[Bioc-devel] Question about org.Dr.eg.db package
James W. MacDonald
jm@cdon @end|ng |rom uw@edu
Fri Aug 14 00:00:15 CEST 2020
Glad to help!
On Thu, Aug 13, 2020 at 5:51 PM Margolin, Gennady (NIH/NICHD) [C] <
gennady.margolin using nih.gov> wrote:
> 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> 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>
> 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)
>
> [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>>
> 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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>
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> --
>
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
--
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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