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API Keys

Most BioMCP workflows run without credentials. Some enrichment and higher-rate access paths improve with API keys. For provider terms, redistribution caveats, and which sources are only indirect provenance, see the source-licensing reference.

Required for prediction section

ALPHAGENOME_API_KEY

Used by variant prediction lookups:

Provider access: https://deepmind.google/science/alphagenome/

export ALPHAGENOME_API_KEY="..."
biomcp get variant "chr7:g.140453136A>T" predict

Additional API keys

ONCOKB_TOKEN

Used for the production biomcp variant oncokb ... helper. BioMCP keeps ONCOKB_TOKEN because OncoKB itself calls the credential a token.

Register at: https://www.oncokb.org/account/register

export ONCOKB_TOKEN="..."
biomcp variant oncokb "BRAF V600E"

NCI_API_KEY

Used for NCI CTS trial calls.

Request access at: https://clinicaltrialsapi.cancer.gov/

export NCI_API_KEY="..."
biomcp search trial -c melanoma --source nci

DISGENET_API_KEY

Required for DisGeNET scored association sections on genes and diseases.

Register at: https://www.disgenet.com/

export DISGENET_API_KEY="..."
biomcp get gene TP53 disgenet
biomcp get disease "breast cancer" disgenet

UMLS_API_KEY

Adds optional clinical crosswalk enrichment to biomcp discover.

Register at: https://uts.nlm.nih.gov/uts/signup-login

export UMLS_API_KEY="..."
biomcp discover "cystic fibrosis"
biomcp --json discover diabetes

NCBI_API_KEY

Improves rate limits for PubTator, PMC OA, and NCBI ID converter (3 → 10 req/sec).

Create one in My NCBI: https://www.ncbi.nlm.nih.gov/account/settings/

export NCBI_API_KEY="..."
biomcp search article -g BRAF --limit 5

S2_API_KEY

Enables authenticated Semantic Scholar article requests. Use it for a dedicated provider quota at 1 req/sec across the optional article search leg, get article enrichment, get article ... tldr, article citations, article references, and article recommendations. Without the key, those paths still work through the shared unauthenticated pool at 1 req/2sec.

Request a key at: https://www.semanticscholar.org/product/api

export S2_API_KEY="..."
biomcp get article 22663011 tldr
biomcp article citations 22663011 --limit 3

OPENFDA_API_KEY

Improves OpenFDA rate limits for drug safety lookups.

Request a key at: https://open.fda.gov/apis/authentication/

export OPENFDA_API_KEY="..."
biomcp search adverse-event --drug pembrolizumab --limit 5

Key management guidance

  • Prefer environment variables over hardcoded values.
  • Do not commit secrets into source control.
  • Set keys in the same environment used by your MCP client.
  • Rotate keys when sharing machines or CI runners.
  • S2_API_KEY is optional. Without it, article search/get/helper paths still work through the shared Semantic Scholar pool at 1 req/2sec. With it, BioMCP sends x-api-key and uses the authenticated quota at 1 req/sec for the same article search/get/helper paths.
  • UMLS_API_KEY is optional; when absent, discover still works with OLS4-only results.

See also: Source Licensing and Terms