biomaRt: Wormbase not working
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@antonio-miguel-de-jesus-domingues-5182
Last seen 8 weeks ago
Germany

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

biomart wormbase • 1.5k views
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Do you have a cut and paste error where you say 'What works is'? This line is the same as the one above.

Valerie

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Well spotted Valery. It has been fixed now.

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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?

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> 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.

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