dgidb-graphql-example.md

dgidb-example

2023-12-15

Querying DGIdb GraphQL API

Load packages:

library("ghql")
library(jsonlite)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ forcats   1.0.0     ✔ readr     2.1.4
## ✔ ggplot2   3.4.4     ✔ stringr   1.5.1
## ✔ lubridate 1.9.3     ✔ tibble    3.2.1
## ✔ purrr     1.0.2     ✔ tidyr     1.3.0

## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter()  masks stats::filter()
## ✖ purrr::flatten() masks jsonlite::flatten()
## ✖ dplyr::lag()     masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Link to the GraphQL schema and create a client object

link <- 'https://dgidb.org/api/graphql'
conn <- GraphqlClient$new(url = link)

Define a query and specify query variables

rawQuery <- '
query($id: [String!]){
  genes(names: $id) {
    nodes {
      name
      interactions {
        drug {
          name
        } 
        interactionAttributes {
          name
          value
        }
      }
      geneCategoriesWithSources {
        name
      }
    }
  }
}'
query <- Query$new()$query('link', rawQuery)

variable <- list(
  id = list("RAMP3", "XPO1")
)

Issue the request:

result <- conn$exec(query$link, variables = variable) %>%
  fromJSON()

I am utterly failing at turning this into a table that preserves the individual key/value interaction attribute pairings.

knitr::kable(
  result$data$genes$nodes
)

name	interactions	geneCategoriesWithSources
XPO1	FELEZONEXOR , SELINEXOR , LEPTOMYCIN B , OSTHOLE , GONIOTHALAMIN , Direct Interaction , Mechanism of Action , true , Exportin-1 inhibitor	CLINICALLY ACTIONABLE, KINASE
RAMP3	STREPTOZOCIN , PRAMLINTIDE ACETATE , PRAMLINTIDE , Direct Interaction , Mechanism of Action , true , Amylin receptor AMY3; CALCR/RAMP3 agonist, Clinical Trial Name , Novel Drug Target , Symlin , Established target	CELL SURFACE , DRUGGABLE GENOME