gatherData {RMassBank} | R Documentation

## Retrieve annotation data

### 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)

[Package RMassBank version 2.14.1 Index]