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Biomedical Data Sources for AI Agents

BioMCP's User Guide is organized around entities such as genes, variants, articles, trials, and drugs. This Sources section flips the lens: it shows what each upstream database is good at, what BioMCP exposes from it, and where the boundary sits when a workflow is mixed-source.

Use these pages when you already know the provider you trust, the keyword you are targeting, or the provenance you need to explain to a reviewer, teammate, or downstream agent.

Source guides

Source Best when you want Guide
PubMed Article search, PubTator annotations, and PMC full-text handoff PubMed
ClinicalTrials.gov Recruiting-study search, structured eligibility, and site details ClinicalTrials.gov
ClinVar Clinical significance and review-status context for variants ClinVar
ClinGen Allele Registry Canonical CAids and bounded aliases for supported RefSeq HGVS identities ClinGen Allele Registry
ClinGen CSpec Versioned VCEP criteria source documents with exact captures ClinGen CSpec
ClinGen ERepo Versioned expert assertions and criterion source facts by CAid ClinGen ERepo
ClinGen LDH Optional bounded article identity observations with exact PMC selectors ClinGen LDH
GenCC Submission-level gene-disease validity assertions GenCC
OpenFDA FAERS, recalls, device events, labels, and U.S. approval context OpenFDA
FDA Orphan Drug Designations and Approvals U.S. orphan-designation context in drug regulatory cards Data Sources
CDC WONDER VAERS Vaccine adverse-event summaries, seriousness breakdowns, and age-distribution context CDC WONDER VAERS
UniProt Canonical protein cards and structure-linked context UniProt
gnomAD Population frequency and gene constraint context gnomAD
Reactome Pathway records, pathway genes, and contained events Reactome
Semantic Scholar TLDRs, citation graphs, references, and recommendations Semantic Scholar
ChEMBL Drug-target activity, mechanism context, and indication enrichment ChEMBL
OpenTargets Target-disease scores, druggability, and disease-gene evidence OpenTargets
SEER Explorer Cancer survival statistics and disease survival section output SEER Explorer
CIViC Clinical variant evidence, therapy context, and disease-associated variants CIViC
OncoKB Oncology actionability tiers and treatment implications for actionable variants OncoKB
cBioPortal Cancer cohort frequencies and local study analytics workflows cBioPortal
DDInter Structured drug-drug interactions, severity levels, and class-oriented partner review DDInter
EMA EU regulatory, safety, and shortage context for medicines EMA
WHO Prequalification WHO-backed medicine and vaccine prequalification search plus global access checks WHO Prequalification
NCBI Genetic Testing Registry Gene-centric genetic tests, GTR diagnostic cards, and local bundle lifecycle NCBI Genetic Testing Registry
WHO Prequalified IVD Infectious-disease diagnostic products, assay formats, and WHO product-card provenance WHO Prequalified IVD
CDC CVX/MVX Vaccine brand-to-antigen bridge for EMA/default lookups and explicit WHO vaccine search CDC CVX/MVX
MedlinePlus Plain-language disease/symptom context for discover MedlinePlus
Cellosaurus Cell line identity, accessions, cross-reference join keys, and curated variants Cellosaurus
PharmacoDB Published drug sensitivity experiments for a cell line or a compound, per dataset PharmacoDB
KEGG KEGG pathway IDs, summary cards, and pathway genes KEGG
PharmGKB / CPIC Pharmacogenomic recommendations, frequencies, and clinical annotations PharmGKB / CPIC
Human Protein Atlas Tissue expression, localization, and cancer-expression context Human Protein Atlas
Monarch Initiative Phenotype-to-disease matching, disease genes, and model evidence Monarch Initiative

Reference and setup

  • Data Sources explains runtime behavior, endpoints, auth mode, and operational caveats.
  • Source Licensing and Terms explains direct vs indirect provenance, redistribution limits, and provider terms.
  • API Keys shows the optional or required environment variables that upgrade selected source paths.