I have been trying to access WormBase using biomaRt in the hope of retrieving information for Transposon genes (eg WBTransposon00000001). I tried the instructions in the most recent vignette but it appears these are not correct:
library(biomaRt)
wormbase=useMart("WS220",dataset="wormbase_gene")
listFilters(wormbase)
listAttributes(wormbase)
getBM(attributes = c("public_name","rnai","rnai_phenotype_phenotype_label"),
filters="gene_name", values=c("unc-26","his-33"),
mart=wormbase)
The error occurs right at the beginning:
useMart("WS220", dataset = "wormbase_gene") :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
Changing to the latest version of the WormBase:
wormbase=useMart("WS235",dataset="wormbase_gene")
Results in the same error. What works is:
wormbase=useMart("ensembl", dataset="celegans_gene_ensembl")
However there is no information on transposons:
grep("Transposon", listAttributes(wormbase)[,1])
integer(0)
grep("Transposon", listAttributes(wormbase)[,2])
integer(0)
grep("transposon", listAttributes(wormbase)[,2])
integer(0)
grep("transposon", listAttributes(wormbase)[,1])
integer(0)
The questions are:
1. Is the vignette wrong or am I missing something?
2. Is data in wormbase_gene and celegans_gene_ensembl the same?
3. Ideas on how to get information on Transposons?
Edit: I forgot to attach the sessionInfo. See bellow.
Cheers
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.29.2
loaded via a namespace (and not attached):
[1] IRanges_2.4.8 parallel_3.2.2 DBI_0.4-1
[4] RCurl_1.95-4.8 Biobase_2.30.0 AnnotationDbi_1.32.3
[7] RSQLite_1.0.0 S4Vectors_0.8.11 BiocGenerics_0.16.1
[10] stats4_3.2.2 bitops_1.0-6 XML_3.98-1.4
Do you have a cut and paste error where you say 'What works is'? This line is the same as the one above.
Valerie
Well spotted Valery. It has been fixed now.
The vignette is very old, and from what I can see a lot of it isn't evaluated, so I suspect you've found an example that is now out-of-date.
Are you able to get information on transposons if you use the web interface at http://www.ensembl.org/biomart ?
You should be able to do almost any search using the R package that you can do with on the website, but I can't see the relevant information in there. Maybe I don't know the correct term to look for under the possible attributes you can return?
> Are you able to get information on transposons if you use the web interface at http://www.ensembl.org/biomart ?
No. Only Searching directly in Wormbase.
Regarding Wormbase and the issue with biomaRt not accessing it, I filled an issue in their github repo and got an answer. Relevant part is:
> Unfortunately WormMart has been retired and the new WormMine is still in a beta, with some data types not yet available.
So I guess this explains why biomaRt can't connect to wormbase. This bit should be removed from the vignette.