[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 23:50:03 CEST 2020
Hi Jim,
Hi Jim,
Awesome, that makes sense now. I was wondering whether org.Dr.eg.db has only functional annotation, which I thought it was as it did not refer to a specific genome, unlike TxDb packages, but then I found what I said in my previous emails.
Thank you very much,
Gennady
From: "James W. MacDonald" <jmacdon using uw.edu>
Reply-To: "jmacdon using u.washington.edu" <jmacdon using u.washington.edu>
Date: Thursday, August 13, 2020 at 5:41 PM
To: "Margolin, Gennady (NIH/NICHD) [C]" <gennady.margolin using nih.gov>
Cc: Vincent Carey <stvjc using channing.harvard.edu>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Question about org.Dr.eg.db package
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(org.Dr.eg.db, "30037", "CHR")
'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 using r-project.org<mailto:bioc-devel using 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 using channing.harvard.edu<mailto: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<mailto:gennady.margolin using nih.gov>>
Cc: "bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>" <bioc-devel using r-project.org<mailto: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)
[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 using r-project.org<mailto:bioc-devel using r-project.org><mailto:bioc-devel using r-project.org<mailto:bioc-devel using 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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