Life science and bioinformatics databases your AI assistant can query
Answering a biological question often means hopping between protein, gene, variant, expression and biodiversity databases, each with its own identifiers and query language. Kahubi connects to UniProt, the Human Protein Atlas, ProteomicsDB, gnomAD, Open Targets, Pharos, the HuBMAP Human Reference Atlas, RCSB PDB structures, NCBI, PRIDE and MetaboLights, plus GBIF, iNaturalist and the Paleobiology Database for organisms and fossils.
The assistant translates your question into each database’s syntax, follows identifiers from one source to the next (gene to protein to structure), and cites accessions such as P38398, ENSG ids, rsIDs, PXD and MTBLS numbers so every claim can be checked.
15 sources you can connect
- TogoMCP (UniProt, ChEMBL, PubChem, PDB, Reactome, NCBI)One service across 30+ life-science databases: proteins, genes, compounds, structures, pathways, variants and MeSH.Official server
- Open Targets PlatformTarget–disease–drug associations with the evidence behind them, from EMBL-EBI.Official server
- Protein structures (PDB, AlphaFold)Search experimental and predicted protein structures, find similar folds, track ligands and fetch annotations.Community server
- NCBI E-utilitiesGene, ClinVar, dbSNP, Taxonomy, Nucleotide, Protein, PMC and other NCBI databases.Hosted by Kahubi
- GBIF (biodiversity occurrences)2.5 billion species occurrence records from museums, surveys and citizen science worldwide.Hosted by Kahubi
- iNaturalistCitizen-science observations with photos, research-grade identifications and places.Hosted by Kahubi
- UniProtThe universal protein knowledgebase: function, disease links, domains, locations and structures for every known protein.Hosted by Kahubi
- Human Protein AtlasWhere every human protein is expressed: tissues, single cells, blood, brain, cancers and subcellular location.Hosted by Kahubi
- Paleobiology DatabaseFossil occurrences, taxa, collections and diversity through geological time.Community server
- Pharos (NIH druggable targets)Target development levels, disease associations, ligands and pathways for the whole human proteome, from NIH NCATS.Hosted by Kahubi
- gnomAD (population variant frequencies)Allele frequencies for 800,000+ exomes and genomes, gene constraint scores and ClinVar overlap.Hosted by Kahubi
- PRIDE Archive (proteomics datasets)The world’s largest repository of mass-spectrometry proteomics datasets, from EMBL-EBI.Hosted by Kahubi
- MetaboLights (metabolomics studies)Curated repository of metabolomics experiments and their metabolites, from EMBL-EBI.Hosted by Kahubi
- ProteomicsDBMass-spectrometry evidence and tissue abundance for human proteins, from TU Munich.Hosted by Kahubi
- Human Reference Atlas (HuBMAP)Which cell types live in each part of the healthy human body, and which genes and proteins identify them.Hosted by Kahubi
Questions researchers ask these sources
“Give me the UniProt entry, known structures and Reactome pathways for human TP53.”
The UniProt accession, PDB IDs and Reactome pathway IDs, each verifiable at the source.
TogoMCP“Which targets have the strongest genetic evidence for Parkinson’s disease, and which already have drugs in development?”
Association scores by evidence type, Ensembl target IDs and known drugs with their clinical phase.
Open Targets Platform“Find experimental structures of the SARS-CoV-2 main protease with a bound ligand below 2 Å resolution.”
PDB IDs with method, resolution and ligand details.
Protein structures“How many pathogenic BRCA2 variants are listed in ClinVar?”
The total count from an Entrez search, plus summaries of the top hits with clinical significance.
NCBI E-utilities“Where has the brown bear been recorded in Sweden since 2020?”
Occurrence records with date, locality, coordinates, dataset and basis of record, plus the total count.
GBIF“Where has the invasive Spanish slug (Arion vulgaris) been observed in Sweden since 2020?”
Research-grade observations with date, place, coordinates and observer.
iNaturalist
Frequently asked questions
Do I need to know each database’s query syntax?
Can it combine results across databases?
Are these databases free for commercial research?
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Search life science sources in one research chat
Free to start. Connect a source in one click and get answers that cite the records they came from.