stale-binary warnings, Python 3.12/Rust 1.95 CI compatibility, self-contained
  local-data spec fixtures, and final v0.8.22 readiness audits before publish.
  (247, 258, 262, 263, 285, 289, 315, 316, 317, 327, 328, 330, 348, 363, 367)
• Recorded the diagnostic-entity, HPO clinical-feature, Obsidian vault,
  biomedical news, post-v0.8.21 shipped-surface, and neural-reranking reviews
  as architecture or deferred work unless runtime wiring shipped in the bullets
  above. (230, 243, 244, 245, 246, 284)