You'll need a current version of R and the AnnotationHub package installed. Then
> library(AnnotationHub) ah *5/39 packages newly attached/loaded, see sessionInfo() for details.* > ah = AnnotationHub() *snapshotDate(): 2019-12-26* > query(ah, "sativa") AnnotationHub with 7 records # snapshotDate(): 2019-12-26 # $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Inparanoid8 # $species: Oryza sativa_subsp._japonica, Oryza sativa_Japonica_Group, Oryza... # $rdataclass: OrgDb, Inparanoid8Db # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["AH10561"]]' title AH10561 | hom.Oryza_sativa.inp8.sqlite AH75771 | org.Camelina_sativa.eg.sqlite AH75823 | org.Lactuca_sativa.eg.sqlite AH75915 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite AH75916 | org.Oryza_sativa_Japonica_Group.eg.sqlite AH75917 | org.Oryza_sativa_subsp._japonica.eg.sqlite AH76047 | org.Cannabis_sativa.eg.sqlite What then do we have? > lett = ah[["AH75823"]] *downloading 1 resources* *retrieving 1 resource* * |======================================================================| 100%* *loading from cache* *Loading required package: AnnotationDbi* *Loading required package: stats4* *Loading required package: Biobase* *Welcome to Bioconductor* * Vignettes contain introductory material; view with* * 'browseVignettes()'. To cite Bioconductor, see* * 'citation("Biobase")', and for packages 'citation("pkgname")'.* *Attaching package: ‘Biobase’* *The following object is masked from ‘package:AnnotationHub’:* * cache* *Loading required package: IRanges* *Loading required package: S4Vectors* *Attaching package: ‘S4Vectors’* *The following object is masked from ‘package:base’:* * expand.grid* > lett OrgDb object: | DBSCHEMAVERSION: 2.1 | DBSCHEMA: NOSCHEMA_DB | ORGANISM: Lactuca sativa | SPECIES: Lactuca sativa | CENTRALID: GID | Taxonomy ID: 4236 | Db type: OrgDb | Supporting package: AnnotationDbi *Please see: help('select') for usage information* > keys(lett)[1:10] [1] "3772783" "3772784" "3772785" "3772786" "3772787" "3772788" "3772789" [8] "3772790" "3772791" "3772792" > select(lett, keys=.Last.value, columns="GENENAME") *'select()' returned 1:1 mapping between keys and columns* GID GENENAME 1 3772783 Ycf2 2 3772784 Ycf2 3 3772785 ribosomal protein S4 4 3772786 envelope membrane protein 5 3772787 ribosomal protein S14 6 3772788 photosystem II protein D1 7 3772789 photosystem I P700 chlorophyll a apoprotein A2 8 3772790 ribosomal protein S15 9 3772791 photosystem II protein K 10 3772792 ribosomal protein L20 > columns(lett) [1] "ACCNUM" "ALIAS" "CHR" "ENTREZID" "EVIDENCE" [6] "EVIDENCEALL" "GENENAME" "GID" "GO" "GOALL" [11] "ONTOLOGY" "ONTOLOGYALL" "PMID" "REFSEQ" "SYMBOL" [16] "UNIGENE" > Please post any followup questions to support.bioconductor.org On Mon, Jan 6, 2020 at 11:25 AM Camila Alves <alves...@umn.edu> wrote: > Hello, > > I am looking for Lactuca sativa (lettuce) annotation to download but I am > not finding it. Do you have it available? > > Thank you, > Camila > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
