Getting proteins associated to a disease

Data Access GraphQL API
1

Hi there community,

I have the following function which was working perfectly. Lately, I realized the size is set to 3000 at max. But I want to get all the proteins for a disease, let’s say 5000. The trick would be to use the cursor to re-run the code twice, however, I do not see the option to retrieve the cursor in the documentation for associatedTargets. Please help me with it.

Thanks in advance,
R

def GetDiseaseAssociatedProteins(disease_id):   
    
    efo_id = str(disease_id)

    query_string = """
        query associatedTargets{
          disease(efoId: $efo_id){
            id
            name
            associatedTargets(page:{size:15000,index:0}){
              count
              rows {
                target {
                  id
                  approvedSymbol
                  proteinIds {
                    id
                    source
                  }
                }
                score
              }
            }
          }
        }

    """
    
    #replace $efo_id with value from efo_id
    query_string = query_string.replace("$efo_id",f'"{efo_id}"')
    
    #variables = {"$efo_id":efo_id}

    # Set base URL of GraphQL API endpoint
    base_url = "https://api.platform.opentargets.org/api/v4/graphql"

    # Perform POST request and check status code of response
    r = requests.post(base_url, json={"query": query_string})
    #print(r.status_code)

    # Transform API response from JSON into Python dictionary and print in console
    api_response = json.loads(r.text)
    
    temp_list = []
    for item in api_response['data']['disease']['associatedTargets']['rows']:
        #print(item['target'])
        #break
        for obj in item['target']['proteinIds']:
            if obj['source'] == 'uniprot_swissprot':
                #print(obj)
                uprot = obj['id']
                source = obj['source']
                score = item['score']
                ensg = item['target']['id']
                name = item['target']['approvedSymbol']
                temp = {'Protein':name,'ENSG':ensg,'UniProt':uprot,'Source':source,'Score':score}
                temp_list.append(temp)
    
    df = pd.DataFrame(temp_list)
    df['disease_id'] = efo_id
    
    return(df)
2

Hi @jrkarki,

Have you looked through some of the other topics on the forum for pagination? This one might be helpful: Retrieving >50 pathways from evidences - #3 by keithzikai.chew

3

Thanks a lot. I solved my problem by reading through an old discussion.

https://community.opentargets.org/t/returning-all-associations-data-using-the-platform-api/324/2