Runtime: Node.js only (MCP server CLI)

What is this?

An MCP (Model Context Protocol) server that gives AI assistants access to NCBI's biomedical databases — PubMed (37M+ articles), PubMed Central (full text), PubTator3 (entity recognition), MeSH (medical vocabulary), BLAST (sequence alignment), dbSNP (genetic variation), ClinVar (clinical variants), PubChem (chemical compounds), Datasets (genes, genomes, taxonomy), and more.

Quick start

Add to your Claude Code .mcp.json:

{
  "mcpServers": {
    "ncbijs": {
      "command": "npx",
      "args": ["-y", "@ncbijs/http-mcp"],
      "env": {
        "NCBI_API_KEY": "",
        "NCBI_TOOL": "my-app",
        "NCBI_EMAIL": "[email protected]"
      }
    }
  }
}

Environment variables

| Variable | Required | Default | Description | | -------------- | -------- | ------------------------------------- | --------------------------------------------------- | | NCBI_API_KEY | No | -- | NCBI API key (raises rate limit from 3 to 10 req/s) | | NCBI_TOOL | No | ncbijs-mcp | Application name (NCBI usage policy) | | NCBI_EMAIL | No | [email protected] | Developer email (NCBI usage policy) |

Get a free API key at https://www.ncbi.nlm.nih.gov/account/settings/

Available tools

Literature search

| Tool | Description | | ---------------- | ---------------------------------------------------------------------- | | search-pubmed | Search PubMed for biomedical articles with filters (date, sort, limit) | | search-related | Find articles related to a given PubMed article, ranked by relevancy | | get-references | Get the reference list of a PubMed article | | get-cited-by | Get articles that cite a given PubMed article |

Full text

| Tool | Description | | ---------------------- | ---------------------------------------------------------------- | | get-full-text | Fetch PMC full-text article as markdown | | get-full-text-chunks | Fetch PMC full-text article split into semantic chunks (for RAG) |

Entity recognition

| Tool | Description | | -------------------- | --------------------------------------------------------------- | | find-entity | Search biomedical entities (genes, diseases, chemicals) by name | | annotate-text | Annotate free text with biomedical named entity recognition | | export-annotations | Export BioC annotations for PubMed articles |

Genomics (NCBI Datasets API v2)

| Tool | Description | | ----------------- | ------------------------------------------------------------------ | | search-gene | Retrieve gene metadata by NCBI Gene ID or symbol + taxon | | lookup-taxonomy | Retrieve taxonomy data (organism name, rank, lineage, gene counts) | | search-genome | Retrieve genome assembly reports by accession or taxon |

Sequence alignment (BLAST)

| Tool | Description | | -------------- | --------------------------------------------------------------------- | | blast-search | Run a BLAST sequence alignment (blastn, blastp, blastx, tblastn, etc) |

Variation and clinical genomics

| Tool | Description | | ---------------- | ------------------------------------------------------------------------ | | lookup-variant | Look up SNP data by RS IDs — placements, allele annotations, frequencies | | search-clinvar | Search ClinVar for clinical variant significance, genes, and traits |

Chemistry (PubChem)

| Tool | Description | | ----------------- | ---------------------------------------------------------------- | | search-compound | Look up chemical compounds by name or CID — properties, synonyms |

Utilities

| Tool | Description | | -------------- | ---------------------------------------------------------------- | | convert-ids | Convert between PMID, PMCID, DOI, and Manuscript IDs | | get-citation | Get formatted citation (CSL-JSON, APA/MLA/AMA/NLM, RIS, MEDLINE) | | mesh-lookup | Look up MeSH medical vocabulary terms by name | | mesh-sparql | Execute SPARQL queries against the NLM MeSH vocabulary |

Example prompts

Once the MCP server is configured, you can ask your AI assistant things like:

• "Search PubMed for recent reviews on CRISPR gene therapy"
• "Get the full text of PMC7886120 and summarize the methods section"
• "What genes and diseases are mentioned in PMID 33024307?"
• "Find the DOI for PMID 33024307"
• "Get an APA citation for PMID 33024307"
• "What MeSH terms relate to Alzheimer's disease?"
• "Find articles related to PMID 33024307"
• "Look up the BRCA1 gene"
• "What genome assemblies exist for E. coli?"
• "Get the taxonomy for Homo sapiens"
• "Run a BLAST search for the sequence ATCGATCGATCG"
• "What do we know about SNP rs7412?"
• "Look up the clinical significance of BRCA1 variants in ClinVar"
• "What are the properties of aspirin in PubChem?"