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

[James W. MacDonald]

It is the wrong place to send the request. This listserv is for package developers. If you want support please use support.bioconductor.org.

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Anatoly Sorokin
Sent: Thursday, April 18, 2024 12:40 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

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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://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$ ). 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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