biomcp-cli 0.8.16

Biomedical MCP CLI - query genes, variants, trials, articles, drugs, diseases

BioMCP

BioMCP gives researchers, clinicians, and agents one command grammar across biomedical APIs that usually require separate search habits, identifiers, and output formats. It keeps results compact and evidence-oriented so you can move from discovery to detail without rewriting the workflow for each source. One command grammar, compact markdown output, 12 remote entities across 15+ data sources, plus local study analytics.

Install

PyPI tool install

uv tool install biomcp-cli
# or: pip install biomcp-cli

This installs the biomcp binary on your PATH.

Binary install

curl -fsSL https://biomcp.org/install.sh | bash

Install skills

Install guided investigation workflows into your agent directory:

biomcp skill install ~/.claude --force

MCP clients

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Remote HTTP server

For shared or remote deployments:

biomcp serve-http --host 127.0.0.1 --port 8080

Remote clients connect to http://127.0.0.1:8080/mcp. Probe routes are GET /health, GET /readyz, and GET /.

Runnable demo:

uv run --script demo/streamable_http_client.py

See Remote HTTP Server for the newcomer guide.

From source

cargo build --release --locked

Quick start

First useful query in under 30 seconds:

uv tool install biomcp-cli
biomcp health --apis-only
biomcp list gene
biomcp search all --gene BRAF --disease melanoma  # unified cross-entity discovery
biomcp get gene BRAF pathways druggability

Command grammar

search <entity> [filters]    → discovery
get <entity> <id> [sections] → focused detail
<entity> <helper> <id>       → cross-entity pivots
enrich <GENE1,GENE2,...>     → gene-set enrichment
batch <entity> <id1,id2,...> → parallel gets
search all [slot filters]    → counts-first cross-entity orientation

Feature highlights

• Federated article search: search article fans out across PubTator3 and Europe PMC, deduplicates by PMID, and can add Semantic Scholar follow-ups when S2_API_KEY is set.
• Cross-entity pivots: move directly from a gene, variant, drug, disease, pathway, protein, or article into the next built-in view.
• Study analytics and charting: downloaded studies support query, cohort, survival, compare, and co-occurrence workflows with native terminal or SVG charts.
• Citation graphs and article helpers: article citations, article references, article recommendations, and article entities support literature navigation from a known paper.
• Gene-set enrichment and batch retrieval: use biomcp enrich for top-level g:Profiler enrichment and biomcp batch for up to 10 focused get calls in one command.

Entities and sources

Entity	Upstream providers used by BioMCP	Example
gene	MyGene.info, UniProt, Reactome, QuickGO, STRING, GTEx, DGIdb, ClinGen	biomcp get gene BRAF pathways
variant	MyVariant.info, ClinVar, gnomAD fields via MyVariant, CIViC, Cancer Genome Interpreter, OncoKB, cBioPortal, GWAS Catalog, AlphaGenome	biomcp get variant "BRAF V600E" clinvar
article	PubMed, PubTator3, Europe PMC, PMC OA, NCBI ID Converter, Semantic Scholar (optional with S2_API_KEY)	biomcp search article -g BRAF --limit 5
trial	ClinicalTrials.gov API v2, NCI CTS API	biomcp search trial -c melanoma -s recruiting
drug	MyChem.info, ChEMBL, OpenTargets, Drugs@FDA, OpenFDA, CIViC	biomcp get drug pembrolizumab targets
disease	MyDisease.info, Monarch Initiative, MONDO, OpenTargets, Reactome, CIViC	biomcp get disease "Lynch syndrome" genes
pathway	Reactome, g:Profiler, Enrichr-backed enrichment sections	biomcp get pathway R-HSA-5673001 genes
protein	UniProt, InterPro, STRING, PDB, AlphaFold	biomcp get protein P15056 domains
adverse-event	OpenFDA FAERS, MAUDE, Recalls	biomcp search adverse-event --drug pembrolizumab
pgx	CPIC, PharmGKB	biomcp get pgx CYP2D6 recommendations
gwas	GWAS Catalog	biomcp search gwas --trait "type 2 diabetes"
phenotype	Monarch Initiative (HPO semantic similarity)	biomcp search phenotype "HP:0001250"

Cross-entity helpers

Pivot between related entities without rebuilding filters.

See the cross-entity pivot guide for when to use a helper versus a fresh search.

biomcp variant trials "BRAF V600E" --limit 5
biomcp variant articles "BRAF V600E"
biomcp drug adverse-events pembrolizumab
biomcp drug trials pembrolizumab
biomcp disease trials melanoma
biomcp disease drugs melanoma
biomcp disease articles "Lynch syndrome"
biomcp gene trials BRAF
biomcp gene drugs BRAF
biomcp gene articles BRCA1
biomcp gene pathways BRAF
biomcp pathway drugs R-HSA-5673001
biomcp pathway articles R-HSA-5673001
biomcp pathway trials R-HSA-5673001
biomcp protein structures P15056
biomcp article entities 22663011
biomcp article citations 22663011 --limit 3
biomcp article references 22663011 --limit 3
biomcp article recommendations 22663011 --limit 3

Gene-set enrichment

biomcp enrich BRAF,KRAS,NRAS --limit 10

Top-level biomcp enrich uses g:Profiler. Gene enrichment sections inside other entity views still reference Enrichr where that is the backing source.

Sections and progressive disclosure

Every get command supports selectable sections for focused output:

biomcp get gene BRAF                    # summary card
biomcp get gene BRAF pathways           # add pathway section
biomcp get gene BRAF civic interactions # multiple sections
biomcp get gene BRAF all                # everything

biomcp get variant "BRAF V600E" clinvar population conservation
biomcp get article 22663011 tldr
biomcp get drug pembrolizumab label targets civic approvals
biomcp get disease "Lynch syndrome" genes phenotypes variants
biomcp get trial NCT02576665 eligibility locations outcomes

In JSON mode, get responses expose _meta.next_commands for the next likely follow-ups, and batch ... --json returns per-entity objects with the same metadata shape.

API keys

Most commands work without credentials. Optional keys improve rate limits or unlock optional enrichments:

export NCBI_API_KEY="..."        # PubTator, PMC OA, NCBI ID converter
export S2_API_KEY="..."          # Semantic Scholar TLDR, citations, references, recommendations
export OPENFDA_API_KEY="..."     # OpenFDA rate limits
export NCI_API_KEY="..."         # NCI CTS trial search (--source nci)
export ONCOKB_TOKEN="..."        # OncoKB variant helper
export ALPHAGENOME_API_KEY="..." # AlphaGenome variant effect prediction

search article still uses PubTator3 + Europe PMC. S2_API_KEY only unlocks optional article enrichment and explicit Semantic Scholar helper commands. References and recommendations can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage.

Multi-worker deployment

BioMCP rate limiting is process-local. For many concurrent workers, run one shared Streamable HTTP biomcp serve-http endpoint so all workers share a single limiter budget:

biomcp serve-http --host 0.0.0.0 --port 8080

Remote clients should connect to http://<host>:8080/mcp. Lightweight process probes are available at GET /health, GET /readyz, and GET /.

Skills

BioMCP ships an embedded agent guide instead of a browsable in-binary catalog. Use biomcp skill to read the embedded BioMCP guide, then install it into your agent directory when you want local copies of the workflow references:

biomcp skill
biomcp skill install ~/.claude --force

See Skills for supported install targets, installed files, and legacy compatibility notes.

Local study analytics

study is BioMCP's local analysis family for downloaded cBioPortal-style datasets. The 12 remote entity commands query upstream APIs for discovery and detail; study commands work on local datasets when you need per-study query, cohort, survival, comparison, or co-occurrence workflows.

Use study download to fetch a dataset into your local study root. Set BIOMCP_STUDY_DIR when you want an explicit dataset location for reproducible scripts and demos; if it is unset, BioMCP falls back to its default study root.

export BIOMCP_STUDY_DIR="$HOME/.local/share/biomcp/studies"
biomcp study download msk_impact_2017
biomcp study query --study msk_impact_2017 --gene TP53 --type mutations --chart bar --theme dark --palette wong -o docs/blog/images/tp53-mutation-bar.svg

See the CLI reference for the full study command family and dataset prerequisites.

Ops

biomcp version          # show version and build info
biomcp health           # check all API connectivity
biomcp update           # self-update to latest release
biomcp update --check   # check for updates without installing
biomcp uninstall        # remove biomcp from ~/.local/bin

Documentation

Full documentation at biomcp.org.

• Getting Started
• Search All Workflow
• Cross-Entity Pivot Guide
• Data Sources
• Quick Reference
• Troubleshooting

Citation

If you use BioMCP in research, cite it via CITATION.cff. GitHub also exposes Cite this repository in the repository sidebar when that file is present.

License

MIT