Parse taxon names from R, using the GBIF name parser API (http://portaldev.gbif.org/developer/species).

gbif_parse.R

gbif_parse <- function(x) {
  # x is a vector of species names
  library(RJSONIO)
  library(RCurl)
  library(plyr)
  u <- "http://api.gbif.org/v1/parser/name"
  res <- fromJSON(
    postForm(u,
      .opts = list(postfields = RJSONIO::toJSON(x),
      httpheader = c('Content-Type' = 'application/json')))
    )
  do.call(rbind.fill, lapply(res, as.data.frame))  
}

gbif_parse_examples.R

library(devtools)
source_url('https://gist.github.com/johnbaums/6971353/raw/gbif_parse.R')

# Examples
gbif_parse('x Agropogon littoralis')
gbif_parse(c("Hovenia dulcis", "Mauryanda barclaiana", "Senecio glastifolius", 
             "Carex buxbaumii", "Alternanthera philoxeroides", "Catapodium marinum", 
             "Secale cereale subsp. cereale", "Verbena supina var. erecta", 
             "Carica papaya", "Impatiens walleriana", "Pennisetum villosum", 
             "Lolium X hybridum", "Hedera helix", "Arrhenatherum elatius var. elatius", 
             "Buddleja lindleyana", "Fallopia sachalinensis", "Trifolium alexandrinum", 
             "Acanthus spinosus", "Impatiens balsamina", "Crassula spathulata"))

spp <- read.delim('http://gbif-ecat.googlecode.com/svn/trunk/ecat-common/src/test/resources/scientific_names.txt', 
                  header=TRUE, sep='\t', comment.char='#', stringsAsFactors=FALSE, 
                  fileEncoding='utf-8')
spp.parsed <- gbif_parse(spp$scientificName)
head(spp.parsed)