run_sparql
Execute SPARQL queries on biological and biomedical RDF databases. Choose a single database or use an endpoint for cross-database queries.
Instructions
Run a SPARQL query on an RDF database. ALWAYS pass database (required; 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, massbank, nbrc, mogplus, hco, mco, togovar, ontology) for single-database queries. For cross-database queries on a shared endpoint, still pass a member database AND add endpoint_name (valid values: sib, pubchem, pdb, ebi, primary, ncbi, ddbj, glycosmos, nims, togovar) or endpoint_url, which take priority over database. Invalid database/endpoint_name values fail immediately with a deterministic error — do not retry. RETURNS the query results as a CSV-formatted string (first row is the header of SELECT variable names).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | Alias for `sparql_query`. | |
| database | Yes | 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, massbank, nbrc, mogplus, hco, mco, togovar, ontology. Do NOT pass an endpoint group name here (e.g. 'ebi', 'sib') — those go in endpoint_name instead. | |
| endpoint_url | No | Direct SPARQL endpoint URL. Use this for explicit control over the endpoint. | |
| sparql_query | No | The SPARQL query to execute. Alias: `query`. | |
| endpoint_name | No | Endpoint name for cross-database queries. One of: sib, pubchem, pdb, ebi, primary, ncbi, ddbj, glycosmos, nims, togovar. Use this when querying multiple databases on the same endpoint. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |