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...
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.
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).
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
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
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).
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.
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.
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.
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
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 listedCheers
Lori, do you think it might be usefull to add also EnsDb for all species in ensemblgenomes to AnnotationHub (starting ev "only" with plants)?
Let's further this discussion off the support site
I've generated the
EnsDb
. You can get the file from here https://www.dropbox.com/sh/wglt28zlfzhjubs/AADzGqJ0zydKRmdqbOsH_Ru5a?dl=0after unzipping you can simply load the sqlite file with
edb <- EnsDb(<sqlite-file>)
Thanks! Meanwhile downloaded the file and everything is working fine.
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
It looks like there are three that could be of interested and utilized.
Dear Cameron,
I create
EnsDb
annotation resources for all species part of the Ensembl core databases which are then available through theAnnotationHub
(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
Hi Johannes,
Could I request the same EnsDb creation for Medicago truncatula?
Thank you very much,
Karen
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 theEnsDb
function.cheers, jo
Dear Johannes, can you tell me how can I access to an EnsDb annotation of Vitis vinifera?
Many thanks,
António
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
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
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:cheers, jo
Many thanks,
works fine,
Best regards,
António