Query ChEMBL using ChEMBL IDs

Retrieve ChEMBL data using a vector of ChEMBL IDs.

Usage

chembl_query(
  query,
  resource = "molecule",
  cache_file = NULL,
  verbose = getOption("verbose"),
  test_service_down = FALSE
)

Arguments

query: character; a vector of ChEMBL IDs.
resource: character; the ChEMBL resource to query. Use [chembl_resources()] to see all available resources.
cache_file: character; the name of the cache file without the file extension. If NULL, results are not cached.
verbose: logical; should a verbose output be printed on the console?
test_service_down: logical; this argument is only used for testing.

Value

The function returns a list of lists, where each element of the list contains a list of respective query results. Results are simplified, if possible.

Details

Each entry in ChEMBL has a unique ID. Data in ChEMBL is organized in databases called resources. An entry may or may not have a record in a particular resource. An entry may have a record in more than one resource, e.g. a compound may be present in both the "molecule" and the "drug" resource. This function queries a vector of ChEMBL IDs from a specific ChEMBL resource.

If you are unsure which ChEMBL resource contains your ChEMBL ID, use this function with the "chembl_id_lookup" resource to find the appropriate resource for a ChEMBL ID. Note that "chembl_id_lookup" is not a separate function but a resource used by chembl_query.

If cache_file is not NULL the function creates a cache directory in the working directory and a cache file in the cache directory. This file is used in subsequent calls of the function. The function first tries to retrieve query results from the cache file and only accesses the webservice if the ChEMBL ID cannot be found in the cache file. The cache file is extended as new ChEMBL ID-s are queried during the session.

Note

Links to the webservice documentation:

References

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., ... & Overington, J. P. (2012). ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic acids research, 40(D1), D1100-D1107.

Examples

if (FALSE) { # \dontrun{
# Might fail if API is not available

# Resource: "activity" - requires activity ID
chembl_query("31863", resource = "activity")
# Resource: "assay" - requires assay ChEMBL ID
chembl_query("CHEMBL615117", resource = "assay")
# Resource: "atc_class" - requires ATC class ID
chembl_query("A01AA01", resource = "atc_class")
# Resource: binding_site - requires site ID
chembl_query(2, resource = "binding_site")
# Resource: biotherapeutic - requires ChEMBL ID
chembl_query("CHEMBL448105", resource = "biotherapeutic")
# Resource: cell_line - requires ChEMBL ID
chembl_query("CHEMBL3307241", resource = "cell_line")
# Resource: chembl_id_lookup - requires ChEMBL ID
chembl_query("CHEMBL1", resource = "chembl_id_lookup")
# Resource: compound_record - requires record ID
chembl_query("1", resource = "compound_record")
# Resource: compound_structural_alert - requires compound structural alert ID
chembl_query("79048021", resource = "compound_structural_alert")
# Resource: document - requires document ChEMBL ID
chembl_query("CHEMBL1158643", resource = "document")
# Resource: document_similarity - requires document 1 ChEMBL ID
chembl_query("CHEMBL1148466", resource = "document_similarity")
# Resource: drug - requires ChEMBL ID
chembl_query("CHEMBL2", resource = "drug")
# Resource: drug_indication - requires drug indication ID
chembl_query("22606", resource = "drug_indication")
# Resource: drug_warning - requires warning ID
chembl_query("1", resource = "drug_warning")
# Resource: go_slim - requires GO ID
chembl_query("GO:0000003", resource = "go_slim")
# Resource: mechanism - requires mechanism ID
chembl_query("13", resource = "mechanism")
# Resource: metabolism - requires metabolism ID
chembl_query("119", resource = "metabolism")
# Resource: molecule - requires ChEMBL ID
chembl_query("CHEMBL1082", resource = "molecule")
chembl_query(c("CHEMBL25", "CHEMBL1082"), resource = "molecule")
# Resource: molecule_form - requires ChEMBL ID
chembl_query("CHEMBL6329", resource = "molecule_form")
# Resource: organism - requires organism class ID (not taxid)
chembl_query("1", resource = "organism")
# Resource: protein_classification - requires protein class ID
chembl_query("1", resource = "protein_classification")
# Resource: similarity - requires SMILES
chembl_query("CC(=O)Oc1ccccc1C(=O)O/70", resource = "similarity")
# Resource: source - requires source ID
chembl_query("1", resource = "source")
# Resource: substructure - requires SMILES
chembl_query("CN(CCCN)c1cccc2ccccc12", resource = "substructure")
# Resource: target - requires target ChEMBL ID
chembl_query("CHEMBL2074", resource = "target")
# Resource: target_component - requires target component ID
chembl_query("1", resource = "target_component")
# Resource: target_relation - requires target ChEMBL ID
chembl_query("CHEMBL2251", resource = "target_relation")
# Resource: tissue - requires tissue ChEMBL ID
chembl_query("CHEMBL3988026", resource = "tissue")
# Resource: xref_source - requires the name of the resource
chembl_query("AlphaFoldDB", resource = "xref_source")
} # }