get_sids: Retrieve Substance IDs (SIDs) from PubChem

In PubChemR: Interface to the 'PubChem' Database for Chemical Data Retrieval

Retrieve Substance IDs (SIDs) from PubChem

Description

This function sends a request to PubChem to retrieve Substance IDs (SIDs) for a given identifier.

Usage

get_sids(
  identifier,
  namespace = "cid",
  domain = "compound",
  searchtype = NULL,
  options = NULL
)

Arguments

identifier	A vector of identifiers, either numeric or character. The type of identifier depends on the namespace and domain parameters. **Note**: identifier must be provided; it cannot be NULL.
namespace	A character string specifying the namespace of the identifier. Possible values depend on the domain parameter and include: - For domain = 'compound': cid, name, smiles, inchi, sdf, inchikey, formula, etc. - For domain = 'substance': sid, sourceid/<source id>, sourceall/<source name>, name, etc. - For domain = 'assay': aid, listkey, type/<assay type>, sourceall/<source name>, etc. For more details, see the Input section of the PUG REST API.
domain	A character string specifying the domain of the query. Possible values are: - compound (default) - substance - assay - Other domains as specified in the API documentation.
searchtype	An optional character string specifying the search type. Possible values depend on the namespace and domain. Examples include: - substructure, superstructure, similarity, identity for structure searches. - fastidentity, fastsimilarity_2d, fastsimilarity_3d, etc. for fast searches. If NULL (default), no search type is specified. For more details, see the Input section of the PUG REST API.
options	A list of additional options for the request. Available options depend on the specific request and the API. Examples include: - For similarity searches: list(Threshold = 95) - For substructure searches: list(MaxRecords = 100) If NULL (default), no additional options are included. For more details, see the Structure Search Operations section of the PUG REST API.

Details

#' For more detailed information, please refer to the PubChem PUG REST API documentation.

Value

An object of class 'PubChemInstance_SIDs', which is a list containing information retrieved from the PubChem database. Substance IDs can be extracted from the returned object using the SIDs function.

Examples

result <- get_sids(
  identifier = c("aspirin", "ibuprofen"),
  namespace = "name"
)

# Extract substance IDs of all compounds
SIDs(result)

PubChemR documentation built on April 4, 2025, 2:18 a.m.