[Bioc-devel] Annotation for Lactuca sativa (Lettuce)

[Camila Alves]

Hello Vicent,

Thank you very much!

Camila

On Mon, Jan 6, 2020 at 10:37 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> 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 <alves013 using 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]]
>>
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