get_json {PubChemR} | R Documentation |
Retrieve JSON Data from PubChem
Description
This function sends a request to PubChem to retrieve JSON data based on the specified parameters. It handles errors and warnings gracefully, providing informative messages when they occur.
Usage
get_json(
identifier,
namespace = "cid",
domain = "compound",
operation = NULL,
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, only a single identifier string (name, smiles, xref; inchi, sdf by POST only). |
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'. |
operation |
Specifies the operation to be performed on the input records. For the 'compound' domain, possible operations include 'record', 'property', 'synonyms', 'sids', 'cids', 'aids', 'assaysummary', 'classification', 'xrefs', and 'description'. The available operations are domain-specific. |
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 parameters passed to |
Value
A list containing the parsed JSON response from PubChem. Returns NULL if an error or warning occurs.
Examples
get_json(
identifier = "aspirin",
namespace = "name"
)