[Bioc-devel] annotation data not updated?
Yu, Guangchuang
gcyu at connect.hku.hk
Thu Nov 2 13:40:31 CET 2017
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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Guangchuang Yu PhD
Postdoc researcher
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: https://guangchuangyu.github.io
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