Question

Ensembl plants at annotationHub?

0

Entering edit mode

Guido Hooiveld ★ 3.0k

@guido-hooiveld-2020

Last seen 1 day ago

Wageningen University, Wageningen, the …

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

ensembl ensembldb plant arabidopsis thaliana annotationhub • 995 views

ADD COMMENT • link updated 8 months ago by Johannes Rainer ★ 1.9k • written 2.8 years ago by Guido Hooiveld ★ 3.0k

score 2 · Accepted Answer · 2018-11-22

2

Entering edit mode

Johannes Rainer ★ 1.9k

@johannes-rainer-6987

Last seen 3 months ago

Italy

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 COMMENT • link 2.8 years ago Johannes Rainer ★ 1.9k

0

Entering edit mode

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 REPLY • link 2.8 years ago Guido Hooiveld ★ 3.0k

2

Entering edit mode

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 REPLY • link 2.8 years ago shepherl 2.8k

0

Entering edit mode

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 REPLY • link 2.8 years ago Johannes Rainer ★ 1.9k

1

Entering edit mode

Let's further this discussion off the support site

ADD REPLY • link 2.8 years ago shepherl 2.8k

0

Entering edit mode

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 REPLY • link 2.8 years ago Johannes Rainer ★ 1.9k

0

Entering edit mode

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

ADD REPLY • link 2.8 years ago Guido Hooiveld ★ 3.0k

0

Entering edit mode

Hi, I am having a similar problem. How do I access the rice data (Oryza sativa Japonica Group) made available through the Ensembl Plant database. Sorry if this is extremely obvious I am new to this, thank you in advance for any help you can provide. Sincerely Cameron

ADD REPLY • link 8 months ago Cameron • 0

0

Entering edit mode

> ah = AnnotationHub()
snapshotDate(): 2020-12-19

> query(ah, "Oryza sativa")
AnnotationHub with 4 records
# snapshotDate(): 2020-12-19
# $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                        
  AH85565 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite
  AH85566 | org.Oryza_sativa_Japonica_Group.eg.sqlite           
  AH85567 | org.Oryza_sativa_subsp._japonica.eg.sqlite

It looks like there are three that could be of interested and utilized.

ADD REPLY • link 8 months ago shepherl 2.8k

0

Entering edit mode

Dear Cameron,

I create EnsDb annotation resources for all species part of the Ensembl core databases which are then available through the AnnotationHub (see also Lori's reply). I don't create these by default for the Ensembl plants, fungi, etc databases.

It would however not be a big problem for me to create them on demand - just let me know what species and Ensembl release you need (unless the resources already available in AnnotationHub - see Lori's reply - are not already sufficient).

cheers, jo

ADD REPLY • link 8 months ago Johannes Rainer ★ 1.9k