downloadChEBI: Download the ChEBI database

In gibbslab/minval: MINimal VALidation for Stoichiometric Reactions

Download the ChEBI database

Description

This function downloads the compounds, formulas, masses and charges from the selected release of the ChEBI database. The ChEBI database (Chemical Entities of Biological Interest), is a database and ontology of molecular entities focused on 'small' chemical compounds.

Usage

downloadChEBI(release = "latest", woAssociations = FALSE)

Arguments

release	A character string with the release number of the ChEBI database version to be downloaded, by default the 'latest' release is downloaded.
woAssociations	A logical value 'TRUE' or 'FALSE' if a light version of the ChEBI database without associations should be returned.

Value

A data.frame with the following data associated to the ChEBI compounds:

• 'ID': The unique identifer

• 'ChEBI': The name recommended for use in biological databases

• 'KEGG': The associated name(s) in the KEGG database

• 'IUPAC': The name(s) generated according to recommendations of IUPAC

• 'MetaCyc': The associated name(s) in the MetaCyc database

• 'ChEMBL': The associated name(s) in the ChEMBL database

• 'FORMULA': The molecular formula

• 'MASS': The molecular mass

• 'MONOISOTOPIC': The molecular monoisotopic mass

• 'CHARGE': The molecular net charge

If woAssociations is 'TRUE' a A data.frame with the following data is returned:

• 'NAME': The name(s) associated in several biological databases

• 'FORMULA': The molecular formula

• 'MASS': The molecular mass

• 'MONOISOTOPIC': The molecular monoisotopic mass

• 'CHARGE': The molecular net charge

Author(s)

Daniel Camilo Osorio <[e-mail]>

See Also

The ChEBI database webpage: https://www.ebi.ac.uk/chebi/

Examples

## Not run: 
# Download ChEBI database with associations
ChEBI <- downloadChEBI(release = '142')

# Download ChEBI database without associations
ChEBI <- downloadChEBI(release = '142', woAssociations = TRUE)
 
## End(Not run)

gibbslab/minval documentation built on May 25, 2022, 5:20 a.m.