Question: Ensembl plants at annotationHub?
gravatar for Guido Hooiveld
12 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:


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 ( ).

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



ADD COMMENTlink modified 12 months ago by Johannes Rainer1.5k • written 12 months ago by Guido Hooiveld2.5k
Answer: Ensembl plants at annotationHub?
gravatar for Johannes Rainer
12 months ago by
Johannes Rainer1.5k
Johannes Rainer1.5k 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 12 months ago by Johannes Rainer1.5k

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!


ADD REPLYlink written 12 months ago by Guido Hooiveld2.5k

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,
# $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"]]' 

  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:
# $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:,
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH66148"]]'


ADD REPLYlink written 12 months ago by shepherl ♦♦ 1.7k

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 12 months ago by Johannes Rainer1.5k

Let's further this discussion off the support site 

ADD REPLYlink written 12 months ago by shepherl ♦♦ 1.7k

I've generated the EnsDb. You can get the file from here

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


ADD REPLYlink written 12 months ago by Johannes Rainer1.5k

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

ADD REPLYlink written 11 months ago by Guido Hooiveld2.5k
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