biorouter

A unified MCP server for 299 life science APIs and databases (281 free, 18 API key). Two tools — findTools and callTools — provide progressive discovery across 857 endpoints with field projection and batch execution.

On top of individual API tools, 19 endpoints orchestrate multi-source queries across 197 providers in parallel — a single call like compound/profile "ibuprofen" fans out to 40+ APIs and returns a merged, deduplicated result.

Installation

{
  "mcpServers": {
    "biorouter": {
      "command": "npx",
      "args": ["-y", "github:achillesrasquinha/biorouter"]
    }
  }
}

Endpoints (19)

High-level orchestrated queries that resolve identifiers, fan out to multiple APIs in parallel, and merge results with ranked provenance.

Endpoint	Description
`compound/profile`	Profile a drug or compound — structure, pharmacology, safety, targets, and clinical data
`compound/interactions`	Map drug interactions — mechanisms, targets, gene interactions, indications, and bioactivity
`compound/similar`	Find structurally similar compounds — fingerprint, substructure, and binding-based similarity
`disease/profile`	Profile a disease — phenotypes, genetics, ontology, therapeutics, and clinical classification
`disease/drugs`	Find drugs for a disease — approved treatments, clinical candidates, and drug-gene interactions
`protein/profile`	Profile a protein — sequence, function, expression, disease associations, and druggability
`protein/interactions`	Map protein interactions — PPIs, signaling, complexes, drug targets, and binding affinities
`protein/structure`	Analyze protein structure — 3D coordinates, domains, disorder, AlphaFold predictions, and classification
`pathway/profile`	Profile a biological pathway — reactions, participants, regulation, and cross-database annotations
`pathway/enrichment`	Analyze gene-set enrichment — GO terms, pathways, and functional categories for a gene list
`variant/annotate`	Annotate a genetic variant — pathogenicity, population frequency, consequence predictions, and pharmacogenomics
`cancer/profile`	Profile the molecular landscape of a cancer — mutations, copy number, clinical evidence, and therapeutic targets
`interaction/check`	Check molecular interactions — PPI evidence, signaling, complexes, and drug-gene links for two entities
`literature/search`	Search biomedical literature — publications, preprints, citations, and semantic annotations
`trial/search`	Search clinical trials — interventional studies, drug development, and precision medicine evidence
`organism/profile`	Profile an organism — taxonomy, genome, model organism resources, ecology, and phylogenetics
`sequence/search`	Search and retrieve sequences — nucleotide, protein, genomic context, alignments, and domain annotations
`data/search`	Search life-science data repositories — genomics, single-cell, proteomics, metabolomics, and imaging archives
`ontology/resolve`	Resolve biomedical terms — map free text, CURIEs, and accessions to ontology concepts across 900+ vocabularies

Providers (299)

Provider	Description	Auth
1000 Genomes (IGSR)	International Genome Sample Resource — population genomics data from the 1000 Genomes Project	Free
Addgene	Addgene — nonprofit plasmid repository for sharing molecular biology reagents	Free
AIRR Data Commons	AIRR Data Commons — adaptive immune receptor repertoire sequencing data	Free
Alliance of Genome Resources	Unified portal for model organism genes, diseases, and orthologs	Free
Allen Brain Atlas	Allen Institute brain gene expression and connectivity data	Free
AmoebaDB	VEuPathDB resource for Entamoeba and free-living amoeba genomics	Free
AlphaFold DB	AI-predicted protein structures from DeepMind	Free
AquaMaps	AquaMaps — predicted species distribution maps for marine and freshwater organisms	Free
ArrayExpress	ArrayExpress — gene expression and functional genomics experiments archive (EBI BioStudies)	Free
ATC Classification	ATC (Anatomical Therapeutic Chemical) drug classification via RxNav/RxClass API	Free
BERN2	BERN2 biomedical named entity recognition — extract genes, diseases, drugs, and other entities from text	Free
Bgee	Gene expression evolution database — expression across species and tissues	Free
BiGG Models	BiGG Models — genome-scale metabolic network reconstructions	Free
BindingDB	Public database of measured binding affinities between proteins and drug-like molecules	Free
BioCyc	BioCyc / MetaCyc — metabolic pathway and genome database collection	Free
Bioregistry	Bioregistry — registry of 1000+ biological databases with identifier patterns and metadata	Free
BioStudies	BioStudies — EBI archive for biological study data linking publications to datasets	Free
bio.tools	ELIXIR bio.tools registry — bioinformatics tools and databases catalog	Free
BioGRID	BioGRID database of protein and genetic interactions	API Key
BioModels	BioModels repository — mathematical models of biological systems in SBML and other formats	Free
BioPortal	NCBO BioPortal — search 900+ biomedical ontologies and annotate text with ontology concepts	API Key
bioRxiv	bioRxiv preprint server — access preprints in biology and related sciences	Free
BMRB	Biological Magnetic Resonance Bank — NMR spectroscopy data for proteins, nucleic acids, and metabolites	Free
BioSamples	EBI BioSamples database — biological sample metadata and attributes	Free
BOLD	Barcode of Life Data Systems — DNA barcode specimens and sequences for species identification	Free
BrainSpan	BrainSpan developmental transcriptome — human brain gene expression across developmental stages	Free
BV-BRC	Bacterial and Viral Bioinformatics Resource Center — pathogen genomics, AMR, and surveillance data	Free
CADD	Combined Annotation Dependent Depletion — variant deleteriousness scoring	Free
CATH	Protein structure classification — hierarchical domain classification of protein structures	Free
Catalogue of Life	Catalogue of Life — global checklist of all known species with authoritative taxonomy	Free
cBioPortal	Cancer genomics portal — explore multidimensional cancer genomics data	Free
CDC Open Data	CDC Open Data — public health datasets via the Socrata Open Data API	Free
CDC WONDER	CDC WONDER — Wide-ranging Online Data for Epidemiologic Research, public health datasets	Free
CDD	NCBI Conserved Domain Database — identify conserved domains in protein sequences	Free
Cellosaurus	Knowledge resource on cell lines — cell line identification and characterization	Free
CELLxGENE	CZ CELLxGENE Discover — single-cell datasets and gene expression	Free
ChEBI (via OLS4)	Chemical Entities of Biological Interest — ontology lookup via EBI OLS4	Free
ChEMBL	Database of bioactive drug-like small molecules	Free
ChemSpider	RSC chemical compound search, structures, and properties database	API Key
CIViC	Clinical Interpretations of Variants in Cancer — curated clinical evidence for variants	Free
ClassyFire	Automated chemical classification using the ChemOnt ontology	Free
ClinGen	Clinical Genome Resource — gene-disease validity and dosage sensitivity curation	Free
ClinGen Allele Registry	ClinGen Allele Registry — canonical allele identifiers linking variants across nomenclatures	Free
NLM Clinical Tables	NLM Clinical Tables — autocomplete and lookup for ICD-10, LOINC, RxTerms, and conditions	Free
ClinicalTrials.gov	Registry of clinical studies conducted around the world	Free
ClinVar	Variant-disease relationship database linking genetic variants to clinical significance	Free
Clustal Omega	EBI Clustal Omega multiple sequence alignment service	Free
COG	Clusters of Orthologous Genes — ortholog classification and functional annotation across prokaryotes	Free
COCONUT	COlleCtion of Open Natural prodUcTs — comprehensive natural products database	Free
Complex Portal	Macromolecular complex database — curated stable protein complexes from EBI	Free
Comparative Toxicogenomics Database	CTD curated chemical-gene-disease interactions for toxicogenomics research	Free
CompTox	EPA CompTox Chemicals Dashboard for toxicology and chemical safety	Free
Crossref	Crossref — scholarly metadata for publications, journals, funders, and DOIs	Free
CryptoDB	VEuPathDB resource for Cryptosporidium genomics	Free
DailyMed	DailyMed drug label information from the National Library of Medicine — SPL documents and prescribing information	Free
DataCite	DataCite — DOI registration and metadata for research datasets and publications	Free
DALI	DALI server — protein structure comparison by 3D alignment	Free
DANDI Archive	DANDI — neurophysiology data integration, brain imaging and electrophysiology datasets	Free
dbGaP	dbGaP (database of Genotypes and Phenotypes) — genotype-phenotype association studies	Free
dbSNP	Database of single nucleotide polymorphisms and other genetic variation	Free
dbVar	NCBI dbVar — database of genomic structural variants (CNVs, insertions, deletions, inversions)	Free
DDBJ	DNA Data Bank of Japan — nucleotide sequence archive	Free
dbfetch	EBI dbfetch — sequence and entry retrieval from EMBL, UniProt, PDB, and 50+ databases	Free
DeepLoc 2.0	DeepLoc 2.0 — protein subcellular localization prediction (DTU BioLib)	Free
DepMap	Cancer Dependency Map — cell line genomic and dependency data	Free
DGIdb	Drug-Gene Interaction Database — mining drug-gene interaction data	Free
DisGeNET	Gene-disease association database	API Key
DisProt	Database of intrinsically disordered proteins and regions	Free
DOAJ	Directory of Open Access Journals — indexing quality open access research	Free
DrugCentral	Drug information resource integrating drug indications, mechanisms, and interactions	Free
eBird	Cornell Lab eBird — bird observations, hotspots, and taxonomy worldwide	API Key
EBI Search	EBI Search — unified search across 400+ EBI databases (UniProt, PDB, SRA, etc.)	Free
EggNOG	Orthologous groups and functional annotation from EggNOG	Free
EMDB	Electron Microscopy Data Bank — 3D cryo-EM density maps and tomograms	Free
EMPIAR	Electron Microscopy Public Image Archive for raw EM data	Free
ENCODE SCREEN	ENCODE SCREEN registry of candidate cis-regulatory elements (cCREs)	Free
ENCODE	Encyclopedia of DNA Elements — functional annotations of the human genome	Free
Enrichr	Enrichr — gene set enrichment analysis against curated gene-set libraries	Free
Ensembl BioMart	Ensembl BioMart bulk annotation and data retrieval service	Free
Ensembl VEP	Variant Effect Predictor — predict functional effects of genetic variants	Free
ENA Portal	ENA Portal API — advanced search across ENA studies, samples, experiments, and assemblies	Free
ENA Taxonomy	EBI ENA Taxonomy — taxonomic classification lookup with lineage and common names	Free
Ensembl	Genome browser and annotation database	Free
ELM	Eukaryotic Linear Motifs — short functional motifs in proteins (cleavage sites, binding motifs, etc.)	Free
EpiGraphDB	EpiGraphDB — epidemiological graph database for Mendelian randomization and causal inference	Free
EU Clinical Trials Register	European Union Clinical Trials Register for searching EU clinical studies	Free
European Variation Archive	European Variation Archive — open-access database of genetic variants across species	Free
Europe PMC	Europe PubMed Central — open-access biomedical literature	Free
Europe PMC Annotations	Text-mined named entities (genes, diseases, GO terms) from publications	Free
European Genome-phenome Archive	EGA metadata API for controlled-access genomic and phenomic datasets	Free
European Nucleotide Archive	Open-access nucleotide sequence data and associated information	Free
Expression Atlas	Gene expression patterns across species and biological conditions (EBI)	Free
FAOSTAT	FAO Statistics — food and agriculture data from the UN FAO	Free
FDA Orange Book	FDA Orange Book drug patent and exclusivity data via openFDA	Free
FHIR R4	FHIR R4 public test server — HL7 FHIR standard for healthcare data interoperability	Free
FishBase	FishBase — comprehensive database of fish species biology, ecology, and taxonomy	Free
FlyBase	FlyBase — Drosophila melanogaster genomics, genetics, and molecular biology	Free
FlyMine	InterMine data warehouse for Drosophila genomics, orthologs, and interactions	Free
FungiDB	VEuPathDB resource for fungal genomics (Aspergillus, Candida, Cryptococcus)	Free
g:Profiler	g:Profiler — functional enrichment and gene ID conversion	Free
GARD	GARD — Genetic and Rare Diseases Information Center from NIH	Free
GBIF	Global Biodiversity Information Facility — species occurrence and taxonomy data worldwide	Free
GDC	NCI Genomic Data Commons — cancer genomics data from TCGA and other programs	Free
Geneshot	Geneshot — gene set discovery from PubMed literature mining (Ma'ayan Lab)	Free
Gene Expression Omnibus	Repository of high-throughput gene expression and genomics datasets	Free
Gene Ontology	Gene Ontology API — GO terms, annotations, and bioentity information	Free
GeneMANIA	GeneMANIA — gene interaction network prediction and visualization	Free
GlyCosmos	GlyCosmos — integrated glycoscience portal for glycan structures, pathways, and diseases	Free
GlyGen	GlyGen — glycoscience data integration and retrieval	Free
GlyTouCan	GlyTouCan — international glycan structure repository	Free
gnomAD	Genome Aggregation Database — population variant frequencies and annotations	Free
GNPS	GNPS — molecular networking and spectral library for mass spectrometry data	Free
GPCRdb	GPCR database — G protein-coupled receptor structures, sequences, and pharmacology	Free
Gramene	Gramene — comparative plant genomics resource for crops and model species	Free
GTEx Portal	Genotype-Tissue Expression project — gene expression across human tissues	Free
GTDB	Genome Taxonomy Database — standardized bacterial and archaeal taxonomy based on genome phylogeny	Free
Guide to Pharmacology	IUPHAR/BPS Guide to Pharmacology database of drug targets and ligands	Free
GWAS Catalog	NHGRI-EBI Catalog of genome-wide association studies	Free
Harmonizome	Unified access to 177 datasets of gene and protein knowledge from Ma'ayan Lab	Free
HGNC	HUGO Gene Nomenclature Committee — approved human gene symbols and names	Free
HMMER	HMMER protein sequence search using profile hidden Markov models	Free
HostDB	VEuPathDB resource for host response to pathogens (human, mouse, macaque)	Free
Human Cell Atlas	Human Cell Atlas data portal — single-cell genomics projects and datasets	Free
HuBMAP	Human BioMolecular Atlas Program — atlas of human body at single-cell resolution	Free
HumanMine	InterMine data warehouse for human genomics, disease, and interactions	Free
Human Metabolome Database	HMDB — comprehensive human metabolite and biomarker database	Free
Human Phenotype Ontology	Human Phenotype Ontology — standardized vocabulary of human phenotypic abnormalities	Free
Human Protein Atlas	Human protein expression and localization data across tissues and cell types	Free
I-TASSER	I-TASSER — protein structure and function prediction server (Zhang Lab)	Free
IEDB	Immune Epitope Database — curated epitope data for immune research	Free
iGEM Registry	iGEM Registry of Standard Biological Parts — synthetic biology parts catalog	Free
IGVF	IGVF — Impact of Genomic Variation on Function consortium data portal	Free
IHEC	International Human Epigenome Consortium — reference epigenome datasets and metadata	Free
ImmPort	Immunology Database and Analysis Portal — shared immunology data	Free
IMPC	International Mouse Phenotyping Consortium — phenotype data for knockout mouse lines	Free
iNaturalist	iNaturalist — citizen-science biodiversity observations and taxa worldwide	Free
IntAct	Molecular interaction database — curated protein-protein interactions	Free
InterPro	Protein families, domains, and functional sites classification	Free
IPD-IMGT/HLA	IPD-IMGT/HLA allele database — HLA allele sequences, nomenclature, and immunogenetics data	Free
iPTMnet	iPTMnet — post-translational modification (PTM) knowledge base for proteins	Free
ITIS	Integrated Taxonomic Information System — authoritative taxonomic information for plants, animals, fungi, and microbes	Free
iTOL	iTOL Interactive Tree of Life — phylogenetic tree upload, annotation, and export	Free
IUCN Red List	IUCN Red List of Threatened Species — conservation status for 150,000+ species	API Key
JASPAR	JASPAR — open-access database of transcription factor binding profiles	Free
KEGG	Kyoto Encyclopedia of Genes and Genomes — pathway and molecular interaction database	Free
LegumeMine	InterMine for legume genomics — soybean, common bean, and other legumes	Free
LIPID MAPS	LIPID MAPS Structure Database for lipid classification and structures	Free
LOINC	LOINC clinical terminology — standardized codes for lab tests, clinical observations, and measurements via FHIR	API Key
LOTUS	Natural products database — open knowledge on natural compounds and their biological sources	Free
MaizeGDB	MaizeGDB — maize genetics and genomics database for corn research	Free
MalaCards	MalaCards — human disease database integrating gene, variant, and pathway data	Free
MassBank	Public repository of mass spectra for metabolite identification	Free
MeSH	Medical Subject Headings vocabulary for indexing biomedical literature	Free
MetaboLights	EMBL-EBI database for metabolomics experiments and derived information	Free
MetExplore	MetExplore — metabolic network analysis platform with 349 organism models	Free
Metabolomics Workbench	Metabolomics Workbench — metabolomics data repository and metadata	Free
METLIN	METLIN metabolite mass spectrometry database for metabolomics research	API Key
MG-RAST	MG-RAST — metagenomics analysis and annotation server for microbiome datasets	Free
MGnify	MGnify — EBI metagenomics analysis and archiving platform	Free
MicrobiomeDB	MicrobiomeDB — microbiome study data including taxonomic and functional profiling	Free
MobiDB	Protein disorder and mobility annotations	Free
ModelSEED	ModelSEED — automated metabolic model reconstruction and biochemistry database	Free
Monarch Initiative	Knowledge graph integrating biological and clinical data for disease discovery	Free
Movebank	Movebank — animal tracking and movement data from global research studies	Free
MSigDB	Molecular Signatures Database — curated gene set collections for enrichment analysis	Free
MyChem.info	Chemical and drug annotation query service — aggregates compound data from multiple sources	Free
MyDisease.info	Disease annotation query service — aggregates disease data from multiple sources	Free
MyGene.info	Gene annotation query service — aggregated gene info from multiple sources	Free
MyGeneset.info	Gene set query service — curated and community gene sets	Free
MyVariant.info	Variant annotation query service — aggregates genetic variant data from multiple sources	Free
RENCI Name Resolution	Translator service mapping text labels to biomedical CURIEs	Free
NASA OSDR	NASA Open Science Data Repository — space biology and radiation genomics datasets	Free
Natural Products Atlas	Database of microbially-derived natural products for drug discovery	Free
NatureServe	NatureServe Explorer — conservation status and biodiversity data for species across the Americas	API Key
NCBI BioSample	Database of biological sample metadata used in experimental assays	Free
NCBI BLAST	NCBI BLAST sequence similarity search — submit queries and retrieve alignment results	Free
NCBI Datasets	NCBI Datasets API v2 — modern REST interface for genes, genomes, and taxonomy	Free
NCBI Gene	Gene-specific information from NCBI Entrez Gene database	Free
NCBI Nucleotide	GenBank and RefSeq nucleotide sequence database	Free
NCBI Protein	Protein sequence database including RefSeq, UniProt, and PDB sequences	Free
NCBI SRA	Sequence Read Archive — raw sequencing data repository	Free
NCBI Taxonomy	Taxonomic classification and nomenclature database	Free
NCBO Annotator	NCBO Annotator — annotate biomedical text with ontology concepts and get ontology recommendations	API Key
NCI Chemical Identifier Resolver	NCI CADD Chemical Identifier Resolver — convert between chemical names, SMILES, InChI, and other formats	Free
NDEx	NDEx Network Data Exchange for biological network models	Free
Nextstrain	Real-time tracking of pathogen evolution for influenza, SARS-CoV-2, and other viruses	Free
NMDC	National Microbiome Data Collaborative — integrated microbiome multi-omics data	Free
RENCI Node Normalization	Translator service normalizing CURIEs to canonical identifiers	Free
NetMHCIIpan	NetMHCIIpan 4.3 — MHC class II binding prediction for peptides across HLA-DR/DP/DQ alleles	Free
NetMHCpan	NetMHCpan 4.1 — MHC class I binding prediction for peptides across HLA alleles	Free
OBIS	Ocean Biodiversity Information System — marine species occurrence and distribution data	Free
OBO Foundry	Registry of 267 interoperable biomedical ontologies (GO, HPO, ChEBI, etc.)	Free
OLS	Ontology Lookup Service — search and browse biomedical ontologies (GO, EFO, HPO, etc.)	Free
OMA	Orthologous Matrix — comprehensive ortholog database	Free
OMIM	Online Mendelian Inheritance in Man — catalog of human genes and genetic disorders	API Key
Ontobee	Ontology term search and browsing across OBO and OWL ontologies	Free
OmniPath	OmniPath — comprehensive signaling network and enzyme-substrate interactions	Free
OncoTree	MSK Cancer Classification — standardized cancer type taxonomy and hierarchy	Free
OneZoom	OneZoom tree of life explorer — interactive visualization and species search across the tree of life	Free
Open Targets	Drug target identification and prioritization platform	Free
Open Tree of Life	Open Tree of Life — comprehensive phylogenetic tree and taxonomy synthesis	Free
OpenAlex	OpenAlex — open catalog of scholarly works, authors, institutions, and concepts	Free
OpenCitations	OpenCitations COCI citation index — open bibliographic citation data for DOIs	Free
openFDA	Open-access FDA data on drugs, devices, and foods including adverse events	Free
ORCID	ORCID — persistent researcher identifiers linking authors to works and affiliations	Free
Orphanet	Orphanet — reference portal for rare diseases and orphan drugs	Free
OrthoDB	Hierarchical catalog of orthologs — gene evolutionary relationships	Free
PANTHER	PANTHER — protein classification, gene ontology, and phylogenetic analysis	Free
Pathway Commons	Integrated biological pathway and interaction data from multiple sources	Free
PDBe	Protein Data Bank in Europe — macromolecular structure data	Free
PDBe Graph API	PDBe Graph API — compounds, protein mappings, and molecule details from PDB	Free
PDBj	Protein Data Bank Japan — PDB search, SQL queries, and chemical component lookup	Free
PGS Catalog	Polygenic Score Catalog — risk prediction scores and trait associations	Free
Proteomic Data Commons	NCI Proteomic Data Commons — proteomics data from cancer research studies	Free
PeptideAtlas	PeptideAtlas — proteomics data repository for peptide and protein identifications	Free
Pfam	Pfam protein families database — protein domain classification via InterPro	Free
Pharos	Illuminating the Druggable Genome — comprehensive target, disease, and ligand knowledge base	Free
PharmVar	Pharmacogene Variation Consortium — pharmacogenomic variant alleles for CYP enzymes	API Key
PharmGKB (CPIC)	CPIC pharmacogenomics knowledge base — drug-gene pairs, clinical guidelines, and pharmacogenomic recommendations	Free
PhyloT	PhyloT — taxonomy-based phylogenetic tree generation from NCBI taxon IDs	Free
pkCSM	pkCSM pharmacokinetics and toxicity prediction using graph-based signatures	Free
Planteome	Planteome — plant trait ontologies and gene annotations for plant biology	Free
PlasmoDB	VEuPathDB resource for Plasmodium (malaria parasite) genomics	Free
PomBase	S. pombe genome database — fission yeast genetics and genomics	Free
PRIDE	PRIDE proteomics archive — mass spectrometry proteomics data repository	Free
Progenetix	Cancer genomics with copy number variation data across tumor types	Free
ProteomeXchange	Centralized proteomics dataset repository linking PRIDE, MassIVE, and other archives	Free
PubChem	Open chemistry database with compound, substance, and bioassay data	Free
PubMed	Biomedical literature search engine (NCBI)	Free
PubTator	PubTator3 biomedical text mining — named entity recognition and annotation of PubMed articles	Free
QuickGO	Gene Ontology browser — fast access to GO term information (EBI)	Free
RCSB PDB	Protein Data Bank — 3D structural data for biological macromolecules	Free
Reactome	Curated biological pathway and reaction database	Free
RegulomeDB	RegulomeDB — annotate and score regulatory variants in the human genome	Free
Rfam	Database of non-coding RNA families and structured RNA elements	Free
Rhea	Expert-curated knowledgebase of biochemical reactions	Free
RNAcentral	RNAcentral — comprehensive non-coding RNA sequence database	Free
ROR	Research Organization Registry — identifying research institutions worldwide	Free
RxNorm	NLM drug terminology for normalized drug names and interactions	Free
SABIO-RK	SABIO-RK enzyme kinetics database — reaction kinetics data and parameters	Free
Semantic Scholar	Semantic Scholar academic paper search — find research papers, citations, and author information	API Key
SGD	Saccharomyces Genome Database — yeast genomics	Free
SigCom LINCS	Signatures of perturbation from the LINCS L1000 gene expression project	Free
SignalP 6.0	SignalP 6.0 — signal peptide prediction for protein sequences (DTU BioLib)	Free
SIGNOR	SIGNOR — signaling network open resource for causal interactions in signaling pathways	Free
Single Cell Portal	Broad Institute Single Cell Portal — explore and share single-cell genomics studies	Free
SNOMED CT	SNOMED CT clinical terminology via FHIR terminology server — look up and search clinical concepts	Free
STITCH	STITCH chemical-protein interaction database — sister project of STRING	Free
STRING	Protein-protein interaction network database	Free
SureChEMBL	Patent chemistry database linking chemical structures to patent documents	Free
SwissADME	SwissADME drug-likeness and pharmacokinetics prediction tool	Free
SWISS-MODEL	SWISS-MODEL Repository — homology models and 3D protein structure predictions	Free
SwissLipids	SwissLipids — curated knowledge resource for lipid biology and lipidomics	Free
TargetMine	Integrated data warehouse for drug target prioritization and biomarker discovery	Free
TCIA	The Cancer Imaging Archive — public access to cancer medical imaging data and collections	Free
TimeTree	TimeTree — divergence time estimates between species pairs	Free
ToxCast	EPA ToxCast high-throughput toxicity assay screening data	Free
ToxoDB	VEuPathDB resource for Toxoplasma gondii and related apicomplexan genomics	Free
TriTrypDB	VEuPathDB resource for trypanosomatid genomics (Trypanosoma, Leishmania)	Free
UCSC Genome Browser	UCSC Genome Browser — genome assemblies, annotations, and track data	Free
UCSC Genome Browser API	Programmatic access to genome search, sequences, tracks, and browser data	Free
UMLS	Unified Medical Language System — biomedical concepts, terminology crosswalk, and semantic network	API Key
UniCarb-DB	UniCarb-DB — glycan structure database with experimentally determined carbohydrate structures	Free
UniChem	UniChem compound cross-referencing — map chemical identifiers across databases	Free
UniParc	UniProt Archive — comprehensive non-redundant protein sequence archive	Free
UniProt	Universal Protein Resource — protein sequence and functional information	Free
UniRef	UniProt Reference Clusters — clustered sets of related protein sequences	Free
USDA NASS	USDA National Agricultural Statistics Service — US crop, livestock, and agricultural census data	API Key
VDJdb	VDJdb — curated database of T-cell receptor sequences and specificities	Free
VEuPathDB	Eukaryotic pathogen genomics — Plasmodium, Toxoplasma, Cryptosporidium, and more	API Key
VertNet	VertNet — vertebrate specimen records from natural history collections worldwide	Free
WHO Global Health Observatory	WHO Global Health Observatory — global health indicators, statistics, and country-level health data	Free
WHO ICD-11	WHO ICD-11 International Classification of Diseases — search and retrieve disease classifications	API Key
Wikidata	Wikidata SPARQL endpoint — structured knowledge base for genes, proteins, diseases, drugs, and species	Free
WikiPathways	Open biological pathway database — community-curated pathway data	Free
WormBase	WormBase C. elegans and nematode genomics via the Alliance of Genome Resources API	Free
WoRMS	World Register of Marine Species — authoritative classification and nomenclature of marine organisms	Free
Zenodo	Open research data repository hosted by CERN — datasets, software, and publications	Free
ZFIN	ZFIN Zebrafish Information Network — zebrafish genomics, genetics, and phenotype data	Free
ZINC	Free database of commercially available compounds for virtual screening	Free
Zooma	EBI annotation tool mapping free text to ontology terms	Free

Example Queries

Beginner

Domain	Role	Category	Query
Clinical Genetics	Medical Resident	Variant lookup	I have a patient with a novel LDLR variant (c.2054C>T) — what does ClinVar say about its pathogenicity, and what's the population allele frequency in gnomAD?
Pharmacogenomics	Clinical Pharmacist	Drug dosing	A patient is a CYP2D6 poor metabolizer — should I adjust the dose for vortioxetine? Check PharmGKB for CPIC guidelines and DailyMed for label language.
Rare Disease	Genetic Counselor	Disease lookup	A family reports a diagnosis of Stargardt disease — what's the inheritance pattern and causative genes? Look in Orphanet and GARD.
Drug Safety	Public Health Analyst	Adverse events	Are there emerging safety signals for semaglutide related to thyroid neoplasms? Check openFDA FAERS data and Europe PMC for recent publications.
Conservation	Conservation Volunteer	Range mapping	Show me the distribution of American pika (Ochotona princeps) observations from iNaturalist and their current IUCN Red List status.
Ecology	Birdwatcher	Migration tracking	Where has the Arctic tern (Sterna paradisaea) been reported in eBird during the last migration season?
Structural Biology	Graduate Student	Protein disorder	What is the experimentally determined structure of FUS protein in PDB, and does AlphaFold predict any low-confidence disordered regions?
Metabolomics	Research Technician	Metabolite ID	What are the known biological roles and pathway associations of sphingosine-1-phosphate in HMDB and LIPID MAPS?
Cancer Genomics	Clinical Research Coordinator	Mutation landscape	What are the most common EGFR mutations in lung adenocarcinoma in cBioPortal, and which ones are clinically actionable in OncoKB?
Synthetic Biology	Synthetic Biology Engineer	Parts registry	Find commonly used promoter parts in the iGEM Registry for E. coli protein expression systems.
Transcriptomics	Bioinformatics Analyst	Gene expression	What is the tissue-specific expression pattern of the CLOCK gene across human organs in GTEx and Human Protein Atlas?
Agriculture	Agricultural Extension Officer	Crop statistics	What are the global rice production trends over the last 20 years from FAOSTAT, and how do they correlate with USDA NASS data for US production?

Intermediate

Domain	Role	Category	Query
Clinical Genetics	Clinical Geneticist	VUS interpretation	I found a VUS in SCN5A (p.Arg1632His) in a patient with suspected long QT syndrome — cross-reference ClinVar, ClinGen gene-disease validity, gnomAD constraint metrics, and Ensembl VEP functional predictions. Is this likely pathogenic?
Pharmacogenomics	Oncology Pharmacist	Dose adjustment	Patient with metastatic colorectal cancer is DPYD heterozygous (c.1905+1G>A) — what fluoropyrimidine dose adjustments does CPIC recommend via PharmGKB, and are there alternative regimens listed in ClinicalTrials.gov?
Rare Disease	Rare Disease Specialist	Diagnostic odyssey	A 3-year-old with developmental delay, hypotonia, and abnormal eye movements — query HPO for matching phenotypes, then cross-reference candidate genes in Monarch Initiative, OMIM, and check if GTR lists available clinical testing panels.
Public Health	Cardiologist	Polygenic risk	A patient's direct-to-consumer test shows elevated polygenic risk score for coronary artery disease — validate the PRS model in PGS Catalog, check if DisGeNET has updated gene-CAD associations, and review ClinicalTrials.gov for prevention trials enrolling based on genetic risk.
Ecology	Invasion Ecologist	Invasive tracking	Compare historical and current distribution of spotted lanternfly (Lycorma delicatula) using GBIF and iNaturalist, and identify potential agricultural impacts from USDA NASS crop regions.
Conservation	Pollinator Biologist	Decline analysis	Analyze citizen-science trends for rusty patched bumble bee (Bombus affinis) from GBIF and iNaturalist, cross-reference with IUCN Red List status changes and US corn production areas from USDA NASS.
Marine Biology	Fisheries Analyst	Stock assessment	Compare Atlantic cod (Gadus morhua) occurrence data from OBIS and FishBase life-history traits with IUCN threat assessments and recent genomic diversity from NCBI SRA.
Wildlife Management	Wildlife Corridor Planner	Connectivity genetics	Map jaguar (Panthera onca) observations from VertNet and GBIF, overlay with Movebank GPS tracking data, and assess genetic connectivity using BOLD barcode clusters.
Structural Biology	Structural Biologist	Integrative modeling	For the nuclear pore complex protein NUP98, compare its experimentally determined structures in PDB with AlphaFold predictions and identify intrinsically disordered regions using DisProt and MobiDB.
Systems Biology	Systems Biologist	Network analysis	What are the protein-protein interaction partners of GPX4 in STRING and IntAct, and which metabolic pathways from KEGG and Reactome are enriched among these interactors relevant to ferroptosis?
Single Cell	Single-Cell Analyst	Cell type markers	Using CELLxGENE and Human Cell Atlas, identify marker genes for oligodendrocyte precursor cells in human brain, then validate their expression specificity across tissues in GTEx and Bgee.
Cancer Genomics	Translational Oncologist	Biomarker validation	Identify actionable BRCA1/BRCA2 alterations across ovarian cancer cohorts in GDC and cBioPortal, then cross-reference with FDA-approved PARP inhibitors in DGIdb and clinical trial outcomes in ClinicalTrials.gov.
Drug Discovery	Medicinal Chemist	PROTAC design	For the SMARCA4 target, retrieve binding ligands from ChEMBL, predict ADME properties using SwissADME and pkCSM, and identify E3 ligase recruiters from BindingDB to design a PROTAC degrader.
Immunology	CAR-T Therapy Developer	Antigen selection	Identify tumor-associated antigens overexpressed in glioblastoma from cBioPortal and DepMap, check for normal tissue expression in Pharos, and retrieve published CAR-T trials from ClinicalTrials.gov and Europe PMC.
Natural Products	Natural Products Chemist	Scaffold discovery	Search COCONUT and LOTUS for natural products with quinone scaffolds, classify their chemical ontology using ClassyFire, and identify analogs with known bioactivity in ChEMBL and PubChem.

Advanced

Domain	Role	Category	Query
Clinical Genetics	Precision Medicine Fellow	Complex interpretation	Patient with suspected mitochondrial disorder carries compound heterozygous POLG variants (c.2243G>C and c.2542G>A). Chain: ClinVar and ClinGen for pathogenicity, gnomAD for allele frequency and constraint, GTEx for POLG tissue expression, MyVariant.info for aggregated annotations, HPO for genotype-phenotype correlation with the patient's seizures and ataxia, and PubMed and Europe PMC for case reports of these specific variants.
Drug Safety	Pharmacovigilance Scientist	Signal investigation	Investigating post-marketing immune-mediated adverse events with tofacitinib — openFDA FAERS for disproportionality analysis, DailyMed for current label warnings, FDA Orange Book for formulation differences, ClinicalTrials.gov for ongoing safety studies, PharmGKB for pharmacogenomic associations with JAK inhibitor toxicity, EpiGraphDB for causal inference, and SNOMED CT and ICD-11 for standardized adverse event coding.
Rare Disease	Rare Disease Diagnostician	Multi-system disorder	Adult patient with progressive ataxia, peripheral neuropathy, and hypogonadism — HPO phenotype matching for candidate genes, filter by ClinGen gene-disease validity, cross-reference OMIM for overlap syndromes, check GTR for available testing, review MalaCards comorbidity patterns, query DisGeNET gene-phenotype networks, search Europe PMC for atypical presentations, and verify ICD-11 coding for research cohort identification.
Ecology	Climate Change Ecologist	Range shift modeling	Identify northward range shifts in American beech (Fagus grandifolia) by comparing GBIF occurrence records over 50 years, integrate Planteome trait data, correlate with USDA NASS forest health surveys, and assess evolutionary capacity using TimeTree divergence and NCBI SRA population genomics.
Marine Biology	Marine Conservation Geneticist	Deep-sea biodiversity	Characterize genetic diversity of newly discovered hydrothermal vent species by integrating OBIS occurrence records, WoRMS taxonomic validation, AquaMaps habitat models, BOLD DNA barcodes, NCBI SRA metagenomic surveys, and phylogenetic placement using Open Tree of Life.
Agriculture	Agricultural Genomics Researcher	Pest resistance	Investigate fall armyworm (Spodoptera frugiperda) resistance evolution by combining GBIF invasion pathways, NCBI Taxonomy strain classification, NCBI SRA Bt-resistance genomics, BOLD haplotype networks, FAOSTAT maize loss data, and MaizeGDB resistance gene orthologs.
Structural Biology	Principal Investigator	Phase separation	For the RNA-binding protein TDP-43, integrate PDB structures, AlphaFold predictions, and DisProt disorder annotations to map its prion-like domain. Then use RNAcentral and ENCODE to identify its RNA targets, cross-reference with Rfam for structured RNA elements, and analyze enriched RNA-binding motifs from JASPAR to understand its role in stress granule formation.
Proteomics	Mitochondrial Biologist	Organellar proteomics	Compile the human mitochondrial proteome using UniProt with DeepLoc and SignalP predictions for targeting sequences. Cross-reference with PRIDE for experimentally detected proteins, map interaction networks in Complex Portal and STRING, identify metabolic enzymes and reactions in SABIO-RK and BiGG Models, then analyze pathway enrichment using Reactome and g:Profiler.
Cancer Genomics	Precision Oncology Scientist	Synthetic lethality	Identify synthetic lethal interactions for IDH1-mutant gliomas using DepMap CRISPR screens, cross-reference with genomic co-occurrence patterns in GDC and Progenetix, validate targets with existing small molecules in ChEMBL and BindingDB, assess druggability via Pharos, and retrieve preclinical evidence from Europe PMC and bioRxiv.
Drug Discovery	ADC Scientist	ADC engineering	For Trop-2 positive triple-negative breast cancer — retrieve tumor expression from cBioPortal and GDC, identify payload candidates from ChEMBL and ZINC with cytotoxic mechanisms in DGIdb, assess linker chemistry using ClassyFire and pkCSM, validate internalization via Open Targets and Pharos, and compile ADC clinical trials from ClinicalTrials.gov.
Immunology	Immunotherapy Researcher	Neoantigen pipeline	Build a neoantigen prioritization pipeline for microsatellite-stable colorectal cancer — extract somatic mutations from GDC, predict MHC-I and MHC-II binding using NetMHCpan and NetMHCIIpan, cross-reference patient HLA types with IPD-IMGT/HLA, validate immunogenicity with IEDB, check TCR repertoire coverage in VDJdb and AIRR Data Commons, and review vaccine trial outcomes in ClinicalTrials.gov.
Cheminformatics	AI-Driven Drug Designer	De novo validation	Validate AI-generated molecules targeting BTK for autoimmune disease — check structural novelty against PubChem, ZINC, and SureChEMBL patents, predict binding affinity using ChEMBL SAR data, assess ADMET with SwissADME and pkCSM, identify off-target risks via Pharos and BindingDB, retrieve BTK pathway biology from Open Targets and KEGG, and survey the competitive landscape in FDA Orange Book and ClinicalTrials.gov.

License

MIT — see LICENSE.

life-science-mcp