chebi_comp_entity: Retrieve Complete Entity from ChEBI

In ropensci/webchem: Chemical Information from the Web

Retrieve Complete Entity from ChEBI

Description

Returns a list of Complete ChEBI entities. ChEBI data are parsed as data.frames ("properties", "chebiid_snd", "synonyms", "iupacnames", "formulae", "regnumbers", "citations", "dblinks", "parents", "children", "comments", "origins") or as a list ("chem_structure") in the list. The SOAP protocol is used https://www.ebi.ac.uk/chebi/webServices.do.

Usage

chebi_comp_entity(chebiid, verbose = getOption("verbose"), ...)

Arguments

chebiid	character; search term (i.e. chebiid).
verbose	logical; should a verbose output be printed on the console?
...	optional arguments

Value

returns a list of data.frames or lists containing a complete ChEBI entity

References

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res.

Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res.

de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C. (2010) Chemical entities of biological interest: an update. Nucleic Acids Res. Degtyarenko, K., Hastings, J., de Matos, P., and Ennis, M. (2009). ChEBI: an open bioinformatics and cheminformatics resource. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis et al., Chapter 14.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v093.i13")}.

Examples

## Not run: 
# might fail if API is not available
chebi_comp_entity('CHEBI:27744')

# multiple inputs
comp <- c('CHEBI:27744', 'CHEBI:27744')
chebi_comp_entity(comp)


## End(Not run)

ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.