[Bioc-devel] annotation data not updated?

Thu Nov 9 15:48:53 CET 2017

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:

> 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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