Re: [Bioc-devel] Question about org.Dr.eg.db package
Glad to help!
On Thu, Aug 13, 2020 at 5:51 PM Margolin, Gennady (NIH/NICHD) [C] <
gennady.margo...@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"
> *Reply-To: *"jmac...@u.washington.edu"
> *Date: *Thursday, August 13, 2020 at 5:41 PM
> *To: *"Margolin, Gennady (NIH/NICHD) [C]"
> *Cc: *Vincent Carey , "
> bioc-devel@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
> 130037 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 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
> 4DBSCHEMA
> ZEBRAFISH_DB
> 5ORGANISM
> Danio rerio
> 6 SPECIES
>Zebrafish
> 7EGSOURCEDATE
> 2019-Jul10
> 8EGSOURCENAME
> Entrez Gene
> 9 EGSOURCEURL
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> 10 CENTRALID
> EG
> 11 TAXID
> 7955
> 12 GOSOURCENAME
> Gene Ontology
> 13GOSOURCEURL
> 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)
> 22GPSOURCEURL
> 23 GPSOURCEDATE
>2017-Nov1
> 24 ENSOURCEDATE
> 2019-Jun24
> 25 ENSOURCENAME
> Ensembl
&g
Re: [Bioc-devel] Question about org.Dr.eg.db package
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"
Reply-To: "jmac...@u.washington.edu"
Date: Thursday, August 13, 2020 at 5:41 PM
To: "Margolin, Gennady (NIH/NICHD) [C]"
Cc: Vincent Carey , "bioc-devel@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
130037 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 mailto:bioc-devel@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
4DBSCHEMA
ZEBRAFISH_DB
5ORGANISM
Danio rerio
6 SPECIES
Zebrafish
7EGSOURCEDATE
2019-Jul10
8EGSOURCENAME
Entrez Gene
9 EGSOURCEURL
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
10 CENTRALID
EG
11 TAXID
7955
12 GOSOURCENAME Gene
Ontology
13GOSOURCEURL
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 B
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
130037 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 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
> 4DBSCHEMA
> ZEBRAFISH_DB
> 5ORGANISM
> Danio rerio
> 6 SPECIES
>Zebrafish
> 7EGSOURCEDATE
> 2019-Jul10
> 8EGSOURCENAME
> Entrez Gene
> 9 EGSOURCEURL
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> 10 CENTRALID
> EG
> 11 TAXID
> 7955
> 12 GOSOURCENAME
> Gene Ontology
> 13GOSOURCEURL
> 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)
> 22GPSOURCEURL
> 23 GPSOURCEDATE
>2017-Nov1
> 24 ENSOURCEDATE
> 2019-Jun24
> 25 ENSOURCENAME
> Ensembl
> 26ENSOURCEURL
> ftp://ftp.ensembl.org/pub/current_fasta
> 27 UPSOURCENAME
> Uniprot
> 28UPSOURCEURL
> http://www.UniProt.org/
> 29 UPSOURCEDATE Mon Oct 21
> 14:32:30 2019
>
> From: Vincent Carey
> Date: Thursday, August 13, 2020 at 2:46 PM
> To: "Margolin, Gennady (NIH/NICHD) [C]"
> Cc: "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&q
Re: [Bioc-devel] Question about org.Dr.eg.db package
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
4DBSCHEMA
ZEBRAFISH_DB
5ORGANISM
Danio rerio
6 SPECIES
Zebrafish
7EGSOURCEDATE
2019-Jul10
8EGSOURCENAME
Entrez Gene
9 EGSOURCEURL
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
10 CENTRALID
EG
11 TAXID
7955
12 GOSOURCENAME Gene
Ontology
13GOSOURCEURL
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)
22GPSOURCEURL
23 GPSOURCEDATE
2017-Nov1
24 ENSOURCEDATE
2019-Jun24
25 ENSOURCENAME
Ensembl
26ENSOURCEURL
ftp://ftp.ensembl.org/pub/current_fasta
27 UPSOURCENAME
Uniprot
28UPSOURCEURL
http://www.UniProt.org/
29 UPSOURCEDATE Mon Oct 21
14:32:30 2019
From: Vincent Carey
Date: Thursday, August 13, 2020 at 2:46 PM
To: "Margolin, Gennady (NIH/NICHD) [C]"
Cc: "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 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
[[alternative HTML version deleted]]
___
Bio
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 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
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Bioc-devel@r-project.org mailing list
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[Bioc-devel] Question about org.Dr.eg.db package
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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
