biomaRt human paralog timeout

Question

[matthew.martin]

I am using the github biomaRt version 2.37.5 am able to successful pull orthologs across a number of species. However, when I switch to trying to pull paralogs I get an curl timing out error. See the below code. I have tried different hosts. I have even limited the attributes to just "ensembl_gene_id" "hsapiens_paralog_ensembl_gene" I have also tried using the "values" parameter and limiting the number of genes to <100. It does not appear to be an actual latency or data volume issue.

Thanks for any pointers!

human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                 dataset = "hsapiens_gene_ensembl",
                 host    = "useast.ensembl.org")

attr <- as.data.table(listAttributes(human))

attributes <- c("ensembl_gene_id", attr[grepl("paralog", name), name][1])

para <- getBM(attributes,
              filters    = "with_hsapiens_paralog",
              values  = TRUE,
              mart     = human)

Answer 1

[matthew.martin]

I suspect that the original request was formatted in such a way that the query blows up (cartesian product).

I therefore first identified the genes with paralogs and then requested the paralog information only for those genes (2 steps instead of 1 essentially).

para.attr <- c("ensembl_gene_id", attr[grepl("paralog", name), name])

hgid <- getBM(attributes = "ensembl_gene_id",
              filters    = "with_hsapiens_paralog",
              values     = TRUE,
              mart       = human)$ensembl_gene_id

para <- getBM(attributes = para.attr,
              filters    = "ensembl_gene_id",
              values     = hgid,
              mart       = human)

Hope this is helpful for someone in the future.