get_aids {PubChemR}

Retrieve Assay IDs (AIDs) from PubChem

Description

This function queries the PubChem database to retrieve Assay IDs (AIDs) based on a given identifier.

Usage

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

Arguments

identifier

A vector of positive integers (e.g., cid, sid, aid) or identifier strings (source, inchikey, formula). In some cases, it may be a single identifier string (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 are combinations of 'substructure', 'superstructure', 'similarity', 'identity' with 'smiles', 'inchi', 'sdf', 'cid'. For fast searches, possible values are 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_AIDs', which is a list containing information retrieved from the PubChem database. Assay IDs can be extracted from the returned object using the getter function AIDs.

Note

To extract assay IDs from returned object, one may use AIDs function. See examples.

See Also

AIDs, get_pug_rest

Examples

# Request for multiple assays
# If assay identifier is unknown or incorrect, an error returns from PubChem Database
aids <- get_aids(
  identifier = c("aspirin", "ibuprofen", "rstudio"),
  namespace = "name"
)

print(aids)

# Return all Assay IDs.
AIDs(aids)