Question: Ensembl plants at annotationHub?
0
gravatar for Guido Hooiveld
6 months ago by
Guido Hooiveld2.4k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.4k wrote:

Hi,

I am regularly using the annotationHub to retrieve/query the Ensembl-based gene annotations (ensembldb). This works fine for e.g human and mouse, but I now would like to obtain info made available through the Ensembl Plant database; specifically for Arabidopsis ( http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index ).

Question: Is such ensembldb available at the annotationHub? I searched for it but could not find it...

Thanks,

Guido

ADD COMMENTlink modified 6 months ago by Johannes Rainer1.4k • written 6 months ago by Guido Hooiveld2.4k
Answer: Ensembl plants at annotationHub?
2
gravatar for Johannes Rainer
6 months ago by
Johannes Rainer1.4k
Italy
Johannes Rainer1.4k wrote:

Dear Guido,

while it is possible to create EnsDb databases also for ensemblgenomes (including plants, funghi etc) I did not do this on a regular basis and was also hesitant to add these to AnnotationHub because I was not sure how many users there will be for these.

Just let me know which species (for which Ensembl/Ensemblgenomes) version you need and I will create the EnsDb for you.

cheers, jo

ADD COMMENTlink written 6 months ago by Johannes Rainer1.4k

Hi Johannes,

Thanks for your offer! As far as I am concerned only an EnsDb for the latest genome info for Arabidopsis would do for now. (EnsemblPlants, release 41, Sept 2018, here).

Thanks a lot for your help!

Guido

ADD REPLYlink written 6 months ago by Guido Hooiveld2.4k
2

Also don't know if its helpful but there is a recent orgDb added to AnnotationHub for Arabidopsis matching the taxonomyid on the reference page you listed

> ah[which(mcols(ah)$taxonomyid==3702)]
AnnotationHub with 5 records
# snapshotDate(): 2018-11-01 
# $dataprovider: UCSC, Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Arabidopsis thaliana
# $rdataclass: TxDb, Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH10456"]]' 

            title                                     
  AH10456 | hom.Arabidopsis_thaliana.inp8.sqlite      
  AH52245 | TxDb.Athaliana.BioMart.plantsmart22.sqlite
  AH52246 | TxDb.Athaliana.BioMart.plantsmart25.sqlite
  AH52247 | TxDb.Athaliana.BioMart.plantsmart28.sqlite
  AH66148 | org.At.tair.db.sqlite
> ah["AH66148"]
AnnotationHub with 1 record
# snapshotDate(): 2018-11-01 
# names(): AH66148
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Arabidopsis thaliana
# $rdataclass: OrgDb
# $rdatadateadded: 2018-10-22
# $title: org.At.tair.db.sqlite
# $description: NCBI gene ID based annotations about Arabidopsis thaliana
# $taxonomyid: 3702
# $genome: NCBI genomes
# $sourcetype: NCBI/ensembl
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.ensembl.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH66148"]]'

Cheers

ADD REPLYlink written 6 months ago by shepherl ♦♦ 1.4k

Lori, do you think it might be usefull to add also EnsDb for all species in ensemblgenomes to AnnotationHub (starting ev "only" with plants)?
 

ADD REPLYlink written 6 months ago by Johannes Rainer1.4k
1

Let's further this discussion off the support site 

ADD REPLYlink written 6 months ago by shepherl ♦♦ 1.4k

I've generated the EnsDb. You can get the file from here https://www.dropbox.com/sh/wglt28zlfzhjubs/AADzGqJ0zydKRmdqbOsH_Ru5a?dl=0

after unzipping you can simply load the sqlite file with edb <- EnsDb(<sqlite-file>)

 

ADD REPLYlink written 6 months ago by Johannes Rainer1.4k

Thanks! Meanwhile downloaded the file and everything is working fine.
 

ADD REPLYlink written 6 months ago by Guido Hooiveld2.4k
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