The goslim_goa_accession attribute seems to have disappeared within ENSEMBL_MART_PLANT of the current release but is still available for ENSEMBL. Is there now an alternative option to get to this attribute? The below used to work fine a few month ago.

Thanks,

Thomas

> library("biomaRt")
> m <- useMart("ENSEMBL_MART_PLANT", dataset="athaliana_eg_gene")
goslimvec <- as.character(getBM(attributes=c("goslim_goa_accession"), mart=m)[,1])
> goslimvec <- as.character(getBM(attributes=c("goslim_goa_accession"), mart=m)[,1])
Error in getBM(attributes = c("goslim_goa_accession"), mart = m) :
  Invalid attribute(s): goslim_goa_accession
Please use the function 'listAttributes' to get valid attribute names

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

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

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

other attached packages:
 [1] systemPipeR_1.0.11      AnnotationDbi_1.28.1    Biobase_2.26.0
 [4] RSQLite_1.0.0           DBI_0.3.1               ShortRead_1.24.0
 [7] GenomicAlignments_1.2.1 BiocParallel_1.0.0      Rsamtools_1.18.2
[10] Biostrings_2.34.0       XVector_0.6.0           GenomicRanges_1.18.3
[13] GenomeInfoDb_1.2.3      IRanges_2.0.1           S4Vectors_0.4.0
[16] BiocGenerics_0.12.1     biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] annotate_1.44.0       AnnotationForge_1.8.1 base64enc_0.1-2
 [4] BatchJobs_1.5         BBmisc_1.8            bitops_1.0-6
 [7] brew_1.0-6            Category_2.32.0       checkmate_1.5.0
[10] codetools_0.2-9       colorspace_1.2-4      digest_0.6.4
[13] edgeR_3.8.5           fail_1.2              foreach_1.4.2
[16] genefilter_1.48.1     ggplot2_1.0.0         GO.db_3.0.0
[19] GOstats_2.32.0        graph_1.44.0          grid_3.1.2
[22] GSEABase_1.28.0       gtable_0.1.2          hwriter_1.3.2
[25] iterators_1.0.7       lattice_0.20-29       latticeExtra_0.6-26
[28] limma_3.22.1          MASS_7.3-35           Matrix_1.1-4
[31] munsell_0.4.2         pheatmap_0.7.7        plyr_1.8.1
[34] proto_0.3-10          RBGL_1.42.0           RColorBrewer_1.1-2
[37] Rcpp_0.11.3           RCurl_1.95-4.5        reshape2_1.4.1
[40] rjson_0.2.15          scales_0.2.4          sendmailR_1.2-1
[43] splines_3.1.2         stringr_0.6.2         survival_2.37-7
[46] tools_3.1.2           XML_3.98-1.1          xtable_1.7-4
[49] zlibbioc_1.12.0

Dear Thomas,

Just to let you know that I've contacted my colleagues in Ensembl genomes and they are looking into this.

I will come back to you asap.

Regards,

Thomas

Dear Thomas,

I am afraid this is a bug in release 25, the goslim_goa_accession attribute should be back in the next Ensembl genomes release planned for March 2015.

Hope this helps,

Regards,

Thomas