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