[Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

[Anatoly Sorokin]

Hi,
sorry if this is the wrong list to send this request, but the landing page
of the org.Hs.eg.db package contains no reference for the bug report.

The most recent version of the org.Hs.eg.db package (3.19.7) misses
the GRPEL1 gene (https://www.ncbi.nlm.nih.gov/gene/80273). It could not be
found either by SYMBOL, or by ENTREZID:

> orgDB = org.Hs.eg.db
> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'ENTREZID'. Please use the
keys method to see a listing of valid arguments.
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys
method to see a listing of valid arguments.

however, in the previous version of the package (3.18.0), it could be found
by both keys:

> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
'select()' returned 1:1 mapping between keys and columns
  ENTREZID SYMBOL                   GENENAME
1    80273 GRPEL1 GrpE like 1, mitochondrial
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
'select()' returned 1:1 mapping between keys and columns
  SYMBOL                   GENENAME ENTREZID
1 GRPEL1 GrpE like 1, mitochondrial    80273

That omission caused an error in our BioNAR package. As this is the only
missing gene in the network for the time being I've fixed this manually in
the vignette, but I'd like to understand is it a real mistake or am I using
the package in the wrong way?

Cheers,
Anatoly

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