Variant to Gene Query for multiple variants in OT Genetics

Data Access GraphQL API
1

Dear Open Target team,

First of all, thank you very much for your valuable work.

I need to perform a Variant to Gene search for multiple variants (>200).

I am trying to find a way to do it through a script that generates a table with the results containing the same parameters as when I search the rsid individually through the browser but I’ve been not able to find what I am looking for in the documentation.

Your guidance would be very appreciated.

Thank you very much!

Paloma

2

Thanks for your question Paloma. For a moderate number of variants, you could use the GraphQL API, which can be access via a browser, or programmatically.

For example, a query in the browser might look something like this:
GraphQL variant to gene query.

You can use a language of your choice to do the query programmatically, e.g. python or R. Here is an example in R:

# Install relevant library for HTTP requests
library(httr)

# Set gene_id variable
variantId <- "17_44352876_C_T"

# Build query string
query_string = "
query v2g($variantId: String!) {
  genesForVariant(variantId: $variantId) {
    gene {
      id
    }
    variant
    overallScore
    distances {
      sourceId
      aggregatedScore
      tissues {
      	distance
      }
    }
  }
}"

# Set base URL of GraphQL API endpoint
base_url <- "https://api.genetics.opentargets.org/graphql"

# Set variables object of arguments to be passed to endpoint
variables <- list("variantId" = variantId)

# Construct POST request body object with query string and variables
post_body <- list(query = query_string, variables = variables)

# Perform POST request
r <- POST(url=base_url, body=post_body, encode='json')

df = content(r)
# Print first entry of V2G data console
head(content(r)$data$genesForVariant, 1)

# Flatten the nested result fields into a dataframe
library(rlist)
list_result = content(r)$data$genesForVariant
x = lapply(list_result, list.flatten)

library(dplyr)
df = bind_rows(x)

Note that if you want to get the information for individual QTL associations, you would need to do a bit more to flatten the resulting nested lists.

3

Thank you very much for your detailed and very helpful response Jeremy! It worked!

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