get_chebiid {webchem}

Retrieve Lite Entity (identifiers) from ChEBI

Description

Returns a data.frame with a ChEBI entity ID (chebiid), a ChEBI entity name (chebiasciiname), a search score (searchscore) and stars (stars) using the SOAP protocol: https://www.ebi.ac.uk/chebi/webServices.do

Usage

get_chebiid(
  query,
  from = c("all", "chebi id", "chebi name", "definition", "name", "iupac name",
    "citations", "registry numbers", "manual xrefs", "automatic xrefs", "formula",
    "mass", "monoisotopic mass", "charge", "inchi", "inchikey", "smiles", "species"),
  match = c("all", "best", "first", "ask", "na"),
  max_res = 200,
  stars = c("all", "two only", "three only"),
  verbose = getOption("verbose"),
  ...
)

Arguments

query

character; search term.

from

character; type of input. "all" searches all types and "name" searches all names. Other options include 'chebi id', 'chebi name', 'definition', 'iupac name', 'citations', 'registry numbers', 'manual xrefs', 'automatic xrefs', 'formula', 'mass', 'monoisotopic mass','charge', 'inchi', 'inchikey', 'smiles', and 'species'

match

character; How should multiple hits be handled?, "all" all matches are returned, "best" the best matching (by the ChEBI searchscore) is returned, "ask" enters an interactive mode and the user is asked for input, "na" returns NA if multiple hits are found.

max_res

integer; maximum number of results to be retrieved from the web service

stars

character; "three only" restricts results to those manualy annotated by the ChEBI team.

verbose

logical; should a verbose output be printed on the console?

...

currently unused

Value

returns a list of data.frames containing a chebiid, a chebiasciiname, a searchscore and stars if matches were found. If not, data.frame(NA) is returned

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 metabfolites. 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). doi:10.18637/jss.v093.i13.

Examples

## Not run: 
# might fail if API is not available
get_chebiid('Glyphosate')
get_chebiid('BPGDAMSIGCZZLK-UHFFFAOYSA-N')

# multiple inputs
comp <- c('Iron', 'Aspirin', 'BPGDAMSIGCZZLK-UHFFFAOYSA-N')
get_chebiid(comp)


## End(Not run)