Hello all, Thanks to James W. MacDonald I was able to figure out how to convert NCBI forms to Enseml forms, however the database provided requires you to know the species before hand (library(org.Hs.eg.db), where Hs is Homo sapiens). I can't seem to find a database that compiles all species, nor can I find a tool that can take an accession number and translate it into its organism's name. I am using R. Thank you for any help, J. Denton edit for clarification: for the accession number translation, an example would be NP_062749.2=Mus Musculus.

If you already know all the species, it's a simple matter of iterating through the available OrgDb packages.

> library(org.Hs.eg.db)
> library(org.Mm.eg.db)

> library(org.Gg.eg.db)

> getIds <- function(x) head(grep("^NP", keys(x, "REFSEQ"), value = TRUE))
> rando <- c(getIds(org.Hs.eg.db), getIds(org.Mm.eg.db), getIds(org.Gg.eg.db))
> theorgs <- c("org.Hs.eg.db","org.Mm.eg.db","org.Gg.eg.db")
> thespecies <- c("Human","Mouse","Chicken")

> fun <- function(x,y) {
         tmp <- mapIds(get(x), y, "SYMBOL", "REFSEQ")
         return(tmp[!is.na(tmp)])
}

> symblst <- lapply(theorgs, fun, y = rando)
'select()' returned 1:1 mapping
between keys and columns
'select()' returned 1:1 mapping
between keys and columns
'select()' returned 1:1 mapping
between keys and columns
> names(symblst) <- thespecies
> symblst
$Human
   NP_570602    NP_000005 
      "A1BG"        "A2M" 
NP_001334352 NP_001334353 
       "A2M"        "A2M" 
NP_001334354    NP_000653 
       "A2M"       "NAT1" 

$Mouse
   NP_031402    NP_033721 
       "Pzp"      "Aanat" 
NP_001185714 NP_001185716 
      "Aatk"       "Aatk" 
NP_001364432 NP_001389718 
      "Aatk"       "Aatk" 

$Chicken
NP_001003718    NP_989428 
     "TENM2"      "TENM2" 
   NP_989429 NP_001263212 
     "FZD10"       "FZD9" 
   NP_989430    NP_989431 
      "FZD4"       "TFAM"