run_sparql
Run SPARQL queries on single biological databases (e.g., UniProt, ChEMBL) or cross-database endpoints to retrieve integrated RDF data.
Instructions
Run a SPARQL query on an RDF database. Specify database (valid values: uniprot, rhea, pubchem, pdb, chembl, chebi, reactome, ensembl, amrportal, mesh, go, taxonomy, mondo, nando, bacdive, mediadive, clinvar, pubmed, pubtator, ncbigene, medgen, ddbj, glycosmos, supercon, bgee, oma, brenda, hgnc, jpostdb) for single-database queries, or endpoint_name (valid values: sib, pubchem, pdb, ebi, primary, ncbi, ddbj, glycosmos, nims) / endpoint_url for cross-database queries on shared endpoints. Invalid database/endpoint_name values fail immediately with a deterministic error — do not retry.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| sparql_query | No | The SPARQL query to execute. Alias: `query`. | |
| database | No | Name of a single RDF database. Must be exactly one of: uniprot, rhea, pubchem, pdb, chembl, chebi, reactome, ensembl, amrportal, mesh, go, taxonomy, mondo, nando, bacdive, mediadive, clinvar, pubmed, pubtator, ncbigene, medgen, ddbj, glycosmos, supercon, bgee, oma, brenda, hgnc, jpostdb. Do NOT pass an endpoint group name here (e.g. 'ebi', 'sib') — those go in endpoint_name instead. | |
| endpoint_name | No | Endpoint name for cross-database queries. One of: sib, pubchem, pdb, ebi, primary, ncbi, ddbj, glycosmos, nims. Use this when querying multiple databases on the same endpoint. | |
| endpoint_url | No | Direct SPARQL endpoint URL. Use this for explicit control over the endpoint. | |
| dbname | No | ||
| db | No | ||
| query | No |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |