[Bioc-devel] annotation data not updated?
Shepherd, Lori
Lori.Shepherd at RoswellPark.org
Wed Nov 15 13:50:14 CET 2017
When this issue was brought up I updated the files that were downloaded when using AnnotationHub so they should be updated as well.
The files were updated but the rdatadateadded was not updated when I added the new files.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of James W. MacDonald <jmacdon at uw.edu>
Sent: Tuesday, November 14, 2017 7:54:54 PM
To: Van Twisk, Daniel
Cc: bioc-devel; Yu, Guangchuang
Subject: Re: [Bioc-devel] annotation data not updated?
On Thu, Nov 9, 2017 at 9:48 AM, Van Twisk, Daniel <
Daniel.VanTwisk at roswellpark.org> wrote:
> Thanks for looking into this. New versions of the OrgDbs and Db0s
> (v3.5.0) are now available that have up-to-date resources. Here is the
> output of the new org.Hs.eg.db
Does this issue affect the OrgDbs on AnnotationHub as well? I am finding
e.g., that the OrgDb for Salmo salar contains GO IDs that no longer exist
in GO.db.
> zz
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Salmo salar
| SPECIES: Salmo salar
| CENTRALID: GID
| Taxonomy ID: 8030
| Db type: OrgDb
| Supporting package: AnnotationDbi
Please see: help('select') for usage information
> sum(!keys(zz, "GOALL") %in% keys(GO.db))
[1] 38
But this isn't true of, for example, the Homo sapiens OrgDb from
AnnotationHub
> z
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMAN_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| EGSOURCEDATE: 2017-Nov6
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: EG
| TAXID: 9606
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL:
ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2017-Nov01
| GOEGSOURCEDATE: 2017-Nov6
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
| GPSOURCEURL:
| GPSOURCEDATE: 2017-Oct9
| ENSOURCEDATE: 2017-Aug23
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.UniProt.org/
| UPSOURCEDATE: Tue Nov 7 20:57:02 2017
Please see: help('select') for usage information
> sum(!keys(z, "GOALL") %in% keys(GO.db))
[1] 0
But I am not sure when they were added, because the human OrgDb has an
rdatadateadded that is obviously not correct, since it precedes the
SOURCEDATEs from the OrgDb itself!
> mcols(hub["AH57973"])$rdatadateadded <------ Human
[1] "2017-10-23"
> mcols(hub["AH58003"])$rdatadateadded <------ Salmo
[1] "2017-10-27"
Best,
Jim
>
> > x <- org.Hs.eg.db
> > x
> OrgDb object:
> | DBSCHEMAVERSION: 2.1
> | Db type: OrgDb
> | Supporting package: AnnotationDbi
> | DBSCHEMA: HUMAN_DB
> | ORGANISM: Homo sapiens
> | SPECIES: Human
> | EGSOURCEDATE: 2017-Nov6
> | EGSOURCENAME: Entrez Gene
> | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> | CENTRALID: EG
> | TAXID: 9606
> | GOSOURCENAME: Gene Ontology
> | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/
> latest-lite/
> | GOSOURCEDATE: 2017-Nov01
> | GOEGSOURCEDATE: 2017-Nov6
> | GOEGSOURCENAME: Entrez Gene
> | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> | KEGGSOURCENAME: KEGG GENOME
> | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
> | KEGGSOURCEDATE: 2011-Mar15
> | GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
> | GPSOURCEURL:
> | GPSOURCEDATE: 2017-Oct9
> | ENSOURCEDATE: 2017-Aug23
> | ENSOURCENAME: Ensembl
> | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
> | UPSOURCENAME: Uniprot
> | UPSOURCEURL: http://www.UniProt.org/
> | UPSOURCEDATE: Tue Nov 7 20:57:02 2017
>
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
> Obenchain, Valerie <Valerie.Obenchain at RoswellPark.org>
> Sent: Thursday, November 2, 2017 12:47:43 PM
> To: Yu, Guangchuang; bioc-devel
> Subject: Re: [Bioc-devel] annotation data not updated?
>
> Guangchuang,
>
> Thanks for reporting this. We've looked into it and there is indeed a more
> recent version of the data. Daniel is working on re-generating the db0 and
> OrgDb packages. We'll post back with more information when the packages are
> ready.
>
> Valerie
>
>
> On 11/02/2017 05:40 AM, Yu, Guangchuang wrote:
>
> Dear all,
>
> I just upgraded BioC to 3.6 and found that the data source of org.Hs.eg.db
> and GO.db is still half year ago.
>
> I was wondering whether these packages had been updated in current release.
>
>
>
> org.Hs.eg.db
>
>
> OrgDb object:
> | DBSCHEMAVERSION: 2.1
> | Db type: OrgDb
> | Supporting package: AnnotationDbi
> | DBSCHEMA: HUMAN_DB
> | ORGANISM: Homo sapiens
> | SPECIES: Human
> | EGSOURCEDATE: *2017-Mar29*
> | EGSOURCENAME: Entrez Gene
> | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> | CENTRALID: EG
> | TAXID: 9606
> | GOSOURCENAME: Gene Ontology
> | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/
> latest-lite/
> | GOSOURCEDATE: *2017-Mar29*
> | GOEGSOURCEDATE: 2017-Mar29
> | GOEGSOURCENAME: Entrez Gene
> | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> | KEGGSOURCENAME: KEGG GENOME
> | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
> | KEGGSOURCEDATE: 2011-Mar15
> | GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
> | GPSOURCEURL:
> | GPSOURCEDATE: 2017-Sep7
> | ENSOURCEDATE: 2017-Mar29
> | ENSOURCENAME: Ensembl
> | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
> | UPSOURCENAME: Uniprot
> | UPSOURCEURL: http://www.UniProt.org/
> | UPSOURCEDATE: Thu Oct 5 16:07:33 2017
>
> Please see: help('select') for usage information
>
>
> GO.db
>
>
> GODb object:
> | GOSOURCENAME: Gene Ontology
> | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/
> latest-lite/
> | GOSOURCEDATE: *2017-Mar29*
> | Db type: GODb
> | package: AnnotationDbi
> | DBSCHEMA: GO_DB
> | GOEGSOURCEDATE: 2017-Mar29
> | GOEGSOURCENAME: Entrez Gene
> | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
> | DBSCHEMAVERSION: 2.1
>
> Please see: help('select') for usage information
>
>
> sessionInfo()
>
>
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel stats4 stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] org.Hs.eg.db_3.4.2 GO.db_3.4.2 AnnotationDbi_1.40.0
> [4] IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0
> [7] BiocGenerics_0.24.0 rvcheck_0.0.9 rmarkdown_1.6
> [10] roxygen2_6.0.1 magrittr_1.5 BiocInstaller_1.28.0
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.13 knitr_1.17 xml2_1.1.1 bit_1.1-12
> [5] R6_2.2.2 rlang_0.1.2 blob_1.1.0 stringr_1.2.0
> [9] tools_3.4.2 DBI_0.7 htmltools_0.3.6 commonmark_1.4
> [13] bit64_0.9-7 rprojroot_1.2 digest_0.6.12 tibble_1.3.4
> [17] memoise_1.1.0 RSQLite_2.0 evaluate_0.10.1 stringi_1.1.5
> [21] compiler_3.4.2 backports_1.1.1 pkgconfig_2.0.1
>
>
>
>
>
>
>
>
>
>
>
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Biostatistician
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