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

Margolin, Gennady (NIH/NICHD) [C] genn@dy@m@rgo||n @end|ng |rom n|h@gov
Thu Aug 13 22:38:48 CEST 2020

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
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)
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 using channing.harvard.edu>
Date: Thursday, August 13, 2020 at 2:46 PM
To: "Margolin, Gennady (NIH/NICHD) [C]" <gennady.margolin using nih.gov>
Cc: "bioc-devel using r-project.org" <bioc-devel using 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)



[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 using r-project.org<mailto:bioc-devel using r-project.org>> wrote:

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,

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