Question

Ensembl plants at annotationHub?

0

Entering edit mode

Guido Hooiveld ★ 3.3k

@guido-hooiveld-2020

Last seen 20 hours 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 • 1.7k views

ADD COMMENT • link updated 16 days ago by António • 0 • written 3.7 years ago by Guido Hooiveld ★ 3.3k

score 2 · Accepted Answer · 2018-11-22

2

Entering edit mode

Johannes Rainer ★ 2.0k

@johannes-rainer-6987

Last seen 13 days 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 3.7 years ago Johannes Rainer ★ 2.0k

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 3.7 years ago Guido Hooiveld ★ 3.3k

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 3.7 years ago shepherl 3.2k

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 3.7 years ago Johannes Rainer ★ 2.0k

1

Entering edit mode

Let's further this discussion off the support site

ADD REPLY • link 3.7 years ago shepherl 3.2k

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 3.7 years ago Johannes Rainer ★ 2.0k

0

Entering edit mode

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

ADD REPLY • link 3.7 years ago Guido Hooiveld ★ 3.3k

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 19 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 19 months ago shepherl 3.2k

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 19 months ago Johannes Rainer ★ 2.0k

0

Entering edit mode

Hi Johannes,

Could I request the same EnsDb creation for Medicago truncatula?

Thank you very much,

Karen

ADD REPLY • link 12 weeks ago karenserrano • 0

0

Entering edit mode

Hi Karen,

I've created the EnsDb (for Ensembl release 106, which corresponds to ensemblgenomes release 53). You can download the file from here. The file is called EnsDb.Mtruncatula.v106.sqlite. You can simply load this database using the EnsDb function.

cheers, jo

ADD REPLY • link 12 weeks ago Johannes Rainer ★ 2.0k

0

Entering edit mode

Dear Johannes, can you tell me how can I access to an EnsDb annotation of Vitis vinifera?

Many thanks,

António

ADD REPLY • link 29 days ago António • 0

0

Entering edit mode

Dear Antonio,

I can create you an EnsDb for Vitis vinifera - could you please tell me from which Ensembl (or Ensemblgenomes) release you want to have it?

thanks, jo

ADD REPLY • link 21 days ago Johannes Rainer ★ 2.0k

0

Entering edit mode

Dear Johannes,

Many thanks for your help. I want it for the last genome assemble release that is the PN40024.v4. If not possible could perfectly be the previous version v3.

best regards,

António

ADD REPLY • link 21 days ago António • 0

0

Entering edit mode

Hi Antonio,

I've created an EnsDb for Ensembl version 107 (which has PN40024.v4). You can download the sqlite file (EnsDb.Vvinifera.v107.sqlite) from here. To use this database:

> library(ensembldb)
> edb <- EnsDb("EnsDb.Vvinifera.v107.sqlite")
> edb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.7
|Creation time: Mon Jul 25 08:22:47 2022
|ensembl_version: 107
|ensembl_host: localhost
|Organism: Vitis vinifera
|taxonomy_id: 29760
|genome_build: PN40024.v4
|DBSCHEMAVERSION: 2.2
| No. of genes: 35134.
| No. of transcripts: 41097.
|Protein data available.

cheers, jo

ADD REPLY • link 16 days ago Johannes Rainer ★ 2.0k

0

Entering edit mode

Many thanks,

works fine,

Best regards,

António

ADD REPLY • link 16 days ago António • 0