Configuration Reference

This page classifies supported operator runtime configuration separately from internal fixture overrides and release/install variables.

Operator API Keys

Variable	Purpose
ALPHAGENOME_API_KEY	Enables get variant <id> predict
DISGENET_API_KEY	Enables gene/disease disgenet sections
NCBI_API_KEY	Improves NCBI E-utilities quota for PubMed, PubTator, PMC OA, and ID Converter paths
NCI_API_KEY	Enables trial operations with --source nci
ONCOKB_TOKEN	Enables the explicit variant oncokb <id> helper
OPENFDA_API_KEY	Improves OpenFDA quota headroom
S2_API_KEY	Enables authenticated Semantic Scholar quota
UMLS_API_KEY	Enables optional discover cross-vocabulary enrichment

Operator Data and Cache Knobs

Variable or file	Purpose
BIOMCP_CACHE_DIR	Overrides the BioMCP cache root
BIOMCP_CACHE_MODE	Cache behavior; infinite is used for local replay/spec cache hits
BIOMCP_CACHE_MAX_AGE	Optional cache age limit, as a positive integer number of seconds
BIOMCP_CACHE_MAX_SIZE	Optional cache size limit
BIOMCP_CACHE_MIN_DISK_FREE	Minimum free disk budget before cache eviction
BIOMCP_STUDY_DIR	Local cBioPortal-style study dataset root
BIOMCP_DDINTER_DIR	Local DDInter download bundle root
BIOMCP_EMA_DIR	Local EMA human-medicines download root
BIOMCP_WHO_DIR	Local WHO Prequalification download root
BIOMCP_CVX_DIR	Local CDC CVX/MVX download root
BIOMCP_GTR_DIR	Local GTR download root
BIOMCP_WHO_IVD_DIR	Local WHO IVD download root
cache.toml	Persistent cache defaults under the resolved config root
RUST_LOG	stderr tracing filter; default CLI behavior is quiet, and tools/biomcp-ci sets error

Cache runtime precedence is environment, then cache.toml, then built-in default. BIOMCP_CACHE_MAX_AGE overrides [cache].max_age_secs; both values are positive integer seconds.

Internal and Measurement Controls

Variable	Purpose
BIOMCP_GENE_GET_STRATEGY	Internal gene retrieval strategy control used for measurement and rollout comparisons
BIOMCP_GENE_OPTIONAL_TIMEOUT_MS	Internal timeout, in milliseconds, for optional gene enrichment branches
BIOMCP_GENE_TIMING_PATH	Internal measurement output path; when set, gene retrieval may write a local JSON timing report to that caller-provided path

Test and Fixture Override Seams

BIOMCP_*_BASE, BIOMCP_*_URL, and fixture process variables are internal fixture overrides unless this page lists them in an operator section. They let BioMCP's own verification harness redirect a source to a local server or fixture file. Do not treat those base-URL overrides as stable operator API.

Known examples include BIOMCP_ALPHAGENOME_BASE, BIOMCP_CANCERHOTSPOTS_BASE, BIOMCP_CBIOPORTAL_BASE, BIOMCP_CBIOPORTAL_DATAHUB_BASE, BIOMCP_CHEMBL_BASE, BIOMCP_CIVIC_BASE, BIOMCP_CLINGEN_BASE, BIOMCP_COMPLEXPORTAL_BASE, BIOMCP_CPIC_BASE, BIOMCP_CTGOV_BASE, BIOMCP_DGIDB_BASE, BIOMCP_DISGENET_BASE, BIOMCP_EMA_REPORT_BASE, BIOMCP_ENRICHR_BASE, BIOMCP_EUROPEPMC_BASE, BIOMCP_FIGSHARE_BASE, BIOMCP_GNOMAD_BASE, BIOMCP_GPROFILER_BASE, BIOMCP_GTEX_BASE, BIOMCP_GWAS_BASE, BIOMCP_HPA_BASE, BIOMCP_HPO_BASE, BIOMCP_INTERPRO_BASE, BIOMCP_KEGG_BASE, BIOMCP_LITSENSE2_BASE, BIOMCP_MEDLINEPLUS_BASE, BIOMCP_MONARCH_BASE, BIOMCP_MUTALYZER_BASE_URL, BIOMCP_MYCHEM_BASE, BIOMCP_MYDISEASE_BASE, BIOMCP_MYGENE_BASE, BIOMCP_MYVARIANT_BASE, BIOMCP_NCBI_IDCONV_BASE, BIOMCP_NCI_CTS_BASE, BIOMCP_NIH_REPORTER_BASE, BIOMCP_OLS4_BASE, BIOMCP_ONCOKB_BASE, BIOMCP_OPENFDA_BASE, BIOMCP_OPENTARGETS_BASE, BIOMCP_PHARMGKB_BASE, BIOMCP_PMC_HTML_BASE, BIOMCP_PMC_OA_BASE, BIOMCP_PUBMED_BASE, BIOMCP_PUBTATOR_BASE, BIOMCP_QUICKGO_BASE, BIOMCP_REACTOME_BASE, BIOMCP_S2_BASE, BIOMCP_SEER_BASE, BIOMCP_STRING_BASE, BIOMCP_UMLS_BASE, BIOMCP_UNIPROT_BASE, BIOMCP_VAERS_BASE, BIOMCP_VARIANTVALIDATOR_BASE_URL, BIOMCP_WIKIPATHWAYS_BASE, BIOMCP_WHO_PQ_URL, BIOMCP_WHO_PQ_API_URL, BIOMCP_WHO_VACCINES_URL, BIOMCP_WHO_IVD_URL, BIOMCP_GTR_TEST_VERSION_URL, BIOMCP_GTR_CONDITION_GENE_URL, BIOMCP_CVX_URL, BIOMCP_CVX_TRADENAME_URL, and BIOMCP_MVX_URL. Internal cBioPortal fixture/source-selection seams include BIOMCP_CBIOPORTAL_STUDY, BIOMCP_CBIOPORTAL_SAMPLE_LIST, and BIOMCP_CBIOPORTAL_MUTATION_PROFILE.

Release and Install Variables

Variable	Purpose
BIOMCP_BIN	Selects a built binary for spec wrappers and local demos
BIOMCP_GITHUB_REPO	Installer repository override
BIOMCP_INSTALL_DIR	Installer destination override
BIOMCP_TAG	Release/tag helper override
BIOMCP_VERSION	Installer/version override
BIOMCP_SPEC_CACHE_HIT	Spec wrapper hint that enables replay-style cache mode when unset by the caller

Observability and Degradation

Variable	Purpose
BIOMCP_DISABLE_KEGG	Operator-supported degradation control that disables KEGG pathway calls when KEGG should be avoided

• Human-facing diagnostics and tracing go to stderr, never JSON stdout.
• JSON query responses use _meta.source_status where a command has structured source availability/auth state to expose.
• biomcp health --apis-only reports API/source connectivity and excluded key-gated rows; full biomcp health also reports local runtime data and cache readiness.
• Optional sources degrade by omission, explicit unavailable notes, or _meta.source_status; they must not fabricate empty-source certainty.
• SourceUnavailable means the source is supported but temporarily unavailable. It is distinct from unsupported sections or invalid command grammar.