gatherPubChem: Retrieve supplemental annotation data from Pubchem

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

Description

Retrieves annotation data for a compound from the internet service Pubchem based on the inchikey generated by babel or Cactus

Usage

gatherPubChem(key)

Arguments

key	An Inchi-Key

Details

The data retrieved is the Pubchem CID, a synonym from the Pubchem database, the IUPAC name (using the preferred if available) and a Chebi link

Value

Returns a list with 4 slots: PcID The Pubchem CID Synonym An arbitrary synonym for the compound name IUPAC A IUPAC-name (preferred if available) Chebi The identification number of the chebi database

Author(s)

Erik Mueller

References

Pubchem REST: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Chebi: http://www.ebi.ac.uk/chebi

See Also

mbWorkflow

Examples

# Gather data for compound ID 131
## Not run: gatherPubChem("QEIXBXXKTUNWDK-UHFFFAOYSA-N")

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