I have been using biomaRt for some time now and it has been working nicely. However, today while trying to convert some ensembl gene ids to uniprotswissprot ids I have been facing some problems. The code and the error are as follows:
#importing the library library(biomart) #since I am working with thaliana - I create the mart object as follows thaliana_mart = useMart(host="plants.ensembl.org", "plants_mart", dataset = "athaliana_eg_gene") #running a sample code where I want to retrieve a uniprotswissprot id getBM(mart = thaliana_mart, attributes = "uniprotswissprot", values = "AT4G21050", filters = "ensembl_gene_id")
Here I expect to get the uniprotswissprot id - Q9SUA9 which is corresponding to AT4G21050, however, I get the following error.
Error in result_create(conn@ptr, statement) : no such table: metadata
Also, something that I should mention : I make requests in bulk. This piece of code is a part of a larger code which runs through 25 ids at a time and does a bunch of other functions. In order to not over-shoot the limit of 55000 requests per hour by ensembl's REST-API, I put the code to "sleep" after one batch of 25 ids for 1800 seconds (half hour).
Can anyone please help me?