I have a list of ~58K ensembl gene ids of h.sapiens for which I need to extract the gene names, descriptions and other annotations from biomart.
The online way is failing primarily because of the huge list I am uploading, hence, I though to give this a try with the BiomaRt R package. I am trying to access ensembl biomart using following commands
source("http://bioconductor.org/biocLite.R") biocLite("biomaRt") library(biomaRt) listEnsembl()
> listEnsembl() Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available. Error: XML content does not seem to be XML:
From the error, it appears to be a problem with the URL - http://www.biomart.org, which I could infact access without any issue.
What I can see is a downtime notice here. Is it something related to this?
Can anybody suggest anything else?
What version of R and biomaRt are you using? I suspect you might have an old version. While the www.biomart.org website still exists, it ceased to be the central reportistory for BioMart instances quite a while ago. All the defaults in the biomaRt package should now point to www.ensembl.org
You can check the version using the command
sessionInfo(), here's mine along with the output i get when running
Working fine for me:
Check to see if an overzealous intrusion prevention device (or a firewall admin) has disabled your access since it seems to be working for others.