Closed Gurlaz closed 5 years ago
I've just tried myself to get biomaRt working with Vectorbase. It will list datasets but won't work with getBM. The manual has a section on other biomarts using Wormbase as an example.
listMarts(host = "biomart.vectorbase.org")
vectorbase = useMart(biomart = "vb_gene_mart_1902",
host = "https://biomart.vectorbase.org",
port = 443)
listDatasets(vectorbase)
vectorbase <- useDataset(mart = vectorbase, dataset = "alvpagwg_eg_gene") #Aedes - change for other organisms
go_ids = getBM(attributes = c("go_id", "external_gene_name", "ensembl_gene_id","refseq_dna"),
filters="external_gene_name",
values=geneUniverse,
mart=vectorbase,
verbose = TRUE)
Before I saw the manual I found @grimbough gist to test if it was on my end or the server and play with urls: https://gist.github.com/grimbough/1e44fbe7ab4e3638671ef5e11e7128db I just copied the XML output from vectorbase's biomart and replaced some info.
I skimmed the biomart manual for the version vectorbase uses (0.7) http://www.biomart.org/other/user-docs.pdf
I just saw today if anyone comes across this, grimbough posted the same for Ensembl Fungi data using biomaRt:
https://support.bioconductor.org/p/116770/#116775
Thank you @cerdelyan, I tried your method and it works. Changing the host name to full and giving it port 443 was the trick. Thanks to you I have my GO ids now.
Thanks @cerdelyan for answering this.
The function getBM() gives me following error:
My script looks like this:
I have tried following https://github.com/grimbough/biomaRt/issues/3 to get individual attributes:
But the error remains the same. I manually checked the website on vector base for biomart, it works fine. I do not understand, if the error is from my end or the website connection timeout. My session info is:
Any ideas are highly appreciated. Thanks!