Query ChEMBL

Retrieve ChEMBL data using a vector of IDs.

Usage

chembl_query(
  query,
  resource = "molecule",
  mode = "ws",
  verbose = getOption("verbose"),
  options = chembl_options(cache_file = NULL, similarity = 70, tidy = TRUE, version =
    "latest"),
  ...
)

Arguments

query: character; a vector of IDs. The type of ID depends on the resource. See examples for more information.
resource: character; the ChEMBL resource to query. Use [chembl_resources()] to see all available resources.
mode: character; either "ws" (default) to use the webservice or "offline" to use a local ChEMBL database. Note, to use the "offline" mode, you need to have a local ChEMBL database. See [db_download_chembl()].
verbose: logical; should a verbose output be printed on the console?
options: function; returns a named list for resource- and mode-specific options. Supported entries: - cache_file: character or NULL; name of the cache file (without extension) used when mode = "ws". If NULL (default), results are not cached. - similarity: numeric; similarity threshold for similarity searches (default 70). - tidy: logical; attempt to convert output to a simpler structure (default TRUE). - version: character; database version to use in "offline" mode (default "latest").
...: additional arguments, only used for internal testing.

Value

The function returns a list of lists, where each element of the list contains a list of respective query results. If `tidy = TRUE` 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 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 mode = "ws" and options$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 cache file is extended as new 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

# Examples with resources that operate on compounds

# Resource: biotherapeutic - requires compound ChEMBL ID
chembl_query("CHEMBL448105", resource = "biotherapeutic")

# Resource: compound_structural_alert - requires compound ChEMBL ID
chembl_query(
  "CHEMBL266429",
  resource = "compound_structural_alert",
  options = chembl_options(tidy = FALSE)
)

# Resource: compound_record - requires compound record ID
chembl_query("1", resource = "compound_record")

# Resource: drug - requires compound ChEMBL ID
chembl_query("CHEMBL2", resource = "drug")

# Resource: molecule - requires compound ChEMBL ID
chembl_query("CHEMBL1082", resource = "molecule")
chembl_query(c("CHEMBL25", "CHEMBL1082"), resource = "molecule")

# Resource: molecule_form - requires compound ChEMBL ID
chembl_query("CHEMBL6329", resource = "molecule_form")

# Resource: similarity - requires compound SMILES
# By default, the function will use 70 as similarity threshold
chembl_query(
  "CC(=O)Oc1ccccc1C(=O)O", resource = "similarity",
  options = chembl_options(similarity = 70)
)

# Resource: substructure - requires compound SMILES
chembl_query("CN(CCCN)c1cccc2ccccc12", resource = "substructure")

# Other Examples

# 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: 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: 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_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: 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: source - requires source ID
chembl_query("1", resource = "source")

# 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")
} # }