PubChemR (version 2.1.4)

get_synonyms: Retrieve Synonyms from PubChem

Description

This function sends a request to PubChem to retrieve synonyms for a given identifier. It returns a list of synonyms corresponding to the provided identifier.

Usage

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

Value

An object of class 'PubChemInstance_Synonyms', which is a list containing information retrieved from the PubChem database. Synonyms data can be extracted from the returned object using the synonyms 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

The PubChem PUG REST API allows for retrieving synonyms related to various domains. The table below summarizes valid combinations for retrieving synonyms: For more detailed information, please refer to the PubChem PUG REST API documentation.

Examples

syns <- get_synonyms(
  identifier = "aspirin",
  namespace = "name"
)

syns

synonyms(syns)