gatherDataBabel: Retrieve annotation data
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Author(s) References See Also Examples

Retrieves annotation data for a compound by using babel, based on the SMILES code and name of the compounds stored in the compound list.

1	gatherDataBabel(id)

`id`	The compound ID.

Composes the "upper part" of a MassBank record filled with chemical data about the compound: name, exact mass, structure, CAS no.. The instrument type is also written into this block (even if not strictly part of the chemical information). Additionally, index fields are added at the start of the record, which will be removed later: id, dbcas, dbname from the compound list.

Additionally, the fields ACCESSION and RECORD_TITLE are inserted empty and will be filled later on.

This function is an alternative to gatherData, in case CTS is down or if information on one or more of the compounds in the compound list are sparse

Returns a list of type list(id= compoundID, ..., 'ACCESSION' = '', 'RECORD_TITLE' = '', ) etc.

Michael Stravs, Erik Mueller

MassBank record format: http://www.massbank.jp/manuals/MassBankRecord_en.pdf

mbWorkflow