PubChemR (version 2.1.3)

get_sids: 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
)

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.

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.

Examples

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

# Extract substance IDs of all compounds
SIDs(result)