Get PubChem Substance ID's Associated With A Compound


Each unique compound is associated with a number of substances. Given a CID it is possible to determine the associated substance ID's.


get.sid.list(cid, quiet=TRUE, from.file=FALSE)



A vector of one or more compound ID's


If FALSE, output is verbose


If TRUE then the first argument is considered to be the name of a file containing the XML data. If FALSE the first argument must be a sequence of compound ID's and the data will be downloaded from the PubChem FTP site


Processing a large number of compound ID's can take a long time. For large numbers of CID's the resultant XML file can be many megabytes. This may take a long time to download. After download it takes approximate 60 sec to process a 23MB data file.

It should also be noted that the data files are downloaded using the R interface to Curl. In addition, the PubChem servers do not allow very large query URL's. This limits the number of compound ID's that can be directly pulled of the PubChem servers to about 1000


A list object, the name of each element is the CID and the value is the SID's that are associated with the compound in question.


Rajarshi Guha

See Also

get.cid, get.assay