This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Ensembl REST API Optional Parameters

Hello,

Can anyone please share an example of how one can specify optional parameters when using VEP through Ensembl REST API? I am following the examples on this page and would like to limit the results to those from canonical transcripts, and only return the maximum allele frequency in any population.

Best, Noushin

P.S. Tagging Emily_Ensembl

ensembl vep
• 3,799 views • link
updated by Ben Moore Ben Moore • written by Noushin N Noushin N

Are you putting this in a script (if so what language), just plugging a URL into a browser or using a REST client? Are you using POST or GET endpoints?

• 0 views • link
written by Emily Emily

Thank you! I am using this in an R script and using POST endpoint.

• 0 views • link
written by Noushin N Noushin N

1 answer

We have Jupyter notebooks that take you through a training course on using the REST API in different coding languages. This page covers how to use POST endpoints in R, and includes how to add optional parameters. Simply, you add them to the endpoint URL after a /. There's even a VEP example in there, although it is a different parameter.

• 0 views • link
written by Emily Emily

Thanks, Emily_Ensembl ! The tutorials were great.

For future reference of myself and others, here is an example of how one would add protein domain annotation and uniprot protein ids to vep results for an input specified in genomic coordinates:

server <- "http://grch37.rest.ensembl.org"
ext <- "/vep/homo_sapiens/region/?domains=1&uniprot=1"
query <- "17 7578407 - G A"

body <- sprintf('{ "variants" : ["%s"] }', query)
r <- httr::POST(paste(server, ext, sep = ""), httr::content_type("application/json"),
                        httr::accept("application/json"), body = body)
annot <- jsonlite::fromJSON(jsonlite::toJSON(httr::content(r)))
• 0 views • link
written by Noushin N Noushin N

Your links are dead (misleading) here, it would be helpful if you could restore them to a more useful state!

• 0 views • link
written by Jon • Jon

Log in to answer this question.

More posts like this