Batch download disease/association scores

[animesh]

I am trying to download association scores from a list of IDs using the api/v4/graphql but it feels cumbersome as i am iterating through the lists and making individual calls then concatenating into a dataframe (python code appended below). Probably there is a better way of doing this, any recommendations will be deeply appreciated

import pandas as pd
import json
import requests
dfENSG=dfENSG.str.strip()#contains #gene_id like "ENSG00000169093"...
colS=pd.DataFrame(columns=["ID","name","disease", "datasourceScores"])
cntG=0;
for gene_id in dfENSG:
    cntG=cntG+1
    print(cntG,gene_id)
    query_string = """
      query target($ensemblId: String!){
        target(ensemblId: $ensemblId){
        id
        approvedSymbol
        associatedDiseases {
          count
          rows {
            disease {
              id
              name
            }
            datasourceScores {
              id
              score
            }
          }
        }
      }
    }
    """
    variables = {"ensemblId": gene_id}
    base_url = "https://api.platform.opentargets.org/api/v4/graphql"
    r = requests.post(base_url, json={"query": query_string, "variables": variables})
    print(r.status_code)
    if r.status_code==200:
        api_response = json.loads(r.text)
        iD=api_response['data']['target']['id']
        print(iD)
        iG=api_response['data']['target']['approvedSymbol']
        print(iG)
        aS=api_response['data']['target']['associatedDiseases']['rows']#[1]['datasourceScores'][0]['score']
        dataOIDP=pd.DataFrame(aS,columns=["disease", "datasourceScores"])
        dataOIDP["ID"]=iD
        dataOIDP["name"]=iG
        colS=pd.concat([colS,dataOIDP])
colS.to_csv("openTargetResults.csv")

[hcornu]

Hi @animesh!

The API is optimised for queries about a single entity or association. For queries about multiple entities or associations, we recommend using one of our other data access points: Google BigQuery or our Data Downloads.

You can find out more information about these in our documentation: Data access - Open Targets Platform Documentation

You can also take a look at some other threads on the Community, for example:

Get marketed drugs for a set of targets with the data downloads

``At Open Targets, we have several ways of accessing our data. If BigQuery falls short for you or you are simply comfortable using Pyspark, in this post, we illustrate what it would be like to reproduce this analysis in BigQuery using our data files downloadable from the Downloads page. Batch search using our data files This snippet is an example of how to extract the drugs that are on the market for a restricted list of targets. from pyspark.sql import SparkSession import pyspark.sql.functio…

Returning all associations data using the Platform API

If I run a targets search with associatedDisease information how can I specify that I want all rows? For example this query says it has 947 associatedDiseases but not all of them are included in the rows: Write your query or mutation here query target_disease { target(ensemblId: “ENSG00000105974”) { id approvedSymbol approvedName associatedDiseases { count rows { score disease { id name } } } } }

Or maybe another user has found a solution?

[animesh]

Thanks @hcornu , will check it out