[Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

[Vincent Carey]

Has this situation been rectified?

On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel <
Daniel.VanTwisk using roswellpark.org> wrote:

> We've made some changes to our annotation generation scripts this release
> and it seems these may have introduced some errors. Thank you for
> identifying this issue and I will try to have some fixes out asap.
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of James W.
> MacDonald <jmacdon using uw.edu>
> Sent: Tuesday, April 23, 2019 11:03:02 AM
> To: Aaron Lun
> Cc: Bioc-devel
> Subject: Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
>
> Looks like the ensembl table of the human.db0 package got polluted with
> *Pan
> troglodytes* genes:
>
> > con <- dbConnect(SQLite(),
> "/R-devel/lib64/R/library/human.db0/extdata/chipsrc_human.sqlite")
> > dbGetQuery(con, "select count(*) from ensembl where ensid like
> 'ENSPTR%';")
>   count(*)
> 1    16207
> > dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';")
>   count(*)
> 1    28973
>
> On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun <
> infinite.monkeys.with.keyboards using gmail.com> wrote:
>
> > Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG0000...?
> >
> >  > library(org.Hs.eg.db)
> >  > mapIds(org.Hs.eg.db, key="GCG", keytype="SYMBOL", column="ENSEMBL")
> > 'select()' returned 1:many mapping between keys and columns
> >                   GCG
> > "ENSPTRG00000000777"
> >
> > Well, at least it still recovers the right identifier... eventually.
> >
> >  > select(org.Hs.eg.db, key="GCG", keytype="SYMBOL", columns="ENSEMBL")
> > 'select()' returned 1:many mapping between keys and columns
> >    SYMBOL            ENSEMBL
> > 1    GCG ENSPTRG00000000777
> > 2    GCG    ENSG00000115263
> >
> > The SYMBOL->Entrez ID relational table seems to be okay:
> >
> >  > Y <- toTable(org.Hs.egSYMBOL)
> >  > Y[which(Y[,2]=="GCG"),]
> >       gene_id symbol
> > 2152    2641    GCG
> >
> > So the cause is the Ensembl->Entrez mappings:
> >
> >  > Z <- toTable(org.Hs.egENSEMBL2EG)
> >  > Z[Z[,1]==2641,]
> >       gene_id         ensembl_id
> > 3028    2641 ENSPTRG00000000777
> > 3029    2641    ENSG00000115263
> >
> > Googling suggests that ENSPTRG00000000777 is an identifier for some
> > other gene in one of the other monkeys. Hardly "Hs" stuff.
> >
> > Session info (not technically R 3.6, but I didn't think that would have
> > been the cause):
> >
> > > R Under development (unstable) (2019-04-11 r76379)
> > > Platform: x86_64-pc-linux-gnu (64-bit)
> > > Running under: Ubuntu 18.04.2 LTS
> > >
> > > Matrix products: default
> > > BLAS:   /home/luna/Software/R/trunk/lib/libRblas.so
> > > LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so
> > >
> > > locale:
> > >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> > >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> > >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> > >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> > >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > >
> > > attached base packages:
> > > [1] parallel  stats4    stats     graphics  grDevices utils
>  datasets
> > > [8] methods   base
> > >
> > > other attached packages:
> > > [1] org.Hs.eg.db_3.8.0   AnnotationDbi_1.45.1 IRanges_2.17.5
> > > [4] S4Vectors_0.21.23    Biobase_2.43.1       BiocGenerics_0.29.2
> > >
> > > loaded via a namespace (and not attached):
> > >  [1] Rcpp_1.0.1      digest_0.6.18   DBI_1.0.0       RSQLite_2.1.1
> > >  [5] blob_1.1.1      bit64_0.9-7     bit_1.1-14      compiler_3.7.0
> > >  [9] pkgconfig_2.0.2 memoise_1.1.0
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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