I am trying to use biomaRt in R to retrieve the corresponding refseqpeptide IDs for a list of refseqdna mRNA transcript ids. However, for some transcripts, no peptide ID is returned, even though other sources clearly indicate an associated peptide for that transcript. For example, "NM_000092" has this problem. Using the martview web interface, I can reproduce the same results. Here is a link.
[EDIT] - converted URL to tinyurl
You can see that I have queried for refseqdna equal to NM000092, and retrieved dna and protein identifiers in both refseq and Ensembl. Only the refseq protein ID is empty. If you look on the NCBI record for NM000092, you'll see that the answer should be NP000083:
/product="collagen alpha-4(IV) chain precursor" /protein_id="NP_000083.3"
Also, if I search on bioDBnet's db2db tool, it does find the associated peptide ID.
Furthermore, searching with IDConverter also yields the correct results, and IDConverter explicitly states that its refseq_peptide info comes from Ensembl, which is presumably the same source as biomart.
So why isn't biomart finding some mRNA-peptide associations that other tools are?