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-boun...@r-project.org> on behalf of Obenchain, Valerie <valerie.obench...@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 This email message may contain legally privileged and/or confidential information. 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