query_database
Read-only
Ask one of the ~60 authoritative databases a question and hand its rows downstream — Ensembl, UniProt, ClinVar, gnomAD, ChEMBL, PubChem, InterPro, STRING, PDB, AlphaFold, the GWAS Catalog, PubMed and the rest.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | cap on rows returned, where the authority honours one. | |
| query | Yes | what to ask, in the authority's own terms — an identifier, a gene symbol, or one of its command forms such as `ensembl_lookup:BRCA2`. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| authority | Yes | which database to ask. Values: pubmed (NCBI PubMed (E-utilities) — literature), pmc-idconv (NCBI PMC ID Converter — literature), europepmc (Europe PMC — literature), openalex (OpenAlex — literature), crossref (Crossref — literature), arxiv (arXiv — literature), biorxiv (bioRxiv — literature), medrxiv (medRxiv — literature), datacite (DataCite — literature), ensembl (Ensembl REST — genomics), ucsc (UCSC Genome Browser API — genomics), biomart (Ensembl BioMart — genomics), mygene (MyGene.info — genomics), ncbi-gene (NCBI Gene (E-utilities) — genomics), hgnc (HGNC (genenames.org) — genomics), gnomad (gnomAD (Broad) — genomics), clinvar (NCBI ClinVar — genomics), dbsnp (NCBI dbSNP — genomics), variation (NCBI Variation Services — genomics), cadd (CADD (Kircher lab) — genomics), gtex (GTEx Portal — genomics), eqtlcatalogue (eQTL Catalogue (EBI) — genomics), gwascatalog (GWAS Catalog (EBI/NHGRI) — genomics), pheweb (PheWeb / FinnGen — genomics), uniprot (UniProt — proteins), interpro (InterPro / Pfam (EBI) — proteins), string (STRING — proteins), proteinatlas (Human Protein Atlas — proteins), alphafold (AlphaFold DB (EBI) — proteins), pdb (RCSB PDB — proteins), emdb (EMDB (EBI) — proteins), complexportal (Complex Portal (EBI) — proteins), intact (IntAct (EBI) — proteins), chembl (ChEMBL (EBI) — chemistry), pubchem (PubChem (NCBI) — chemistry), chebi (ChEBI (EBI) — chemistry), bindingdb (BindingDB — chemistry), zinc (ZINC (CartBlanche, UCSF) — chemistry), rhea (Rhea (EBI) — chemistry), clinicaltrials (ClinicalTrials.gov — clinical), openfda (openFDA — clinical), opentargets (Open Targets Platform — clinical), civic (CIViC — clinical), clingen (ClinGen (erepo.genome.network) — clinical), cosmic (COSMIC via NLM Clinical Tables — clinical), depmap (Cell Model Passports (Sanger) — clinical), cbioportal (cBioPortal — clinical), geo (NCBI GEO — omics), arrayexpress (ArrayExpress / BioStudies (EBI) — omics), pride (PRIDE (EBI) — omics), metabolights (MetaboLights (EBI) — omics), mgnify (MGnify (EBI) — omics), encode (ENCODE Project — omics), jaspar (JASPAR (Elixir) — omics), unibind (UniBind (Univ. of Oslo) — omics), cellguide (CellGuide (CZI CELLxGENE) — cells), panglaodb (PanglaoDB — cells), antibodyregistry (Antibody Registry (RRID) — cells), ols (OLS4 (EBI) — ontology), quickgo (QuickGO (EBI) — ontology), identifiers-org (identifiers.org registry — ontology), ncbi-taxonomy (NCBI Taxonomy (E-utilities) — ontology), reactome (Reactome — ontology), kegg (KEGG — ontology), rfam (Rfam (EBI) — ontology), grantsgov (Grants.gov — funding). |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | how many rows came back | |
| results | Yes | the rows the authority returned — wire into filter_items, check_rows or summarize_rows | |
| envelope | Yes | the whole response, for a row shape this node's `results` does not name | |
| authority | Yes | which authority answered, stated rather than implied | |
| endpoints | Yes | the URLs actually called — the provenance a methods section needs | |
| retrievedAt | Yes | when it was fetched, because a live lookup is a fact about a moment |