Releases: genomoncology/biomcp
v0.7.1
What's Changed
- chore(deps): Bump astral-sh/setup-uv from 6 to 7 by @dependabot[bot] in #76
- oncokbapi by @azingalis-go in #77
Full Changelog: v0.7.0...v0.7.1
Contributors
Assets 2
v0.7.0
Adds --assembly option to biomcp variant get command, allowing users to specify genome assembly (hg19 or hg38) when retrieving variant annotations from MyVariant.info API.
Problem: The MyVariant.info API supports an assembly query parameter, but this was not exposed in the BioMCP CLI or MCP tools, forcing users to work exclusively with hg19 coordinates.
Solution: Added full assembly parameter support across the entire variant getter stack with comprehensive testing and documentation.
v0.6.9
v0.6.8
v0.6.7
Summary of Changes Made:
- Fixed Character Encoding Issue
- Modified getter.py to explicitly use UTF-8 encoding when reading resource files
- This fixes the Windows cp1252 encoding error
- Removed External Sequential-Thinking References
- Updated docs/blog/researcher-persona-resource.md:
- Removed the separate sequential-thinking server from the JSON config
- Changed references from "Sequential Thinking MCP" to "built-in sequential thinking"
- Updated text to clarify the think tool is included in BioMCP
v0.6.6
Fix Windows compatibility and update Docker documentation
Fix fcntl import error on Windows (Issue ModuleNotFoundError: No module named 'fcntl' #57)
Added conditional import with try/except for fcntl module
File locking now only applies on Unix systems
Windows users get full functionality without file locking
Refactored cache functions to reduce complexity
Add Docker build instructions to README (Issue Docker image not found #58)
Added docker build command before docker run
Clarifies that biomcp:latest is a local build, not from Docker Hub
v0.6.5
-
feat: Add comprehensive OpenFDA integration with 12 new tools
Implements full OpenFDA API integration providing access to FDA regulatory data
for drug safety, device events, approvals, recalls, and shortages.New Modules:
- adverse_events.py: Search/retrieve drug adverse event reports (FAERS)
- device_events.py: Search/retrieve device malfunction reports (MAUDE)
- drug_labels.py: Search/retrieve FDA drug labels (SPL)
- drug_approvals.py: Search/retrieve drug approval records (Drugs@FDA)
- drug_recalls.py: Search/retrieve drug recall notices (Enforcement)
- drug_shortages.py: Search/retrieve drug shortage data with 24hr caching
Key Features:
- 12 new MCP tools (6 searchers + 6 getters) for AI agent integration
- Flexible API key support via parameter, env var (OPENFDA_API_KEY), or none
- Smart device search with wildcard matching (no hardcoding)
- Robust handling of polymorphic FDA fields (string/list types)
- Genomics device filtering for precision medicine focus
- Rate limiting: 40 req/min (no key) or 240 req/min (with key)
CLI Enhancements:
- New 'biomcp openfda' command with 6 subcommands
- All commands support --api-key parameter
- Pagination support with --page and --limit
Documentation:
- Added openfda-prompts.md with 30+ example prompts
- Updated MCP tools reference (now 35 tools total)
- Comprehensive API key usage examples
- Integration patterns for complex safety analyses
Testing & Quality:
- All quality checks passing (ruff, mypy, pre-commit)
- MCP integration tests updated for new tool count
- API key priority handling verified
- Endpoint registry updated with FDA endpoints
This integration enables comprehensive FDA regulatory data access for
drug safety assessment, post-market surveillance, and treatment planning
in precision oncology workflows.
Co-authored-by: Justin Yeakley [email protected]
v0.6.4
Restructure and improve documentation
- Simplified navigation structure from 10 to 5 top-level sections
- Removed expandable/collapsible navigation in favor of clean sections display
- Fixed code block horizontal scrolling issues across all documentation
- Converted grid card layouts to stacked format for better readability
- Removed all emojis from headers for professional appearance
- Made documentation more concise, especially the overview page
- Fixed broken anchor links and embedded ASCII diagrams inline
- Removed unnecessary sections (migrations, breaking changes, feedback)
- Synced outdated docs changelog with main CHANGELOG.md (v0.4.0 → v0.6.2)
- Added CSS improvements for code block wrapping and responsive design
- Improved overall user experience with cleaner, flatter navigation
The documentation now provides optimal onboarding, clear navigation paths,
and professional presentation suitable for production deployment.
v0.6.3
Add NCI Clinical Trials Search API integration
Integrates the National Cancer Institute's Clinical Trials Search API to provide
enhanced cancer trial search capabilities alongside existing ClinicalTrials.gov support.
New Features
Core NCI Integration
- Added dual source support for trial search/getter (ClinicalTrials.gov + NCI)
- Implemented NCI API key handling via environment variable or parameter
- Added advanced trial filters: biomarkers, prior therapy, brain metastases
New NCI-Specific Tools (6 MCP tools + CLI commands)
- Organizations: Search/get cancer centers, hospitals, research institutions
- Interventions: Search/get drugs, devices, procedures, biologicals
- Biomarkers: Search trial eligibility biomarkers (reference genes, branches)
- Diseases: Search NCI's controlled vocabulary of cancer conditions
API Features
- Real-time access to NCI's curated cancer trials database
- Support for all NCI API parameters and filters
- Automatic cBioPortal integration for gene searches
- Proper parameter mapping (org_city, org_state_or_province, etc.)
- Comprehensive error handling for Elasticsearch limits
Documentation
- Added NCI tutorial with example prompts:
docs/tutorials/nci-prompts.md - Created API parameter reference:
docs/api-changes/nci-api-parameters.md - Updated CLAUDE.md with NCI usage instructions and parameter notes
CLI Integration
# New commands
biomcp organization search "MD Anderson" --api-key YOUR_KEY
biomcp intervention search pembrolizumab --type Drug --api-key YOUR_KEY
biomcp biomarker search --name "PD-L1" --api-key YOUR_KEY
biomcp disease search melanoma --source nci --api-key YOUR_KEY
# Enhanced trial commands
biomcp trial search --condition melanoma --source nci --api-key YOUR_KEY
biomcp trial get NCT04280705 --source nci --api-key YOUR_KEY
Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/