Databases

The AI Chat agent can query 37 bioinformatics databases across 8 categories. These are accessible via the query_bio_database and query_entrez_database tools.

How to Query Databases

Just ask the AI in plain English. The agent automatically selects the right database and translates your question into an API call. For example:

• “Find the 3D structure of BRCA1” → queries pdb
• “What clinical trials exist for lung cancer?” → queries clinicaltrials
• “Search PubMed for CRISPR gene editing” → queries pubmed via query_entrez_database

Complete Database Reference

Protein (6)

UniProtProtein sequence and annotation

AlphaFoldProtein structure predictions

InterProProtein domain and feature predictions

PDB3D structures of proteins and nucleic acids

PRIDEProteomics data repository

EMDBElectron Microscopy Data Bank

Genomic (7)

EnsemblGenome annotation database

UCSCUCSC Genome Browser

dbSNPSingle Nucleotide Polymorphisms

gnomADGenome Aggregation Database

GWAS CatalogGenome-wide association study catalog

ENCODEEncyclopedia of DNA Elements

SynapseSynapse collaborative research platform

Pathway (4)

KEGGKyoto Encyclopedia of Genes and Genomes

ReactomePathway knowledge base

STRINGProtein-protein interactions

Open TargetsOpen Targets genetics

Clinical (5)

ClinVarClinical variation database

ClinicalTrials.govClinical trials registry

DailyMedDrug labeling information

OpenFDAFDA drug and device data

cBioPortalCancer genomics data

Chemical (3)

PubChemChemical information database

ChEMBLBioactive drug-like molecules

UniChemCross-referencing chemical identifiers

Annotation (5)

JASPARTranscription factor bindings

RegulomeDBFunctional regulatory elements

ReMapRegulatory mappings

QuickGOGene Ontology annotations

MonarchPhenotype-genotype associations

Literature (2)

PubMedBiomedical literature (NCBI)

NCBINCBI databases (Gene, Protein, Nucleotide)

Other (5)

GEOGene Expression Omnibus

WoRMSWorld Register of Marine Species

PaleobiologyPaleobiology Database

Guide to PharmacologyGuide to Pharmacology

Mouse PhenomeMouse Phenome Database