gatherData: Retrieve annotation data

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Retrieves annotation data for a compound from the internet services CTS, Pubchem, Chemspider and Cactvs, based on the SMILES code and name of the compounds stored in the compound list.

Usage

gatherData(id)

Arguments

id	The compound ID.

Details

Composes the "upper part" of a MassBank record filled with chemical data about the compound: name, exact mass, structure, CAS no., links to PubChem, KEGG, ChemSpider. 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, dataused to indicate the used identifier for CTS search (smiles or dbname).

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

Value

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

Author(s)

Michael Stravs

References

Chemical Translation Service: http://uranus.fiehnlab.ucdavis.edu:8080/cts/homePage cactus Chemical Identifier Resolver: http://cactus.nci.nih.gov/chemical/structure MassBank record format: http://www.massbank.jp/manuals/MassBankRecord_en.pdf Pubchem REST: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Chemspider InChI conversion: https://www.chemspider.com/InChI.asmx

See Also

mbWorkflow

Examples

# Gather data for compound ID 131
## Not run: gatherData(131)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.