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Conduit

mcp server

scikit

A unified life science data layer for your AI agents - genomics, proteomics, drug discovery, clinical trials across 300+ databases.

achillesrasquinha/scikitcommunitylistedunreviewed
Use tool

Set up

Runs on your computer. Pick your agent and operating system.

Before you start

  • Node.js 20 or newer
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "scikit": {
      "command": "npx",
      "args": [
        "-y",
        "biorouter"
      ]
    }
  }
}

same format Cursor, GitHub Copilot CLI, Junie, JetBrains AI Assistant, Augment (Auggie CLI), Factory Droid, Kiro, Devin CLI +12

Values in angle brackets are placeholders. Restart Claude Desktop after editing its config.Claude Desktop docs

README

synced Oct 23, 2026

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.

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

Providers (299)

ProviderDescriptionAuth
1000 Genomes (IGSR)International Genome Sample Resource — population genomics data from the 1000 Genomes ProjectFree
AddgeneAddgene — nonprofit plasmid repository for sharing molecular biology reagentsFree
AIRR Data CommonsAIRR Data Commons — adaptive immune receptor repertoire sequencing dataFree
Alliance of Genome ResourcesUnified portal for model organism genes, diseases, and orthologsFree
Allen Brain AtlasAllen Institute brain gene expression and connectivity dataFree
AmoebaDBVEuPathDB resource for Entamoeba and free-living amoeba genomicsFree
AlphaFold DBAI-predicted protein structures from DeepMindFree
AquaMapsAquaMaps — predicted species distribution maps for marine and freshwater organismsFree
ArrayExpressArrayExpress — gene expression and functional genomics experiments archive (EBI BioStudies)Free
ATC ClassificationATC (Anatomical Therapeutic Chemical) drug classification via RxNav/RxClass APIFree
BERN2BERN2 biomedical named entity recognition — extract genes, diseases, drugs, and other entities from textFree
BgeeGene expression evolution database — expression across species and tissuesFree
BiGG ModelsBiGG Models — genome-scale metabolic network reconstructionsFree
BindingDBPublic database of measured binding affinities between proteins and drug-like moleculesFree
BioCycBioCyc / MetaCyc — metabolic pathway and genome database collectionFree
BioregistryBioregistry — registry of 1000+ biological databases with identifier patterns and metadataFree
BioStudiesBioStudies — EBI archive for biological study data linking publications to datasetsFree
bio.toolsELIXIR bio.tools registry — bioinformatics tools and databases catalogFree
BioGRIDBioGRID database of protein and genetic interactionsAPI Key
BioModelsBioModels repository — mathematical models of biological systems in SBML and other formatsFree
BioPortalNCBO BioPortal — search 900+ biomedical ontologies and annotate text with ontology conceptsAPI Key
bioRxivbioRxiv preprint server — access preprints in biology and related sciencesFree
BMRBBiological Magnetic Resonance Bank — NMR spectroscopy data for proteins, nucleic acids, and metabolitesFree
BioSamplesEBI BioSamples database — biological sample metadata and attributesFree
BOLDBarcode of Life Data Systems — DNA barcode specimens and sequences for species identificationFree
BrainSpanBrainSpan developmental transcriptome — human brain gene expression across developmental stagesFree
BV-BRCBacterial and Viral Bioinformatics Resource Center — pathogen genomics, AMR, and surveillance dataFree
CADDCombined Annotation Dependent Depletion — variant deleteriousness scoringFree
CATHProtein structure classification — hierarchical domain classification of protein structuresFree
Catalogue of LifeCatalogue of Life — global checklist of all known species with authoritative taxonomyFree
cBioPortalCancer genomics portal — explore multidimensional cancer genomics dataFree
CDC Open DataCDC Open Data — public health datasets via the Socrata Open Data APIFree
CDC WONDERCDC WONDER — Wide-ranging Online Data for Epidemiologic Research, public health datasetsFree
CDDNCBI Conserved Domain Database — identify conserved domains in protein sequencesFree
CellosaurusKnowledge resource on cell lines — cell line identification and characterizationFree
CELLxGENECZ CELLxGENE Discover — single-cell datasets and gene expressionFree
ChEBI (via OLS4)Chemical Entities of Biological Interest — ontology lookup via EBI OLS4Free
ChEMBLDatabase of bioactive drug-like small moleculesFree
ChemSpiderRSC chemical compound search, structures, and properties databaseAPI Key
CIViCClinical Interpretations of Variants in Cancer — curated clinical evidence for variantsFree
ClassyFireAutomated chemical classification using the ChemOnt ontologyFree
ClinGenClinical Genome Resource — gene-disease validity and dosage sensitivity curationFree
ClinGen Allele RegistryClinGen Allele Registry — canonical allele identifiers linking variants across nomenclaturesFree
NLM Clinical TablesNLM Clinical Tables — autocomplete and lookup for ICD-10, LOINC, RxTerms, and conditionsFree
ClinicalTrials.govRegistry of clinical studies conducted around the worldFree
ClinVarVariant-disease relationship database linking genetic variants to clinical significanceFree
Clustal OmegaEBI Clustal Omega multiple sequence alignment serviceFree
COGClusters of Orthologous Genes — ortholog classification and functional annotation across prokaryotesFree
COCONUTCOlleCtion of Open Natural prodUcTs — comprehensive natural products databaseFree
Complex PortalMacromolecular complex database — curated stable protein complexes from EBIFree
Comparative Toxicogenomics DatabaseCTD curated chemical-gene-disease interactions for toxicogenomics researchFree
CompToxEPA CompTox Chemicals Dashboard for toxicology and chemical safetyFree
CrossrefCrossref — scholarly metadata for publications, journals, funders, and DOIsFree
CryptoDBVEuPathDB resource for Cryptosporidium genomicsFree
DailyMedDailyMed drug label information from the National Library of Medicine — SPL documents and prescribing informationFree
DataCiteDataCite — DOI registration and metadata for research datasets and publicationsFree
DALIDALI server — protein structure comparison by 3D alignmentFree
DANDI ArchiveDANDI — neurophysiology data integration, brain imaging and electrophysiology datasetsFree
dbGaPdbGaP (database of Genotypes and Phenotypes) — genotype-phenotype association studiesFree
dbSNPDatabase of single nucleotide polymorphisms and other genetic variationFree
dbVarNCBI dbVar — database of genomic structural variants (CNVs, insertions, deletions, inversions)Free
DDBJDNA Data Bank of Japan — nucleotide sequence archiveFree
dbfetchEBI dbfetch — sequence and entry retrieval from EMBL, UniProt, PDB, and 50+ databasesFree
DeepLoc 2.0DeepLoc 2.0 — protein subcellular localization prediction (DTU BioLib)Free
DepMapCancer Dependency Map — cell line genomic and dependency dataFree
DGIdbDrug-Gene Interaction Database — mining drug-gene interaction dataFree
DisGeNETGene-disease association databaseAPI Key
DisProtDatabase of intrinsically disordered proteins and regionsFree
DOAJDirectory of Open Access Journals — indexing quality open access researchFree
DrugCentralDrug information resource integrating drug indications, mechanisms, and interactionsFree
eBirdCornell Lab eBird — bird observations, hotspots, and taxonomy worldwideAPI Key
EBI SearchEBI Search — unified search across 400+ EBI databases (UniProt, PDB, SRA, etc.)Free
EggNOGOrthologous groups and functional annotation from EggNOGFree
EMDBElectron Microscopy Data Bank — 3D cryo-EM density maps and tomogramsFree
EMPIARElectron Microscopy Public Image Archive for raw EM dataFree
ENCODE SCREENENCODE SCREEN registry of candidate cis-regulatory elements (cCREs)Free
ENCODEEncyclopedia of DNA Elements — functional annotations of the human genomeFree
EnrichrEnrichr — gene set enrichment analysis against curated gene-set librariesFree
Ensembl BioMartEnsembl BioMart bulk annotation and data retrieval serviceFree
Ensembl VEPVariant Effect Predictor — predict functional effects of genetic variantsFree
ENA PortalENA Portal API — advanced search across ENA studies, samples, experiments, and assembliesFree
ENA TaxonomyEBI ENA Taxonomy — taxonomic classification lookup with lineage and common namesFree
EnsemblGenome browser and annotation databaseFree
ELMEukaryotic Linear Motifs — short functional motifs in proteins (cleavage sites, binding motifs, etc.)Free
EpiGraphDBEpiGraphDB — epidemiological graph database for Mendelian randomization and causal inferenceFree
EU Clinical Trials RegisterEuropean Union Clinical Trials Register for searching EU clinical studiesFree
European Variation ArchiveEuropean Variation Archive — open-access database of genetic variants across speciesFree
Europe PMCEurope PubMed Central — open-access biomedical literatureFree
Europe PMC AnnotationsText-mined named entities (genes, diseases, GO terms) from publicationsFree
European Genome-phenome ArchiveEGA metadata API for controlled-access genomic and phenomic datasetsFree
European Nucleotide ArchiveOpen-access nucleotide sequence data and associated informationFree
Expression AtlasGene expression patterns across species and biological conditions (EBI)Free
FAOSTATFAO Statistics — food and agriculture data from the UN FAOFree
FDA Orange BookFDA Orange Book drug patent and exclusivity data via openFDAFree
FHIR R4FHIR R4 public test server — HL7 FHIR standard for healthcare data interoperabilityFree
FishBaseFishBase — comprehensive database of fish species biology, ecology, and taxonomyFree
FlyBaseFlyBase — Drosophila melanogaster genomics, genetics, and molecular biologyFree
FlyMineInterMine data warehouse for Drosophila genomics, orthologs, and interactionsFree
FungiDBVEuPathDB resource for fungal genomics (Aspergillus, Candida, Cryptococcus)Free
g:Profilerg:Profiler — functional enrichment and gene ID conversionFree
GARDGARD — Genetic and Rare Diseases Information Center from NIHFree
GBIFGlobal Biodiversity Information Facility — species occurrence and taxonomy data worldwideFree
GDCNCI Genomic Data Commons — cancer genomics data from TCGA and other programsFree
GeneshotGeneshot — gene set discovery from PubMed literature mining (Ma'ayan Lab)Free
Gene Expression OmnibusRepository of high-throughput gene expression and genomics datasetsFree
Gene OntologyGene Ontology API — GO terms, annotations, and bioentity informationFree
GeneMANIAGeneMANIA — gene interaction network prediction and visualizationFree
GlyCosmosGlyCosmos — integrated glycoscience portal for glycan structures, pathways, and diseasesFree
GlyGenGlyGen — glycoscience data integration and retrievalFree
GlyTouCanGlyTouCan — international glycan structure repositoryFree
gnomADGenome Aggregation Database — population variant frequencies and annotationsFree
GNPSGNPS — molecular networking and spectral library for mass spectrometry dataFree
GPCRdbGPCR database — G protein-coupled receptor structures, sequences, and pharmacologyFree
GrameneGramene — comparative plant genomics resource for crops and model speciesFree
GTEx PortalGenotype-Tissue Expression project — gene expression across human tissuesFree
GTDBGenome Taxonomy Database — standardized bacterial and archaeal taxonomy based on genome phylogenyFree
Guide to PharmacologyIUPHAR/BPS Guide to Pharmacology database of drug targets and ligandsFree
GWAS CatalogNHGRI-EBI Catalog of genome-wide association studiesFree
HarmonizomeUnified access to 177 datasets of gene and protein knowledge from Ma'ayan LabFree
HGNCHUGO Gene Nomenclature Committee — approved human gene symbols and namesFree
HMMERHMMER protein sequence search using profile hidden Markov modelsFree
HostDBVEuPathDB resource for host response to pathogens (human, mouse, macaque)Free
Human Cell AtlasHuman Cell Atlas data portal — single-cell genomics projects and datasetsFree
HuBMAPHuman BioMolecular Atlas Program — atlas of human body at single-cell resolutionFree
HumanMineInterMine data warehouse for human genomics, disease, and interactionsFree
Human Metabolome DatabaseHMDB — comprehensive human metabolite and biomarker databaseFree
Human Phenotype OntologyHuman Phenotype Ontology — standardized vocabulary of human phenotypic abnormalitiesFree
Human Protein AtlasHuman protein expression and localization data across tissues and cell typesFree
I-TASSERI-TASSER — protein structure and function prediction server (Zhang Lab)Free
IEDBImmune Epitope Database — curated epitope data for immune researchFree
iGEM RegistryiGEM Registry of Standard Biological Parts — synthetic biology parts catalogFree
IGVFIGVF — Impact of Genomic Variation on Function consortium data portalFree
IHECInternational Human Epigenome Consortium — reference epigenome datasets and metadataFree
ImmPortImmunology Database and Analysis Portal — shared immunology dataFree
IMPCInternational Mouse Phenotyping Consortium — phenotype data for knockout mouse linesFree
iNaturalistiNaturalist — citizen-science biodiversity observations and taxa worldwideFree
IntActMolecular interaction database — curated protein-protein interactionsFree
InterProProtein families, domains, and functional sites classificationFree
IPD-IMGT/HLAIPD-IMGT/HLA allele database — HLA allele sequences, nomenclature, and immunogenetics dataFree
iPTMnetiPTMnet — post-translational modification (PTM) knowledge base for proteinsFree
ITISIntegrated Taxonomic Information System — authoritative taxonomic information for plants, animals, fungi, and microbesFree
iTOLiTOL Interactive Tree of Life — phylogenetic tree upload, annotation, and exportFree
IUCN Red ListIUCN Red List of Threatened Species — conservation status for 150,000+ speciesAPI Key
JASPARJASPAR — open-access database of transcription factor binding profilesFree
KEGGKyoto Encyclopedia of Genes and Genomes — pathway and molecular interaction databaseFree
LegumeMineInterMine for legume genomics — soybean, common bean, and other legumesFree
LIPID MAPSLIPID MAPS Structure Database for lipid classification and structuresFree
LOINCLOINC clinical terminology — standardized codes for lab tests, clinical observations, and measurements via FHIRAPI Key
LOTUSNatural products database — open knowledge on natural compounds and their biological sourcesFree
MaizeGDBMaizeGDB — maize genetics and genomics database for corn researchFree
MalaCardsMalaCards — human disease database integrating gene, variant, and pathway dataFree
MassBankPublic repository of mass spectra for metabolite identificationFree
MeSHMedical Subject Headings vocabulary for indexing biomedical literatureFree
MetaboLightsEMBL-EBI database for metabolomics experiments and derived informationFree
MetExploreMetExplore — metabolic network analysis platform with 349 organism modelsFree
Metabolomics WorkbenchMetabolomics Workbench — metabolomics data repository and metadataFree
METLINMETLIN metabolite mass spectrometry database for metabolomics researchAPI Key
MG-RASTMG-RAST — metagenomics analysis and annotation server for microbiome datasetsFree
MGnifyMGnify — EBI metagenomics analysis and archiving platformFree
MicrobiomeDBMicrobiomeDB — microbiome study data including taxonomic and functional profilingFree
MobiDBProtein disorder and mobility annotationsFree
ModelSEEDModelSEED — automated metabolic model reconstruction and biochemistry databaseFree
Monarch InitiativeKnowledge graph integrating biological and clinical data for disease discoveryFree
MovebankMovebank — animal tracking and movement data from global research studiesFree
MSigDBMolecular Signatures Database — curated gene set collections for enrichment analysisFree
MyChem.infoChemical and drug annotation query service — aggregates compound data from multiple sourcesFree
MyDisease.infoDisease annotation query service — aggregates disease data from multiple sourcesFree
MyGene.infoGene annotation query service — aggregated gene info from multiple sourcesFree
MyGeneset.infoGene set query service — curated and community gene setsFree
MyVariant.infoVariant annotation query service — aggregates genetic variant data from multiple sourcesFree
RENCI Name ResolutionTranslator service mapping text labels to biomedical CURIEsFree
NASA OSDRNASA Open Science Data Repository — space biology and radiation genomics datasetsFree
Natural Products AtlasDatabase of microbially-derived natural products for drug discoveryFree
NatureServeNatureServe Explorer — conservation status and biodiversity data for species across the AmericasAPI Key
NCBI BioSampleDatabase of biological sample metadata used in experimental assaysFree
NCBI BLASTNCBI BLAST sequence similarity search — submit queries and retrieve alignment resultsFree
NCBI DatasetsNCBI Datasets API v2 — modern REST interface for genes, genomes, and taxonomyFree
NCBI GeneGene-specific information from NCBI Entrez Gene databaseFree
NCBI NucleotideGenBank and RefSeq nucleotide sequence databaseFree
NCBI ProteinProtein sequence database including RefSeq, UniProt, and PDB sequencesFree
NCBI SRASequence Read Archive — raw sequencing data repositoryFree
NCBI TaxonomyTaxonomic classification and nomenclature databaseFree
NCBO AnnotatorNCBO Annotator — annotate biomedical text with ontology concepts and get ontology recommendationsAPI Key
NCI Chemical Identifier ResolverNCI CADD Chemical Identifier Resolver — convert between chemical names, SMILES, InChI, and other formatsFree
NDExNDEx Network Data Exchange for biological network modelsFree
NextstrainReal-time tracking of pathogen evolution for influenza, SARS-CoV-2, and other virusesFree
NMDCNational Microbiome Data Collaborative — integrated microbiome multi-omics dataFree
RENCI Node NormalizationTranslator service normalizing CURIEs to canonical identifiersFree
NetMHCIIpanNetMHCIIpan 4.3 — MHC class II binding prediction for peptides across HLA-DR/DP/DQ allelesFree
NetMHCpanNetMHCpan 4.1 — MHC class I binding prediction for peptides across HLA allelesFree
OBISOcean Biodiversity Information System — marine species occurrence and distribution dataFree
OBO FoundryRegistry of 267 interoperable biomedical ontologies (GO, HPO, ChEBI, etc.)Free
OLSOntology Lookup Service — search and browse biomedical ontologies (GO, EFO, HPO, etc.)Free
OMAOrthologous Matrix — comprehensive ortholog databaseFree
OMIMOnline Mendelian Inheritance in Man — catalog of human genes and genetic disordersAPI Key
OntobeeOntology term search and browsing across OBO and OWL ontologiesFree
OmniPathOmniPath — comprehensive signaling network and enzyme-substrate interactionsFree
OncoTreeMSK Cancer Classification — standardized cancer type taxonomy and hierarchyFree
OneZoomOneZoom tree of life explorer — interactive visualization and species search across the tree of lifeFree
Open TargetsDrug target identification and prioritization platformFree
Open Tree of LifeOpen Tree of Life — comprehensive phylogenetic tree and taxonomy synthesisFree
OpenAlexOpenAlex — open catalog of scholarly works, authors, institutions, and conceptsFree
OpenCitationsOpenCitations COCI citation index — open bibliographic citation data for DOIsFree
openFDAOpen-access FDA data on drugs, devices, and foods including adverse eventsFree
ORCIDORCID — persistent researcher identifiers linking authors to works and affiliationsFree
OrphanetOrphanet — reference portal for rare diseases and orphan drugsFree
OrthoDBHierarchical catalog of orthologs — gene evolutionary relationshipsFree
PANTHERPANTHER — protein classification, gene ontology, and phylogenetic analysisFree
Pathway CommonsIntegrated biological pathway and interaction data from multiple sourcesFree
PDBeProtein Data Bank in Europe — macromolecular structure dataFree
PDBe Graph APIPDBe Graph API — compounds, protein mappings, and molecule details from PDBFree
PDBjProtein Data Bank Japan — PDB search, SQL queries, and chemical component lookupFree
PGS CatalogPolygenic Score Catalog — risk prediction scores and trait associationsFree
Proteomic Data CommonsNCI Proteomic Data Commons — proteomics data from cancer research studiesFree
PeptideAtlasPeptideAtlas — proteomics data repository for peptide and protein identificationsFree
PfamPfam protein families database — protein domain classification via InterProFree
PharosIlluminating the Druggable Genome — comprehensive target, disease, and ligand knowledge baseFree
PharmVarPharmacogene Variation Consortium — pharmacogenomic variant alleles for CYP enzymesAPI Key
PharmGKB (CPIC)CPIC pharmacogenomics knowledge base — drug-gene pairs, clinical guidelines, and pharmacogenomic recommendationsFree
PhyloTPhyloT — taxonomy-based phylogenetic tree generation from NCBI taxon IDsFree
pkCSMpkCSM pharmacokinetics and toxicity prediction using graph-based signaturesFree
PlanteomePlanteome — plant trait ontologies and gene annotations for plant biologyFree
PlasmoDBVEuPathDB resource for Plasmodium (malaria parasite) genomicsFree
PomBaseS. pombe genome database — fission yeast genetics and genomicsFree
PRIDEPRIDE proteomics archive — mass spectrometry proteomics data repositoryFree
ProgenetixCancer genomics with copy number variation data across tumor typesFree
ProteomeXchangeCentralized proteomics dataset repository linking PRIDE, MassIVE, and other archivesFree
PubChemOpen chemistry database with compound, substance, and bioassay dataFree
PubMedBiomedical literature search engine (NCBI)Free
PubTatorPubTator3 biomedical text mining — named entity recognition and annotation of PubMed articlesFree
QuickGOGene Ontology browser — fast access to GO term information (EBI)Free
RCSB PDBProtein Data Bank — 3D structural data for biological macromoleculesFree
ReactomeCurated biological pathway and reaction databaseFree
RegulomeDBRegulomeDB — annotate and score regulatory variants in the human genomeFree
RfamDatabase of non-coding RNA families and structured RNA elementsFree
RheaExpert-curated knowledgebase of biochemical reactionsFree
RNAcentralRNAcentral — comprehensive non-coding RNA sequence databaseFree
RORResearch Organization Registry — identifying research institutions worldwideFree
RxNormNLM drug terminology for normalized drug names and interactionsFree
SABIO-RKSABIO-RK enzyme kinetics database — reaction kinetics data and parametersFree
Semantic ScholarSemantic Scholar academic paper search — find research papers, citations, and author informationAPI Key
SGDSaccharomyces Genome Database — yeast genomicsFree
SigCom LINCSSignatures of perturbation from the LINCS L1000 gene expression projectFree
SignalP 6.0SignalP 6.0 — signal peptide prediction for protein sequences (DTU BioLib)Free
SIGNORSIGNOR — signaling network open resource for causal interactions in signaling pathwaysFree
Single Cell PortalBroad Institute Single Cell Portal — explore and share single-cell genomics studiesFree
SNOMED CTSNOMED CT clinical terminology via FHIR terminology server — look up and search clinical conceptsFree
STITCHSTITCH chemical-protein interaction database — sister project of STRINGFree
STRINGProtein-protein interaction network databaseFree
SureChEMBLPatent chemistry database linking chemical structures to patent documentsFree
SwissADMESwissADME drug-likeness and pharmacokinetics prediction toolFree
SWISS-MODELSWISS-MODEL Repository — homology models and 3D protein structure predictionsFree
SwissLipidsSwissLipids — curated knowledge resource for lipid biology and lipidomicsFree
TargetMineIntegrated data warehouse for drug target prioritization and biomarker discoveryFree
TCIAThe Cancer Imaging Archive — public access to cancer medical imaging data and collectionsFree
TimeTreeTimeTree — divergence time estimates between species pairsFree
ToxCastEPA ToxCast high-throughput toxicity assay screening dataFree
ToxoDBVEuPathDB resource for Toxoplasma gondii and related apicomplexan genomicsFree
TriTrypDBVEuPathDB resource for trypanosomatid genomics (Trypanosoma, Leishmania)Free
UCSC Genome BrowserUCSC Genome Browser — genome assemblies, annotations, and track dataFree
UCSC Genome Browser APIProgrammatic access to genome search, sequences, tracks, and browser dataFree
UMLSUnified Medical Language System — biomedical concepts, terminology crosswalk, and semantic networkAPI Key
UniCarb-DBUniCarb-DB — glycan structure database with experimentally determined carbohydrate structuresFree
UniChemUniChem compound cross-referencing — map chemical identifiers across databasesFree
UniParcUniProt Archive — comprehensive non-redundant protein sequence archiveFree
UniProtUniversal Protein Resource — protein sequence and functional informationFree
UniRefUniProt Reference Clusters — clustered sets of related protein sequencesFree
USDA NASSUSDA National Agricultural Statistics Service — US crop, livestock, and agricultural census dataAPI Key
VDJdbVDJdb — curated database of T-cell receptor sequences and specificitiesFree
VEuPathDBEukaryotic pathogen genomics — Plasmodium, Toxoplasma, Cryptosporidium, and moreAPI Key
VertNetVertNet — vertebrate specimen records from natural history collections worldwideFree
WHO Global Health ObservatoryWHO Global Health Observatory — global health indicators, statistics, and country-level health dataFree
WHO ICD-11WHO ICD-11 International Classification of Diseases — search and retrieve disease classificationsAPI Key
WikidataWikidata SPARQL endpoint — structured knowledge base for genes, proteins, diseases, drugs, and speciesFree
WikiPathwaysOpen biological pathway database — community-curated pathway dataFree
WormBaseWormBase C. elegans and nematode genomics via the Alliance of Genome Resources APIFree
WoRMSWorld Register of Marine Species — authoritative classification and nomenclature of marine organismsFree
ZenodoOpen research data repository hosted by CERN — datasets, software, and publicationsFree
ZFINZFIN Zebrafish Information Network — zebrafish genomics, genetics, and phenotype dataFree
ZINCFree database of commercially available compounds for virtual screeningFree
ZoomaEBI annotation tool mapping free text to ontology termsFree

Example Queries

Beginner

DomainRoleCategoryQuery
Clinical GeneticsMedical ResidentVariant lookupI 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?
PharmacogenomicsClinical PharmacistDrug dosingA patient is a CYP2D6 poor metabolizer — should I adjust the dose for vortioxetine? Check PharmGKB for CPIC guidelines and DailyMed for label language.
Rare DiseaseGenetic CounselorDisease lookupA family reports a diagnosis of Stargardt disease — what's the inheritance pattern and causative genes? Look in Orphanet and GARD.
Drug SafetyPublic Health AnalystAdverse eventsAre there emerging safety signals for semaglutide related to thyroid neoplasms? Check openFDA FAERS data and Europe PMC for recent publications.
ConservationConservation VolunteerRange mappingShow me the distribution of American pika (Ochotona princeps) observations from iNaturalist and their current IUCN Red List status.
EcologyBirdwatcherMigration trackingWhere has the Arctic tern (Sterna paradisaea) been reported in eBird during the last migration season?
Structural BiologyGraduate StudentProtein disorderWhat is the experimentally determined structure of FUS protein in PDB, and does AlphaFold predict any low-confidence disordered regions?
MetabolomicsResearch TechnicianMetabolite IDWhat are the known biological roles and pathway associations of sphingosine-1-phosphate in HMDB and LIPID MAPS?
Cancer GenomicsClinical Research CoordinatorMutation landscapeWhat are the most common EGFR mutations in lung adenocarcinoma in cBioPortal, and which ones are clinically actionable in OncoKB?
Synthetic BiologySynthetic Biology EngineerParts registryFind commonly used promoter parts in the iGEM Registry for E. coli protein expression systems.
TranscriptomicsBioinformatics AnalystGene expressionWhat is the tissue-specific expression pattern of the CLOCK gene across human organs in GTEx and Human Protein Atlas?
AgricultureAgricultural Extension OfficerCrop statisticsWhat 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

DomainRoleCategoryQuery
Clinical GeneticsClinical GeneticistVUS interpretationI 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?
PharmacogenomicsOncology PharmacistDose adjustmentPatient 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 DiseaseRare Disease SpecialistDiagnostic odysseyA 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 HealthCardiologistPolygenic riskA 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.
EcologyInvasion EcologistInvasive trackingCompare historical and current distribution of spotted lanternfly (Lycorma delicatula) using GBIF and iNaturalist, and identify potential agricultural impacts from USDA NASS crop regions.
ConservationPollinator BiologistDecline analysisAnalyze 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 BiologyFisheries AnalystStock assessmentCompare 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 ManagementWildlife Corridor PlannerConnectivity geneticsMap jaguar (Panthera onca) observations from VertNet and GBIF, overlay with Movebank GPS tracking data, and assess genetic connectivity using BOLD barcode clusters.
Structural BiologyStructural BiologistIntegrative modelingFor 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 BiologySystems BiologistNetwork analysisWhat 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 CellSingle-Cell AnalystCell type markersUsing 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 GenomicsTranslational OncologistBiomarker validationIdentify 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 DiscoveryMedicinal ChemistPROTAC designFor 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.
ImmunologyCAR-T Therapy DeveloperAntigen selectionIdentify 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 ProductsNatural Products ChemistScaffold discoverySearch 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

DomainRoleCategoryQuery
Clinical GeneticsPrecision Medicine FellowComplex interpretationPatient 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 SafetyPharmacovigilance ScientistSignal investigationInvestigating 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 DiseaseRare Disease DiagnosticianMulti-system disorderAdult 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.
EcologyClimate Change EcologistRange shift modelingIdentify 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 BiologyMarine Conservation GeneticistDeep-sea biodiversityCharacterize 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.
AgricultureAgricultural Genomics ResearcherPest resistanceInvestigate 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 BiologyPrincipal InvestigatorPhase separationFor 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.
ProteomicsMitochondrial BiologistOrganellar proteomicsCompile 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 GenomicsPrecision Oncology ScientistSynthetic lethalityIdentify 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 DiscoveryADC ScientistADC engineeringFor 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.
ImmunologyImmunotherapy ResearcherNeoantigen pipelineBuild 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.
CheminformaticsAI-Driven Drug DesignerDe novo validationValidate 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.

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