CLI Reference¶

BioMCP provides one command family with entity-oriented subcommands.

Global options¶

--json: return structured JSON output
--no-cache: bypass HTTP cache for the current command

--json normally returns structured output, but biomcp cache path is a plain-text exception. biomcp cache stats, biomcp cache clean, and biomcp cache clear respect --json on success. biomcp cache clear still refuses non-TTY destructive runs with plain stderr unless you pass --yes.

Core command patterns¶

biomcp search <entity> [filters]
biomcp get <entity> <id> [section...]

Section names are positional trailing arguments after <id>.

Evidence metadata¶

get responses include outbound evidence links in markdown output where available. In JSON mode, links are exposed under _meta.evidence_urls and can include Ensembl, OMIM, NCBI Gene, and UniProt URLs. Section-level provenance is exposed under _meta.section_sources.

Top-level commands¶

biomcp search ...
biomcp get ...
biomcp discover <query>
biomcp enrich <GENE1,GENE2,...> [--limit N]
biomcp batch <entity> <id1,id2,...> [--sections ...] [--source ...]
biomcp chart [type]
biomcp cache path
biomcp cache stats
biomcp cache clean [--max-age <duration>] [--max-size <size>] [--dry-run]
biomcp cache clear [--yes]
biomcp ema sync
biomcp health [--apis-only]
biomcp list [entity]
biomcp study list
biomcp study download [--list] [<study_id>]
biomcp study filter --study <id> [--mutated <symbol>] [--amplified <symbol>] [--deleted <symbol>] [--expression-above <gene:threshold>] [--expression-below <gene:threshold>] [--cancer-type <type>]
biomcp study query --study <id> --gene <symbol> --type <mutations|cna|expression>
biomcp study cohort --study <id> --gene <symbol>
biomcp study survival --study <id> --gene <symbol> [--endpoint <os|dfs|pfs|dss>]
biomcp study compare --study <id> --gene <symbol> --type <expression|mutations> --target <symbol>
biomcp study co-occurrence --study <id> --genes <g1,g2,...>
biomcp skill
biomcp skill install [dir]
biomcp skill list                 # list embedded worked examples
biomcp mcp
biomcp serve
biomcp serve-http [--host 127.0.0.1] [--port 8080]
biomcp update [--check]
biomcp uninstall
biomcp version

Worked examples are also addressable directly:

biomcp skill 01
biomcp skill article-follow-up

biomcp health --apis-only is the upstream inventory smoke test. Full biomcp health also reports local readiness rows such as EMA local data, cache dir status, and cache-limit warnings when the managed HTTP cache is over size or below the configured disk-free floor.

biomcp cache path is a local-CLI-only operator command. It prints the managed HTTP cache path as plain text and ignores the global --json flag.

biomcp cache stats is the companion local-CLI operator command. It reports the resolved cache path, total blob inventory, referenced blob bytes used for enforcement, orphan count, age range, and the resolved cache limits including min_disk_free; under --json, it returns the same contract as a JSON object.

biomcp cache clean [--max-age <duration>] [--max-size <size>] [--dry-run] is the targeted maintenance command for the same cache family. It always removes orphan blobs, can optionally evict entries older than a duration or LRU-evict to a byte target, and keeps the same structured report under --json.

biomcp cache clear [--yes] is the destructive sibling for the same managed HTTP cache tree. It wipes <resolved cache_root>/http completely, never touches the sibling downloads/ directory, prompts for confirmation when stdin is a TTY, and refuses non-interactive runs with plain stderr unless you pass --yes. Successful --json output uses { "bytes_freed": <number|null>, "entries_removed": <number> }.

Search command families¶

Discover¶

biomcp discover ERBB1
biomcp discover "chest pain"
biomcp --json discover diabetes

Use discover when the user starts with free text rather than a known entity type. Markdown output groups resolved concepts by type and suggests concrete follow-up BioMCP commands. JSON adds _meta.discovery_sources alongside the standard _meta.next_commands and _meta.section_sources metadata.

All (cross-entity)¶

biomcp search all --gene BRAF --disease melanoma
biomcp search all --gene BRAF --counts-only
biomcp search all --keyword "immunotherapy resistance" --since 2024-01-01
biomcp search all --gene BRAF --debug-plan

Gene¶

biomcp search gene BRAF --limit 10 --offset 0

Disease¶

biomcp search disease -q melanoma --source mondo --limit 10 --offset 0

PGx¶

biomcp search pgx -g CYP2D6 --limit 10
biomcp search pgx -d warfarin --limit 10

Phenotype (Monarch semsim)¶

biomcp search phenotype "HP:0001250 HP:0001263" --limit 10

GWAS¶

biomcp search gwas -g TCF7L2 --limit 10
biomcp search gwas --trait "type 2 diabetes" --limit 10

Article¶

biomcp search article -g BRAF -d melanoma --since 2024-01-01 --limit 5 --offset 0
biomcp --json search article -g BRAF --debug-plan --limit 5

Trial¶

biomcp search trial -c melanoma --status recruiting --source ctgov --limit 5 --offset 0

Variant¶

biomcp search variant -g BRAF --hgvsp V600E --limit 5 --offset 0

Drug¶

biomcp search drug -q "kinase inhibitor" --limit 5 --offset 0
biomcp search drug Keytruda --limit 5
biomcp search drug Keytruda --region eu --limit 5

Pathway¶

biomcp search pathway -q "MAPK signaling" --limit 5 --offset 0
biomcp search pathway -q "Pathways in cancer" --limit 5 --offset 0

Protein¶

biomcp search protein -q kinase --limit 5 --offset 0
biomcp search protein -q kinase --all-species --limit 5

Adverse event¶

biomcp search adverse-event --drug pembrolizumab --serious --limit 5 --offset 0
biomcp search adverse-event --type device --manufacturer Medtronic --limit 5
biomcp search adverse-event --type device --product-code PQP --limit 5

Get command families¶

Gene¶

biomcp get gene BRAF
biomcp get gene BRAF pathways ontology diseases protein
biomcp get gene BRAF go interactions civic expression hpa druggability clingen constraint
biomcp get gene BRAF all

Disease¶

biomcp get disease melanoma
biomcp get disease MONDO:0005105 genes phenotypes
biomcp get disease MONDO:0005105 variants models
biomcp get disease MONDO:0005105 pathways prevalence civic
biomcp get disease MONDO:0005105 all

PGx¶

biomcp get pgx CYP2D6
biomcp get pgx codeine recommendations frequencies
biomcp get pgx warfarin annotations

Article¶

biomcp get article 22663011
biomcp get article 22663011 fulltext
biomcp get article 22663011 tldr
biomcp article batch 22663011 24200969

S2_API_KEY is optional. With it, BioMCP sends authenticated Semantic Scholar requests at 1 req/sec for search article, get article, get article ... tldr, article batch, and the explicit article citations|references|recommendations helpers. Without it, those same paths use the shared unauthenticated pool at 1 req/2sec.

Trial¶

biomcp get trial NCT02576665
biomcp get trial NCT02576665 eligibility

Variant¶

biomcp get variant "BRAF V600E"
biomcp get variant "BRAF V600E" predict
biomcp get variant rs7903146 gwas

Drug¶

biomcp get drug pembrolizumab
biomcp get drug Keytruda regulatory --region eu
biomcp get drug Ozempic safety --region eu
biomcp get drug carboplatin shortage

Omitting --region on a plain name/alias search drug checks both U.S. and EU data. If you omit --region while using structured filters such as --target or --indication, BioMCP stays on the U.S. MyChem path. Explicit --region eu or --region all with structured filters still errors. For get drug, use --region only with regulatory, safety, shortage, or all; approvals stays U.S.-only.

Pathway¶

biomcp get pathway R-HSA-5673001
biomcp get pathway R-HSA-5673001 genes
biomcp get pathway hsa05200
biomcp get pathway hsa05200 genes

Protein¶

biomcp get protein P15056
biomcp get protein P15056 domains interactions
biomcp get protein P15056 complexes

Adverse event¶

biomcp get adverse-event 10222779
biomcp get adverse-event 10222779 reactions outcomes
biomcp get adverse-event 10222779 concomitant guidance all

Enrichment¶

biomcp enrich BRAF,KRAS,NRAS --limit 10
biomcp enrich BRAF,KRAS,NRAS --limit 10 --json

Batch mode¶

Batch is limited to 10 IDs per command.

biomcp batch gene BRAF,TP53
biomcp batch gene BRAF,TP53 --sections pathways,interactions
biomcp batch trial NCT02576665,NCT03715933 --source nci
biomcp batch variant "BRAF V600E","KRAS G12D" --json

MCP mode¶

biomcp serve runs the stdio MCP server.
biomcp serve-http runs the MCP Streamable HTTP server.
Streamable HTTP clients connect to /mcp.
Probe routes: /health, /readyz, and /.
biomcp serve-sse remains available only as a hidden compatibility command that points users back to biomcp serve-http.

See also: docs/reference/mcp-server.md.

Helper command families¶

biomcp variant trials "BRAF V600E"
biomcp variant articles "BRAF V600E"
biomcp variant oncokb "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 drugs hsa05200
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

Chart reference¶

Use biomcp chart to list chart families and biomcp chart <type> for the embedded help page for one chart type.

biomcp chart
biomcp chart violin

Local study analytics¶

study is BioMCP's local cBioPortal analytics family for downloaded cBioPortal-style datasets. Unlike the 12 remote entity commands, study operates on files in your local study root instead of querying remote APIs for each request.

Use BIOMCP_STUDY_DIR when you want an explicit study root for reproducible downloads and examples; if it is unset, BioMCP falls back to its default study root. biomcp study download --list shows downloadable IDs, and biomcp study download <study_id> installs a study into that local root.

Use this	When
`biomcp search/get/<entity>`	You want live API-backed discovery or detail across the 12 remote entity commands
`biomcp study download`	You need to fetch a cBioPortal-style study dataset into your local study root
`biomcp study ...` analytics commands	You already have local study files and want cohort, query, survival, compare, or co-occurrence analysis

Study command examples¶

biomcp study list
biomcp study download --list
biomcp study download msk_impact_2017
biomcp study query --study msk_impact_2017 --gene TP53 --type mutations
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
biomcp study filter --study brca_tcga_pan_can_atlas_2018 --mutated TP53 --amplified ERBB2 --expression-above ERBB2:1.5
biomcp study cohort --study brca_tcga_pan_can_atlas_2018 --gene TP53
biomcp study survival --study brca_tcga_pan_can_atlas_2018 --gene TP53 --endpoint os
biomcp study compare --study brca_tcga_pan_can_atlas_2018 --gene TP53 --type expression --target ERBB2
biomcp study compare --study brca_tcga_pan_can_atlas_2018 --gene TP53 --type mutations --target PIK3CA
biomcp study co-occurrence --study msk_impact_2017 --genes TP53,KRAS

Dataset requirements¶

study list shows locally available studies.
study download fetches remote datasets into the local study root.
study filter intersects mutation, CNA, expression, and clinical filters.
study query supports mutations, cna, and expression per-gene summaries.
study cohort, study survival, and study compare require data_mutations.txt and data_clinical_sample.txt.
study survival also requires data_clinical_patient.txt with canonical {ENDPOINT}_STATUS and {ENDPOINT}_MONTHS columns.
Expression workflows require a supported expression matrix file.