get_cids {PubChemR}

Retrieve Compound IDs (CIDs) from PubChem

Description

This function sends a request to PubChem to retrieve Compound IDs (CIDs) for given identifier(s).

Usage

get_cids(
  identifier,
  namespace = "name",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

identifier

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.

namespace

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.

domain

Specifies the domain of the query. Possible values are 'substance', 'compound', 'assay', 'gene', 'protein', 'pathway', 'taxonomy', 'cell', 'sources', 'sourcetable', 'conformers', 'annotations', 'classification', and 'standardize'.

searchtype

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'.

options

Additional arguments to be passed to the PubChem Database API.

Value

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.

Note

To extract compoud IDs from returned object, one may use CIDs function. See examples.

See Also

CIDs, get_pug_rest

Examples

compound <- get_cids(
  identifier = "aspirin",
  namespace = "name"
)

print(compound)

# Extract compound IDs.
CIDs(compound)