Is ther an annotation package for sheep (Ovis aries)
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@078471bb
Last seen 15 months ago
Spain

Hi,

I wonder if there is a sheep-specific genome database package for sheep, such as EnsDb.Hsapiens.v86 in human. I could only find a package for Affymetrix data in sheep.

Thank you, Priscila

sheep database_package Annotation • 1.2k views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

Yes, there is!

An EnsDb for sheep can be obtained through the so-called AnnotationHub.

See James' and my posts in the thread linked to for all code. Note that these were used to obtain a EnsDb for rat, but the code is easily changed.

EnsDb.Rnorvegicus for Rnor6

The key difference is thus to query for sheep (and not rat):

> library(AnnotationHub)
> library(ensembldb)
> library(AnnotationForge)
> 
> ## start an AnnotationHub instance/connection.
> ah <- AnnotationHub()
snapshotDate(): 2022-10-31
> 
> ## query for available Sheep EnsDb
> EnsDb.sheep <- query(ah, c("EnsDb", "Ovis aries"))
> EnsDb.sheep
AnnotationHub with 21 records
# snapshotDate(): 2022-10-31
# $dataprovider: Ensembl
# $species: Ovis aries
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53225"]]' 

             title                           
  AH53225  | Ensembl 87 EnsDb for Ovis Aries 
  AH53729  | Ensembl 88 EnsDb for Ovis Aries 
  AH56695  | Ensembl 89 EnsDb for Ovis Aries 
  AH57777  | Ensembl 90 EnsDb for Ovis Aries 
  AH60796  | Ensembl 91 EnsDb for Ovis Aries 
  ...        ...                             
  AH95797  | Ensembl 104 EnsDb for Ovis aries
  AH98100  | Ensembl 105 EnsDb for Ovis aries
  AH100696 | Ensembl 106 EnsDb for Ovis aries
  AH104917 | Ensembl 107 EnsDb for Ovis aries
  AH109389 | Ensembl 108 EnsDb for Ovis aries
> 
>
> ## Fetch the v108 EnsDb and put it in the cache.
> EnsDb.sheep <- EnsDb.sheep[["AH109389"]]
downloading 1 resources
retrieving 1 resource
loading from cache
> 
> ##check
> columns(EnsDb.sheep)
 [1] "CANONICALTRANSCRIPT" "DESCRIPTION"         "ENTREZID"           
 [4] "EXONID"              "EXONIDX"             "EXONSEQEND"         
 [7] "EXONSEQSTART"        "GCCONTENT"           "GENEBIOTYPE"        
[10] "GENEID"              "GENEIDVERSION"       "GENENAME"           
[13] "GENESEQEND"          "GENESEQSTART"        "INTERPROACCESSION"  
[16] "ISCIRCULAR"          "PROTDOMEND"          "PROTDOMSTART"       
[19] "PROTEINDOMAINID"     "PROTEINDOMAINSOURCE" "PROTEINID"          
[22] "PROTEINSEQUENCE"     "SEQCOORDSYSTEM"      "SEQLENGTH"          
[25] "SEQNAME"             "SEQSTRAND"           "SYMBOL"             
[28] "TXBIOTYPE"           "TXCDSSEQEND"         "TXCDSSEQSTART"      
[31] "TXEXTERNALNAME"      "TXID"                "TXIDVERSION"        
[34] "TXISCANONICAL"       "TXNAME"              "TXSEQEND"           
[37] "TXSEQSTART"          "TXSUPPORTLEVEL"      "UNIPROTDB"          
[40] "UNIPROTID"           "UNIPROTMAPPINGTYPE" 
>
> ## and so on...
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It worked great, thank you so much!

I only have a problem I couldn´t solve.

The package was generated for a specific sheep breed (Texel) with this annotation: https://www.ensembl.org/Ovis_aries/Info/Annotation

I would like to create it for this annotation because it is the general sheep annotation that most people use: https://www.ensembl.org/Ovis_aries_rambouillet/Info/Annotation

I don´t know how to do it; I guess I have to find the specific EnsDb record, but I couldn´t do it...

Thank you!

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Ahh, that is a pity!

I (also) wasn't able to find on the AnnotationHub an EnsDb for your specific sheep breed...

Yet, you could try to generate one yourselves. See the help page of the function makeEnsembldbPackage (from the library ensembldb) for few suggestions.

BTW: I know from experience that querying the Ensembl database using the Ensembl Perl API may be challenging, but parsing the GTF/GFF file obtained from Ensembl may be sufficient for you.

Alternatively, you may file a request for your specific EnsDb at the GitHub pages of ensembldb (https://github.com/jorainer/ensembldb/issues); whenever his time permits, Johannes Rainer (the maintainer) is known to kindly generate a specific EnsDb upon request.

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