## -----------------------------------------------------------------------------
library(BridgeDbR)

## -----------------------------------------------------------------------------
code <- getOrganismCode("Rattus norvegicus")
code

## -----------------------------------------------------------------------------
fullName <- getFullName("Ce")
fullName
code <- getSystemCode("ChEBI")
code

## -----------------------------------------------------------------------------
getMatchingSources("HMDB00555")
getMatchingSources("ENSG00000100030")

## ----eval=FALSE---------------------------------------------------------------
#  getBridgeNames()

## ----eval=FALSE---------------------------------------------------------------
#  dbLocation <- getDatabase("Rattus norvegicus", location = getwd())

## ----eval=FALSE---------------------------------------------------------------
#  getwd()
#  dbLocation <- ("/home/..../BridgeDb/wikidata_diseases.bridge")

## ----eval=FALSE---------------------------------------------------------------
#  mapper <- loadDatabase(dbLocation)

## ----eval=FALSE---------------------------------------------------------------
#  location <- getDatabase("Homo sapiens")
#  mapper <- loadDatabase(location)
#  map(mapper, "L", "196410", "X")

## ----eval=FALSE---------------------------------------------------------------
#  input <- data.frame(
#      source = rep("Ch", length(data[, 2])),
#      identifier = data[, 2]
#  )
#  wikidata <- maps(mapper, input, "Wd")

## ----eval=FALSE---------------------------------------------------------------
#  ## Set the working directory to download the Metabolite mapping file
#  location <- "data/metabolites.bridge"
#  checkfile <- paste0(getwd(), "/", location)
#  
#  ## Download the Metabolite mapping file (if it doesn't exist locally yet):
#  if (!file.exists(checkfile)) {
#      download.file(
#          "https://figshare.com/ndownloader/files/26001794",
#          location
#      )
#  }
#  # Load the ID mapper:
#  mapper <- BridgeDbR::loadDatabase(checkfile)

## ----eval=FALSE---------------------------------------------------------------
#  map(mapper, "456", source = "Cs", target = "Ck")

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()