The built-in directory contains 43 database connectors in this version. Ask OpenScience to search a named database or retrieve a record by its identifier.
For example: "Find the UniProt record for human BRCA1, report its accession, and link the source." Include the organism, reference assembly, or identifier version when it matters.
Public records may be accessible without a key, but availability, rate limits, licensing, and full-text access depend on the source. Some databases require credentials or a local dataset. A missing result is not proof that a record does not exist.
These are built-in database connections. Use Connectors and MCP for external tool servers, Skills for procedures, and Literature reviews for a review workflow.
Biology
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| BioSimulators | biosimulators | Find simulation tools by name, KiSAO algorithm, or model format (SBML, CellML, NeuroML, BNGL). Registry lookup only. | Structured record |
| KEGG | kegg | KEGG pathway maps, modules, orthologs, compounds, and reactions. | fasta |
| Reactome | reactome | Curated biological pathways, reactions, and molecular events. | Structured record |
| WikiPathways | wikipathways | Community-curated biological pathways across many species. | Structured record |
Chemistry
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| BindingDB | bindingdb | Measured protein-ligand binding affinities; query by UniProt accession. | Structured record |
| ChEBI | chebi | Chemical Entities of Biological Interest ontology terms (EMBL-EBI). | Structured record |
| ChEMBL | chembl | Bioactive drug-like small molecules with curated bioactivity data (EMBL-EBI). | Structured record |
| Guide to PHARMACOLOGY | gtopdb | IUPHAR/BPS ligands, drugs, and their molecular targets. | Structured record |
| PubChem | pubchem | Chemical compounds, structures, and properties from NCBI PubChem. | sdf |
| SureChEMBL | surechembl | Chemistry extracted from the patent literature (EMBL-EBI). | Structured record |
Clinical
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| ClinVar | clinvar | Clinically-interpreted variants: pathogenicity classification, conditions, and gene. | Structured record |
Genomics
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| ArrayExpress / BioStudies | arrayexpress | Functional genomics experiments (microarray & sequencing) archived on EMBL-EBI BioStudies. | Structured record |
| DepMap | depmap | Cancer Dependency Map — released CRISPR/RNAi, omics, and drug-sensitivity dataset metadata. | Structured record |
| Ensembl | ensembl | Genes, transcripts, and cross-references by symbol or Ensembl stable id. | fasta |
| Expression Atlas | expression-atlas | Bulk gene & protein expression across tissues, conditions, and species (EMBL-EBI GXA). | Structured record |
| gnomAD | gnomad | Population allele frequencies (genome/exome) for genes and variants. | Structured record |
| GTEx | gtex | Genotype-Tissue Expression — median gene expression across human tissues. | Structured record |
| MyGene.info | mygene | Gene annotation lookup (symbol, name, Entrez/Ensembl ids) across species. | Structured record |
| MyVariant.info | myvariant | Aggregated variant annotation (dbSNP, ClinVar, CADD, dbNSFP) by HGVS or rsID. | Structured record |
| NCBI dbSNP | dbsnp | Reference SNP (rsID) records: alleles, position, function class, and clinical significance. | Structured record |
| NCBI Gene | ncbi-gene | Gene records (symbol, aliases, locus, summary) from NCBI Entrez Gene. | Structured record |
| NCBI GEO | geo | Gene Expression Omnibus — functional genomics Series, DataSets, and platforms. | Structured record |
| Open Targets | opentargets | Target-disease-drug associations for drug target identification. | Structured record |
| Single Cell Expression Atlas | single-cell-atlas | Single-cell RNA-seq experiments with cell-type expression across species (EMBL-EBI GXA sc). | Structured record |
| UCSC Genome Browser | ucsc | Search genome assemblies for genes/positions and retrieve reference sequence. | Structured record |
Literature
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| arXiv | arxiv | Preprint metadata and abstracts in physics, math, CS, quantitative biology, and more. Paper text must be retrieved separately from the returned PDF link. | Structured record |
| bioRxiv / medRxiv | biorxiv | Biology and health-sciences preprints (bioRxiv + medRxiv) via Cold Spring Harbor. Keyword search ranks only the ~100 most recent postings per server, so no match does not mean no such preprint; search by DOI for an exact record, or use europepmc/openalex for older preprints. | Structured record |
| Crossref | crossref | Cross-publisher DOI metadata: titles, authors, venues, references, and citations. | Structured record |
| Europe PMC | europepmc | Life-science literature metadata and abstracts (PubMed, PMC, Agricola, patents) via EBI. | Structured record |
| OpenAlex | openalex | Open scholarly graph of works, authors, venues, and concepts (successor to MAG). | Structured record |
| PubMed | pubmed | Biomedical literature abstracts and citations from NCBI (MEDLINE/PubMed). | Structured record |
| Semantic Scholar | semantic-scholar | AI-powered academic graph: abstracts, citations, references, and influence. | Structured record |
Proteomics
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| BioGRID | biogrid | Curated protein and genetic interactions (needs a free BioGRID access key). | Structured record |
| Human Protein Atlas | hpa | Tissue, cell, pathology, and subcellular protein expression across the human proteome. | Structured record |
| IntAct | intact | EMBL-EBI molecular interaction database (protein, RNA, small molecule). | Structured record |
| InterPro | interpro | Integrated protein families, domains, and functional sites with GO annotations. | Structured record |
| Pfam | pfam | Pfam protein families and domains (member database of InterPro). | Structured record |
| STRING | string-db | Known and predicted protein-protein interaction networks. | Structured record |
| UniProt | uniprot | Protein sequences with function, GO terms, domains, and pathways (UniProtKB). | fasta, txt |
Structure
| Source and documentation | Identifier | Records and uses | Declared formats |
|---|---|---|---|
| AlphaFold DB | alphafold | AlphaFold-predicted protein structures with per-residue confidence (pLDDT). | pdb, cif |
| PDBe | pdbe | Protein Data Bank in Europe — 3D structures with EBI annotations and cross-references. | cif |
| RCSB PDB | rcsb-pdb | Experimentally determined 3D structures of proteins, nucleic acids, and complexes. | pdb, cif |
| SIFTS | sifts | UniProt↔PDB residue-level structure mappings (best PDB structures per protein). | Structured record |
How to search and fetch
Choose a source above and ask for a bounded query. Select an identifier from the results, then request a structured record or one of that source's declared formats. See Database workflows for complete examples, output checks, and source-error handling.
Check source records
Ask for the exact accession, DOI, or source URL and the retrieval date. Confirm whether a result is a record, abstract, full text, prediction, or experimental observation before citing it.
If access fails, narrow the query, check identifiers, and inspect the reported source error. Do not replace a missing record with an uncited guess.