Question

Ensembl plants at annotationHub?

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Guido Hooiveld ★ 3.8k

@guido-hooiveld-2020

Last seen 22 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 • 4.2k views

ADD COMMENT • link updated 7 weeks ago by karenserrano • 0 • written 5.1 years ago by Guido Hooiveld ★ 3.8k

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Bruno • 0

@d209d072

Last seen 12 weeks ago

France

Hi Johannes,

First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant community ^^ I have been trying to find a good Arabidopsis thaliana annotation for single cell ATAC seq analysis, and downloaded the Arabidopsis Annotation you created 4.5 years ago. But Unfortunately R display the error "Annotation must be a GRanges object" Despite trying to convert it using different program but did not succeed. Would you have a solution about that ?

Thank you very much in advance for your help,

Bruno

ADD COMMENT • link 6 months ago Bruno • 0

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You did not show the code that resulted in that error, so we have to guess what you did. Yet, the R package Signac contains the function GetGRangesFromEnsDb() (link). May be that is worth looking at? Or did you already do so and refered to it as 'different program'?

Note that Signac is not a Bioconductor package, and therefore questions on Signac are best asked on its own website. Yet, if the function works fine on another EnsDb, then it is (indeed) related to the Arabidopsis EnsDb.

ADD REPLY • link 6 months ago Guido Hooiveld ★ 3.8k

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Hi Guido,

Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the annotation for my dataset. I had tried makeGRangesFromEnsDb() without success but I missed the GetGRangesFromEnsDb(). It works using Johannes Annotation.

Thanks again

ADD REPLY • link 6 months ago Bruno • 0

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Hi Johannes,

I used with success your previous EnsDb annotation Arabidopsis thaliana but many new genes are not annotated on that previous version. Would it be possible to have a new EnsDb annotation for Arabidopsis thaliana ? The newest gene annotation is called Arabidopsis_thaliana.TAIR10.55 on Tair. Would you also be able to provide a tutorial on how to do it, so people stop bothering you ? I could not find anything that works online.

Thank you very much for your help,

ADD REPLY • link 3 months ago Bruno • 0

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Hi Bruno,

there is information available in the ensembldb vignette on how to build an EnsDb directly from the Ensembl MySQL database(s) - but it's not straight forward to get the Ensembl Perl API and required Perl version installed properly.

I've created the EnsDb for arabidopsis thaliana (genome build TAIR10) for Ensembl release 110 (the current version). You can download the sqlite file from here. Please let me know if that was not the version you were looking for.

Best, jo

ADD REPLY • link 3 months ago Johannes Rainer ★ 2.0k

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Hi Jo,

It works like a charm. Thanks a lot for your help !! Bru

ADD REPLY • link 3 months ago Bruno • 0

score 2 · Accepted Answer · 2018-11-22

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Johannes Rainer ★ 2.0k

@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 5.1 years ago Johannes Rainer ★ 2.0k

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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 5.1 years ago Guido Hooiveld ★ 3.8k

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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 5.1 years ago shepherl 3.6k

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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 5.1 years ago Johannes Rainer ★ 2.0k

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Let's further this discussion off the support site

ADD REPLY • link 5.1 years ago shepherl 3.6k

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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 5.0 years ago Johannes Rainer ★ 2.0k

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

ADD REPLY • link 5.0 years ago Guido Hooiveld ★ 3.8k

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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 2.9 years ago Cameron • 0

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> 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 2.9 years ago shepherl 3.6k

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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 2.9 years ago Johannes Rainer ★ 2.0k

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Hi Johannes,

Could I request the same EnsDb creation for Medicago truncatula?

Thank you very much,

Karen

ADD REPLY • link 19 months ago karenserrano • 0

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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 19 months ago Johannes Rainer ★ 2.0k

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Thank you, this helped a lot! If it's not too much trouble, would it be possible to get the same for "Rhizophagus irregularis DAOM 181602=DAOM 197198 (ASM43914v3)"?

Many thanks,

Karen

ADD REPLY • link 14 months ago karenserrano • 0

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Dear Karen,

I had a look at the Ensemblgenomes site for this fungus (here), but could not find the actual MySQL database that contains the gene, protein etc annotations. Without that I can not create the EnsDb.

In fact, for fungi, these are all available databases - could you maybe have a look through them to see if you could identify the one containing annotations for that species? I'm not familiar with fungi genus and species collections...

ADD REPLY • link 14 months ago Johannes Rainer ★ 2.0k

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Hi Johannes, Thanks for trying... I could not find it there in those databases. It is in the list of genomes in the parent directory, but I don't see that file in any of the sql databases.

https://fungi.ensembl.org/Rhizophagus_irregularis_daom_181602_daom_197198_gca_002897155/Info/Index

Also sorry for the very delayed response :)

ADD REPLY • link 7 weeks ago karenserrano • 0

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

Many thanks,

António

ADD REPLY • link 17 months ago António • 0

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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 16 months ago Johannes Rainer ★ 2.0k

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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 16 months ago António • 0

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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 months ago Johannes Rainer ★ 2.0k

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Many thanks,

works fine,

Best regards,

António

ADD REPLY • link 16 months ago António • 0