This function sends a request to PubChem to retrieve Compound IDs (CIDs) for given identifier(s).
get_cids(
identifier,
namespace = "name",
domain = "compound",
searchtype = NULL,
options = NULL
)An object of class 'PubChemInstance_CIDs', which is a list containing information retrieved from the PubChem database. Compound IDs can be extracted from the returned object using the CIDs function.
A vector of positive integers (e.g., cid, sid, aid) or identifier strings (e.g., source, inchikey, formula). In some cases, only a single identifier string is required (e.g., name, smiles, xref; inchi, sdf by POST only). Multiple elements can be included as a vector. See Notes for details.
Specifies the namespace for the query. For the 'compound' domain, possible values include 'cid', 'name', 'smiles', 'inchi', 'sdf', 'inchikey', 'formula', 'substructure', 'superstructure', 'similarity', 'identity', 'xref', 'listkey', 'fastidentity', 'fastsimilarity_2d', 'fastsimilarity_3d', 'fastsubstructure', 'fastsuperstructure', and 'fastformula'. For other domains, the possible namespaces are domain-specific.
Specifies the domain of the query. Possible values are 'substance', 'compound', 'assay', 'gene', 'protein', 'pathway', 'taxonomy', 'cell', 'sources', 'sourcetable', 'conformers', 'annotations', 'classification', and 'standardize'.
Specifies the type of search to be performed. For structure searches, possible values include combinations of 'substructure', 'superstructure', 'similarity', 'identity' with 'smiles', 'inchi', 'sdf', or 'cid'. For fast searches, possible values include combinations of 'fastidentity', 'fastsimilarity_2d', 'fastsimilarity_3d', 'fastsubstructure', 'fastsuperstructure' with 'smiles', 'smarts', 'inchi', 'sdf', 'cid', or 'fastformula'.
Additional arguments to be passed to the PubChem Database API.
CIDs, get_pug_rest
compound <- get_cids(
identifier = "aspirin",
namespace = "name"
)
print(compound)
# Extract compound IDs.
CIDs(compound)
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