Question: biomaRt retrieving only NAs for Oryza sativa gene descriptions/annotations
0
gravatar for jennareeg
3 months ago by
jennareeg0
jennareeg0 wrote:

I am trying to retrieve Oryza sativa protein coding genes with their annotations. When running this code months ago, it worked fine. Now when I run it, I get a data frame with the list of gene IDs, chromosome names, start and stop positions, but only NAs in the description column. I need some help figuring out how to get the gene annotations again!

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("biomaRt", version = "3.8")

library("biomaRt")

rice_mart <- useMart("plants_mart", 
                           dataset="osativa_eg_gene", 
                           host="plants.ensembl.org")

rice_genes <- getBM(attributes = c("ensembl_gene_id",
                                "chromosome_name",
                                "start_position",
                                "end_position", 
                                "description"), 
                                filters = "biotype", 
                                values = "protein_coding", 
                                mart=rice_mart)

sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] biomaRt2.38.0 GenomicRanges1.34.0 GenomeInfoDb1.18.2 IRanges2.16.0 S4Vectors0.20.1
[6] BiocGenerics
0.28.0

loaded via a namespace (and not attached): [1] Rcpp1.0.1 BiocManager1.30.4 compiler3.5.3 XVector0.22.0
[5] prettyunits1.0.2 bitops1.0-6 tools3.5.3 progress1.2.0
[9] zlibbioc1.28.0 digest0.6.18 bit1.1-14 RSQLite2.1.1
[13] memoise1.1.0 pkgconfig2.0.2 rlang0.3.4 DBI1.0.0
[17] rstudioapi0.10 curl3.3 yaml2.2.0 xfun0.6
[21] GenomeInfoDbData1.2.0 stringr1.4.0 httr1.4.0 knitr1.22
[25] hms0.4.2 bit640.9-7 Biobase2.42.0 R62.4.0
[29] AnnotationDbi1.44.0 XML3.98-1.19 blob1.1.1 magrittr1.5
[33] assertthat0.2.1 stringi1.4.3 RCurl1.95-4.12 crayon1.3.4

annotation • 134 views
ADD COMMENTlink modified 3 months ago by Mike Smith3.8k • written 3 months ago by jennareeg0
Answer: biomaRt retrieving only NAs for Oryza sativa gene descriptions/annotations
1
gravatar for Mike Smith
3 months ago by
Mike Smith3.8k
EMBL Heidelberg / de.NBI
Mike Smith3.8k wrote:

It looks to me like the description is blank if you use the web interface too e.g Ensembl Plants BioMart

If that's the case then you'll need to contact Ensembl to find out why the underlying dataset has changed. It looks like the rice genome was update in the last release, so maybe this is related

Details on genome updates: ... - Rice (Oryza sativa): updated gene annotation to RAP-DB version 2018-11-26 and added stable_id mappings to previous annotation

ADD COMMENTlink modified 3 months ago • written 3 months ago by Mike Smith3.8k
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