medical-research-toolkit

--- name: medical-research-toolkit license: MIT-0 description: Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data. --- # Medical Research Toolkit Query 14+ biomedical databases for drug repurposing, target discovery, clinical evidence, and literature research — all via a unified MCP endpoint. ## Availability and data flow This document describes a third-party hosted MCP endpoint, not a bundled server or a verified live service. Queries sent to that endpoint leave the local machine and are handled by its operator. Use only non-identifying public research terms; do not transmit patient records, private files, passwords or API keys. Check current endpoint availability, supported tools, terms and access requirements before relying on examples. Examples below were not executed as part of this release review. This is research support, not a diagnosis or treatment recommendation. Separate trial status, approval status and evidence strength in outputs. Do not infer efficacy or causality from a database match or spontaneous adverse-event report. ## Example request ```bash # Find drugs for myasthenia gravis curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"chembl_find_drugs_by_indication","arguments":{"indication":"myasthenia gravis","max_results":10}},"id":1}' ``` Validate the actual response schema and source records before reporting results; an example request is not proof of a successful search. --- ## Quick Recipes ### Find Drugs for a Disease ```bash curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"chembl_find_drugs_by_indication","arguments":{"indication":"myasthenia gravis","max_results":20}},"id":1}' ``` Returns: Approved + investigational drugs with max phase reached ### Find Disease Targets ```bash # First: Find disease ID curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"opentargets_search","arguments":{"query":"myasthenia gravis","entity_type":"disease"}},"id":1}' # Returns: disease ID (e.g., EFO_0004991) # Then: Get targets curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"opentargets_get_associations","arguments":{"disease_id":"EFO_0004991","size":20}},"id":2}' ``` Returns: Top disease targets ranked by evidence strength (0-1 score) ### Search Literature ```bash curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"pubmed_search_articles","arguments":{"diseases":["myasthenia gravis"],"keywords":["immunotherapy"],"max_results":20}},"id":1}' ``` Returns: PubMed articles on myasthenia gravis immunotherapy ### Find Active Clinical Trials ```bash curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"ctg_search_studies","arguments":{"condition":"myasthenia gravis","recruitment_status":"RECRUITING","max_results":20}},"id":1}' ``` Returns: Actively recruiting trials for the disease ### Check Drug Safety ```bash curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"openfda_search_adverse_events","arguments":{"drug_name":"eculizumab","limit":50}},"id":1}' ``` Returns: FDA adverse event reports—check for serious outcomes, death, hospitalization --- ## What You Get **14+ Integrated Databases** | Database | What's Inside | Use For | |----------|---------------|---------| | **ChEMBL** | 2M drugs, bioactivity data | Finding approved/investigational drugs | | **OpenTargets** | Disease-target links + evidence | Identifying therapeutic targets | | **PubMed** | 35M+ articles + preprints | Literature review & validation | | **ClinicalTrials.gov** | 400K+ active trials | Finding ongoing studies | | **OpenFDA** | Adverse events, drug labels | Safety assessment | | **OMIM** | Genetic diseases, genes → phenotypes | Understanding disease genetics | | **Reactome** | Pathways, protein interactions | Mechanism understanding | | **UniProt** | Protein sequences, annotations | Protein properties | | **KEGG** | Metabolic & disease pathways | Systems-level view | | **GWAS Catalog** | Genetic associations | Variant discovery | | **Pathway Commons** | Integrated pathway data | Network analysis | | **MyGene.info** | Gene annotations | ID mapping | | **MyVariant.info** | Variant effects | Variant interpretation | | + more | | | --- ## Use Cases ### 🧬 Drug Repurposing Find non-standard-care drugs for rare/complex diseases: 1. Find disease targets (OpenTargets) 2. Search for drugs targeting those genes (ChEMBL) 3. Check ongoing trials (ClinicalTrials) 4. Verify safety (OpenFDA, PubMed) ### 🔬 Target Discovery Identify novel therapeutic targets: 1. Find disease associations (OpenTargets, GWAS) 2. Get pathway context (Reactome, KEGG) 3. Review literature (PubMed) 4. Check protein properties (UniProt) ### 📋 Clinical Evidence Review Compile evidence for a hypothesis: 1. Search trials (ClinicalTrials.gov) 2. Find literature (PubMed) 3. Check FDA data (OpenFDA) ### 📊 Literature Mining Systematically search biomedical research: 1. PubMed: search literature by gene, disease, drug or chemical; verify query results and coverage. 2. Preprints: bioRxiv, medRxiv 3. Filter by keywords, date, study type --- ## API Endpoint **Production (No setup needed):** ``` https://mcp.cloud.curiloo.com/tools/unified/mcp ``` All 14+ databases unified into one endpoint. ## Package contents and local deployment This package contains this guide only. The reference guides and example workflow previously linked here are not bundled, so those links have been removed. Use the examples included in this document and the original database documentation; do not claim missing reference files were consulted. A local server is not included. Do not execute the previous unpinned package-install recipe automatically. If local deployment is needed, first review the server project's source, release, dependencies and configuration, then obtain authorization for the concrete installation. ## API Keys Most APIs are **free, no key required**. Optional keys for higher rate limits: | Database | Key? | Why | Get Key | |----------|------|-----|---------| | ChEMBL | No | Public data | (not needed) | | OpenTargets | No | Public data | (not needed) | | PubMed | No | Public data | (not needed) | | ClinicalTrials | No | Public data | (not needed) | | **OMIM** | **Yes** | Proprietary data | https://omim.org/api | | OpenFDA | Optional | Higher rate limits | https://open.fda.gov | | NCI Clinical Trials | Optional | Higher rate limits | https://clinicaltrialsapi.cancer.gov | --- ## Service limits Authentication, quotas, caching and charges can change and differ between the hosted intermediary and original databases. No specific request allowance, cache duration or zero-cost guarantee is established by this guide. Verify current terms and report access failures explicitly. --- ## Common Patterns ### Batch Query Loop ```bash # Search multiple targets for gene in CHRNE RAPSN LRP4; do curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d "{\"jsonrpc\":\"2.0\",\"method\":\"tools/call\",\"params\":{\"name\":\"chembl_find_drugs_by_target\",\"arguments\":{\"target_name\":\"$gene\",\"max_results\":10}},\"id\":1}" sleep 1 # Be nice to the API done ``` ### ID Conversion Need to convert IDs between databases? ```bash curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"nodenorm_get_normalized_nodes","arguments":{"curie":"HGNC:11998"}},"id":1}' ``` Returns: Equivalent IDs in NCBI Gene, Uniprot, Ensembl, MyGene, etc. --- ## Troubleshooting **No results?** - Try alternative terms (gene symbol vs protein name) - Check spelling - Use standardized IDs (gene symbols, disease names) - Some APIs use specific ID formats (EFO vs MONDO, etc.) **Too many results?** - Add filters (max_results, phase, recruitment status) - Use `limit` or `size` parameters - Combine with other databases to narrow focus **API key errors?** - OMIM requires API key — get from https://omim.org/api - Other databases optional — request key if hitting rate limits --- ## Next Steps 1. **Pick a use case** (drug repurposing, target discovery, etc.) 2. **Read the relevant database guide** from References section 3. **Copy a quick recipe** from above 4. **Customize parameters** for your disease/gene/drug 5. **Scale up** — build your full research workflow --- ## Resources - **Source Code**: https://github.com/pascalwhoop/medical-mcps - **Author**: Pascal Brockmeyer (@pascalwhoop) - **Organization**: Every Cure (https://www.everycure.org) - **License**: MIT --- ## Getting Help - Database not working? → Check [Troubleshooting](#troubleshooting) - Want detailed guide? → See [Complete References](#complete-references) - Need a workflow example? Use the included Quick Recipes and record which requests actually succeeded. - Question about the host agent? Consult its installed documentation; no host-specific setup guide is bundled.

存档时间线

版本索引永久保留；内容副本只保留最新 1 份，更早版本仅留索引与哈希（存档时间线的证据链不会因此断裂）。

下载存档内容副本