life-science-mcp

A unified MCP server for 110 life science APIs and databases.

Installation

{
  "mcpServers": {
    "life-science": {
      "command": "npx",
      "args": ["-y", "life-science-mcp"]
    }
  }
}

Providers (110)

Provider	Description
AlphaFold DB	AI-predicted protein structures from DeepMind
BERN2	Biomedical named entity recognition and normalization
Bgee	Gene expression evolution across species and tissues
BiGG Models	Metabolic network reconstructions and flux balance models
BioModels	Mathematical models of biological systems (SBML)
bioRxiv	Preprint server for biology
BioSamples	EBI biological sample metadata and attributes
BOLD Systems	Barcode of Life DNA barcode data
Catalogue of Life	Global index of species names and taxonomy
cBioPortal	Multidimensional cancer genomics data
Cellosaurus	Cell line identification and characterization
ChEBI	Chemical Entities of Biological Interest via OLS4
ChEMBL	Bioactive drug-like small molecules
CIViC	Clinical Interpretations of Variants in Cancer
ClinicalTrials.gov	Registry of clinical studies worldwide
ClinVar	Genetic variants linked to clinical significance
DailyMed	FDA drug labeling and packaging information
dbSNP	Single nucleotide polymorphisms and genetic variation
DGIdb	Drug-gene interaction data
DisGeNET	Gene-disease associations
EMDB	Electron Microscopy Data Bank for 3D structures
ENA	European Nucleotide Archive sequence data
ENCODE	Encyclopedia of DNA Elements regulatory data
Enrichr	Gene set enrichment analysis platform
Ensembl	Genome browser and annotation
Europe PMC	Open-access biomedical literature
Expression Atlas	Gene expression patterns across species and conditions
FishBase	Comprehensive fish species database
GBIF	Global Biodiversity Information Facility
GDC	NCI Genomic Data Commons (TCGA and more)
Gene Ontology	Functional gene annotations and ontology
GEO	Gene Expression Omnibus high-throughput datasets
GlyGen	Integrated glycoscience data for glycans and glycoproteins
GlyTouCan	International glycan structure repository
gnomAD	Genome Aggregation Database allele frequencies
GPCRdb	G protein-coupled receptor database
g:Profiler	Functional enrichment and gene ID conversion
GTEx	Gene expression across human tissues
Guide to Pharmacology	Drug targets and ligands
GWAS Catalog	Genome-wide association studies
HGNC	Approved human gene symbols and names
HMDB	Human Metabolome Database
HPO	Human Phenotype Ontology
Human Protein Atlas	Protein expression and localization across tissues
IEDB	Immune Epitope Database and Analysis Resource
iNaturalist	Citizen science biodiversity observations
IntAct	Curated protein-protein interactions
InterPro	Protein families, domains, and functional sites
JASPAR	Transcription factor binding profiles
KEGG	Pathway and molecular interaction database
LIPID MAPS	Lipid classification and structures
MassBank	Mass spectra for metabolite identification
MeSH	Medical Subject Headings vocabulary
MetaboLights	Metabolomics experiments and derived information
Metabolomics Workbench	Metabolomics data repository and tools
MGnify	EBI metagenomics analysis and archiving
Monarch Initiative	Knowledge graph for disease discovery
MyChem.info	Aggregated chemical and drug annotations
MyDisease.info	Aggregated disease annotations
MyGene.info	Aggregated gene annotations
MyVariant.info	Aggregated genetic variant annotations
Natural Products Atlas	Microbially-derived natural products
NCBI BioSample	Biological sample metadata for experimental assays
NCBI Gene	Gene-specific information from Entrez
NCBI Nucleotide	GenBank and RefSeq sequences
NCBI Protein	Protein sequences from RefSeq, UniProt, PDB
NCBI Taxonomy	Taxonomic classification and nomenclature
NCI Chemical Identifier Resolver	Chemical name/structure resolution and conversion
NDEx	Biological network models exchange
OBIS	Ocean Biodiversity Information System
OLS	Ontology Lookup Service for biomedical ontologies
OmniPath	Signaling pathway and molecular interaction network
OpenCitations	Open citation index and bibliometrics
openFDA	FDA data on drugs, devices, and adverse events
Open Targets	Drug target identification and prioritization
Open Tree of Life	Comprehensive synthetic phylogenetic tree
Orphanet	Rare disease and orphan drug information
OrthoDB	Gene evolutionary relationships and orthologs
PANTHER	Protein classification and evolutionary analysis
PDBe	Protein Data Bank in Europe
PharmGKB	Pharmacogenomics knowledge (via CPIC)
PRIDE	Proteomics identifications database
PubChem	Open chemistry database
PubMed	Biomedical literature search engine
PubTator	Biomedical text mining and entity annotation
QuickGO	Gene Ontology browser
RCSB PDB	3D structural data for biological macromolecules
Reactome	Curated biological pathway database
Rfam	Non-coding RNA families and structured RNA elements
Rhea	Expert-curated biochemical reactions
RNAcentral	Non-coding RNA sequence database
SABIO-RK	Enzyme kinetics and biochemical reaction data
Semantic Scholar	AI-powered academic paper search and analysis
SNOMED CT	Standardized clinical terminology (via FHIR)
STITCH	Chemical-protein interaction network
STRING	Protein-protein interaction networks
SwissLipids	Curated knowledge on lipid biology
TCIA	The Cancer Imaging Archive
UCSC Genome Browser	Genome browser, tracks, and annotations
UniChem	Chemical structure cross-referencing
UniParc	Non-redundant protein sequence archive
UniProt	Protein sequence and functional information
UniRef	Clustered protein sequence sets
WHO GHO	World Health Organization Global Health Observatory
WikiPathways	Community-curated biological pathways
WormBase	C. elegans and nematode genomics
WoRMS	World Register of Marine Species
ZINC	Commercially available compounds for virtual screening

Example Queries

Beginner

Category	Query
Gene lookup	What is the approved gene symbol for p53 and what chromosome is it on?
Chemistry	Give me the molecular formula, weight, and canonical SMILES for metformin.
Functional annotation	What biological process GO terms are annotated to the human insulin receptor gene INSR?
Clinical trials	Find open clinical trials recruiting patients with glioblastoma.
Taxonomy	What species are in the family Felidae and how are they classified?
Structural biology	Retrieve the AlphaFold-predicted structure confidence (pLDDT) for human serum albumin.
Pharmacovigilance	What are the known side effects of ibuprofen in FDA adverse event reports?
Pathways	Look up the glycolysis pathway and list the enzymes involved.

Intermediate

Category	Query
Pharmacogenomics	My patient had an unexpected bleeding event on standard-dose warfarin — are there CYP2C9 or VKORC1 variants that could explain abnormal metabolism, and do clinical dosing guidelines exist for those genotypes?
Drug metabolism	CYP3A4 metabolizes over half of all prescribed drugs — which of its protein interaction partners in liver tissue are also drug-metabolizing enzymes, and do any share substrates that could cause undocumented interactions?
Post-GWAS	A GWAS hit near FOXP3 is associated with autoimmune disease but the mechanism is unknown — what regulatory elements overlap this locus in ENCODE, what pathways is FOXP3 in, and are there phenotypically similar rare diseases caused by FOXP3 mutations?
Drug repurposing	Imatinib was designed for BCR-ABL, but what other kinase targets does it hit, are any of those targets implicated in non-cancer diseases, and are there trials testing imatinib for those conditions?
Evolutionary biology	The FOXP2 "language gene" is highly conserved — how does its protein domain architecture compare across human, mouse, zebrafish, and songbird, and are any domains under positive selection in the human lineage?
Marine ecology	Lionfish (Pterois volitans) are invasive in the Caribbean — where are they being observed now vs. their native Indo-Pacific range, what native species occupy the same phylogenetic niche, and has anyone studied how their gut microbiome shifts in the invaded habitat?
Metabolic disease	Branched-chain amino acids are elevated in pre-diabetic patients — which enzymatic pathways degrade them, are the genes for those enzymes differentially expressed in diabetic vs. healthy pancreatic islets, and do any of those enzymes have known drug modulators?
Undiagnosed disease	A child presents with seizures, intellectual disability, and microcephaly — what genes are associated with all three HPO phenotypes simultaneously, which of those genes have pathogenic variants in ClinVar, and are any located in the patient's candidate region on chromosome 7q?

Expert

Category	Query
Adverse drug reaction	A patient on both acetaminophen and isoniazid develops liver failure — could isoniazid's CYP2E1 induction increase NAPQI formation beyond the glutathione detox capacity? Find the enzymes, check if the patient's population has high-frequency CYP2E1 variants that compound the risk, map the oxidative stress cascade, and see if this specific drug combination has a disproportionate signal in FDA adverse event data.
Resistance mechanism	A melanoma patient initially responded to vemurafenib (BRAF V600E inhibitor) but progressed after 8 months — what bypass resistance mechanisms are reported in the literature, do any involve kinases with existing approved inhibitors, what does the structural basis of drug-resistant BRAF look like, and are there combination trials enrolling patients with acquired resistance?
Gut-brain axis	The gene SLC6A4 (serotonin transporter) appears in both depression GWAS and gut microbiome association studies — is there a mechanistic link? Find its expression across gut and brain tissues, identify which gut bacterial metabolites interact with serotonin pathways, check if SLC6A4 polymorphisms alter transporter kinetics, and search for clinical evidence connecting microbiome composition to SSRI treatment response.
Neoantigen prioritization	A tumor exome reveals a novel frameshift in TP53 — predict the neoantigen peptides, determine which patient HLA alleles could present them, check whether those HLA alleles are common or rare in the patient's population, verify the mutant region has high structural confidence and isn't in a disordered domain, confirm the gene is expressed in the tumor tissue type, and rule out homology to self-proteins that would cause tolerance.
Cryptic species discovery	DNA barcodes from a deep-sea vent survey match no known species — find the closest sequences in GenBank, place the organism on the tree of life, check if the vent location has been previously surveyed in OBIS or GBIF, identify whether related organisms have characterized genomes or metagenomes, and search preprints for any recent reports from the same vent system.
Polypharmacy risk	An elderly patient takes metformin, atorvastatin, amlodipine, and omeprazole — map every CYP enzyme involved in metabolizing these four drugs, find shared enzymes where competitive inhibition could alter plasma levels, check if any of the patient's known pharmacogenomic variants affect those specific enzymes, look up FDA adverse event co-occurrence signals for each pairwise drug combination, and identify which interactions lack clinical guideline coverage.

License

MIT — see LICENSE.

life-science-mcp

life-science-mcp

Installation

Providers (110)

Example Queries

Beginner

Intermediate

Expert

License

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