biomcp

Certified

Features

• Structured access to clinical trials, biomedical literature, and genomic variants.
• Natural language queries to specialized databases without requiring specific syntax knowledge.
• Consistent interface supporting biomedical research workflows.
• Functions as an MCP server for AI assistants and agents.
• Integration with key biomedical data sources like PubTator3/PubMed, ClinicalTrials.gov, and MyVariant.info.

Tools

1. search

   Search biomedical literature, clinical trials, and genetic variants with integrated AI reasoning.

   This tool provides comprehensive access to biomedical data from PubMed/PubTator3, ClinicalTrials.gov,
   and MyVariant.info. It supports three powerful search modes:
   
   ## 1. SEQUENTIAL THINKING MODE (Recommended for Complex Queries)
   Use domain="thinking" to engage systematic AI reasoning before searching.
   This is ESSENTIAL for complex biomedical research questions.
   
   Example:
   ```
   await search(
       domain="thinking",
       thought="I need to analyze the relationship between BRAF mutations and melanoma treatment options...",
       thoughtNumber=1,
       totalThoughts=3,
       nextThoughtNeeded=True
   )
   ```
   
   ## 2. UNIFIED QUERY LANGUAGE
   Use the 'query' parameter with field-based syntax for precise cross-domain searches.
   
   Syntax:
   - Basic: "gene:BRAF"
   - AND logic: "gene:BRAF AND disease:melanoma"
   - OR logic: "gene:PTEN AND (R173 OR Arg173 OR 'position 173')"
   - Domain-specific: "trials.condition:melanoma AND trials.phase:3"
   
   Common fields:
   - Cross-domain: gene, disease, variant, chemical/drug
   - Articles: pmid, title, abstract, journal, author
   - Trials: trials.condition, trials.intervention, trials.phase, trials.status
   - Variants: variants.hgvs, variants.rsid, variants.significance
   
   Example:
   ```
   await search(
       query="gene:BRAF AND disease:melanoma AND trials.phase:3",
       max_results_per_domain=20
   )
   ```
   
   ## 3. DOMAIN-SPECIFIC SEARCH
   Use the 'domain' parameter with specific filters for targeted searches.
   
   Domains:
   - "article": Search PubMed/PubTator3 for research articles and preprints
   - "trial": Search ClinicalTrials.gov for clinical studies
   - "variant": Search MyVariant.info for genetic variants
   
   Example:
   ```
   await search(
       domain="article",
       genes=["BRAF", "NRAS"],
       diseases=["melanoma"],
       page_size=50
   )
   ```
   
   ## IMPORTANT NOTES:
   - ALWAYS start with sequential thinking (domain="thinking") for research questions
   - The tool returns results in OpenAI MCP format: {"results": [{"id", "title", "text", "url"}, ...]}
   - Search results do NOT include metadata (per OpenAI MCP specification)
   - Use the fetch tool to get detailed metadata for specific records
   - Use get_schema=True to explore available search fields
   - Use explain_query=True to understand query parsing (unified mode)
   - Domain-specific searches use AND logic for multiple values
   - For OR logic, use the unified query language
   
   ## RETURN FORMAT:
   All search modes return results in this format:
   ```json
   {
       "results": [
           {
               "id": "unique_identifier",
               "title": "Human-readable title",
               "text": "Summary or snippet of content",
               "url": "Link to full resource"
           }
       ]
   }
   ```
   

2. fetch

   Fetch comprehensive details for a specific biomedical record.

   This tool retrieves full information for articles, clinical trials, or genetic variants
   using their unique identifiers. It returns data in a standardized format suitable for
   detailed analysis and research.
   
   ## IDENTIFIER FORMATS:
   - Articles: PMID (PubMed ID) - e.g., "35271234"
   - Trials: NCT ID (ClinicalTrials.gov ID) - e.g., "NCT04280705"
   - Variants: HGVS notation or dbSNP ID - e.g., "chr7:g.140453136A>T" or "rs121913254"
   
   ## DOMAIN-SPECIFIC OPTIONS:
   
   ### Articles (domain="article"):
   - Returns full article metadata, abstract, and full text when available
   - Includes annotations for genes, diseases, chemicals, and variants
   - detail="full" attempts to retrieve full text content
   
   ### Clinical Trials (domain="trial"):
   - detail=None or "protocol": Core study information
   - detail="locations": Study sites and contact information
   - detail="outcomes": Primary/secondary outcomes and results
   - detail="references": Related publications and citations
   - detail="all": Complete trial record with all sections
   
   ### Variants (domain="variant"):
   - Returns comprehensive variant information including:
     - Clinical significance and interpretations
     - Population frequencies
     - Gene/protein effects
     - External database links
   - detail parameter is ignored (always returns full data)
   
   ## RETURN FORMAT:
   All fetch operations return a standardized format:
   ```json
   {
       "id": "unique_identifier",
       "title": "Record title or name",
       "text": "Full content or comprehensive description",
       "url": "Link to original source",
       "metadata": {
           // Domain-specific additional fields
       }
   }
   ```
   
   ## EXAMPLES:
   
   Fetch article with annotations:
   ```
   await fetch(
       domain="article",
       id_="35271234"
   )
   ```
   
   Fetch complete trial information:
   ```
   await fetch(
       domain="trial",
       id_="NCT04280705",
       detail="all"
   )
   ```
   
   Fetch variant with clinical interpretations:
   ```
   await fetch(
       domain="variant",
       id_="rs121913254"
   )
   ```