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[Bioc-devel] Question about org.Dr.eg.db package

James W. MacDonald

Thu, Aug 13, 2020 2:36 PM

Hi Gennady,

That information should probably be cleaned up, and the BiMaps that point
to the location data removed. While the OrgDbs do contain position
information, it's been deprecated, which you would find if you tried to
query using select():

'select()' returned 1:1 mapping between keys and columns
  ENTREZID CHR
1    30037   5
Warning message:
In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select()
  with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
  object instead.

The rationale being that the OrgDb packages are intended to contain
functional annotations, which are not based on any build, and instead are
current as of the construction of the OrgDb package. Since positional
information should be based on a genome release, those data have been
migrated to the TxDb and EnsDb packages, which are based on a given release.

Put a different way, the data in an OrgDb package is downloaded from NCBI
as of a particular date, and the positional data we get are whatever we got
from NCBI on that date. This is obviously a problem for the positional
data, because what we get isn't necessarily build-specific. We get the TxDb
data from the UCSC Genome Browser, which is build specific, so we can tell
end users exactly what build the data come from. Ideally these data would
be defunct in the OrgDb packages, but it hasn't happened yet.

Best,

Jim



On Thu, Aug 13, 2020 at 4:39 PM Margolin, Gennady (NIH/NICHD) [C] via

Bioc-devel <bioc-devel at r-project.org> wrote:

Hi Vincent,

Thank you for responding.

Here is from the R documentation help page from this package (I have
version 3.10.0 (I doubt anything changed with the latest one, which is
3.11.4)):

-------------------------------------------------
org.Dr.egCHRLOC {org.Dr.eg.db}
Entrez Gene IDs to Chromosomal Location
Description
org.Dr.egCHRLOC is an R object that maps entrez gene identifiers to the
starting position of the gene. The position of a gene is measured as the
number of base pairs.
The CHRLOCEND mapping is the same as the CHRLOC mapping except that it
specifies the ending base of a gene instead of the start.
??
-------------------------------------------------

This output also does not show any genome version:

org.Dr.eg_dbInfo()

                 name
       value
1     DBSCHEMAVERSION
         2.1
2             Db type
       OrgDb
3  Supporting package
 AnnotationDbi
4            DBSCHEMA
ZEBRAFISH_DB
5            ORGANISM
 Danio rerio
6             SPECIES
   Zebrafish
7        EGSOURCEDATE
  2019-Jul10
8        EGSOURCENAME
 Entrez Gene
9         EGSOURCEURL
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
10          CENTRALID
          EG
11              TAXID
        7955
12       GOSOURCENAME
 Gene Ontology
13        GOSOURCEURL
ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
14       GOSOURCEDATE
  2019-Jul10
15     GOEGSOURCEDATE
  2019-Jul10
16     GOEGSOURCENAME
 Entrez Gene
17      GOEGSOURCEURL
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
18     KEGGSOURCENAME
 KEGG GENOME
19      KEGGSOURCEURL
ftp://ftp.genome.jp/pub/kegg/genomes
20     KEGGSOURCEDATE
  2011-Mar15
21       GPSOURCENAME                          UCSC Genome Bioinformatics
(Danio rerio)
22        GPSOURCEURL
23       GPSOURCEDATE
   2017-Nov1
24       ENSOURCEDATE
  2019-Jun24
25       ENSOURCENAME
     Ensembl
26        ENSOURCEURL
ftp://ftp.ensembl.org/pub/current_fasta
27       UPSOURCENAME
     Uniprot
28        UPSOURCEURL
http://www.UniProt.org/
29       UPSOURCEDATE                                          Mon Oct 21
14:32:30 2019

From: Vincent Carey <stvjc at channing.harvard.edu>
Date: Thursday, August 13, 2020 at 2:46 PM
To: "Margolin, Gennady (NIH/NICHD) [C]" <gennady.margolin at nih.gov>
Cc: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Question about org.Dr.eg.db package

This should probably be posed to the support site.  What version of the
package are you using?  Where
are you seeing coordinates?  I would expect those to be obtained from the
TxDb package, or perhaps
from AnnotationHub.

columns(org.Dr.eg.db)

 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"
"ENSEMBLTRANS"

 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"

[11] "GO"           "GOALL"        "IPI"          "ONTOLOGY"
 "ONTOLOGYALL"

[16] "PATH"         "PFAM"         "PMID"         "PROSITE"      "REFSEQ"

[21] "SYMBOL"       "UNIGENE"      "UNIPROT"      "ZFIN"


On Thu, Aug 13, 2020 at 2:13 PM Margolin, Gennady (NIH/NICHD) [C] via
Bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
wrote:
Hello,

I have a short question ? how do I figure the genome version for
org.Dr.eg.db package? I couldn?t see it in the DESCRIPTION and also it?s
not in org.Dr.eg_dbInfo() output. It would be nice to know if this is
danRer11/GRCz11 or some other assembly, as there are coordinates present in
the DB.

Thank you,
Gennady

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Thread (6 messages)

Margolin, Gennady (NIH/NICHD) [C] Question about org.Dr.eg.db package Aug 13 Vincent Carey Question about org.Dr.eg.db package Aug 13 Margolin, Gennady (NIH/NICHD) [C] Question about org.Dr.eg.db package Aug 13 James W. MacDonald Question about org.Dr.eg.db package Aug 13 Margolin, Gennady (NIH/NICHD) [C] Question about org.Dr.eg.db package Aug 13 James W. MacDonald Question about org.Dr.eg.db package Aug 13