Only getting 25 results from UniProt REST ID Mapping

Question

[ngarber]

Hello again! I'm trying to map Ensembl Proteins to UniProtKB using the REST API, but although I have 237 items in the list, only 25 results are returned.

Here is my code snippet:

ensembl_id_list = data_df["Ensembl_ID"].tolist() #Returns 237 IDs
ensembl_id_list = list(dict.fromkeys(ensembl_id_list)) #Removes duplicates

URL = 'https://rest.uniprot.org/idmapping'

params = {
   'from': 'Ensembl_Protein',
   'to': 'UniProtKB',
   'ids': ' '.join(ensembl_id_list)
}

response = requests.post(f'{URL}/run', params)
job_id = response.json()['jobId']
job_status = requests.get(f'{URL}/status/{job_id}')
d = job_status.json()

ensembl_to_uniprot_dict = {}

#Retry getting results every 1 sec until they are ready
loop_end = ""
while loop_end != "Done":
   if d.get("job_status") == 'FINISHED' or d.get('results'):
      loop_end = "Done"
      job_results = requests.get(f'{URL}/results/{job_id}')
      results = job_results.json()
      for obj in results['results']:
         ensembl_to_uniprot_dict[obj["from"]] = obj["to"]
         #print(f'{obj["from"]}\t{obj["to"]}')
      break
   time.sleep(1)

But when I query len(ensembl_to_uniprot_dict), it's only 25 entries long. What's going on and how do I fix it?

Answer 1

[Andrzej Zielezinski]

UniProt is now undergoing major changes. In the meantime you can use job_results = requests.get(f'{URL}/results/{job_id}/?size=500'). Unfortunately, 500 is the upper limit for the number of retrieved items from UniProt's REST API. Thus if your query list of ids is longer than 500, you might want to divide the list into smaller sublists of max 500 elements each.

[ngarber]

It works!! Thanks so much; adding that /size=500 fixed the issue. My list is 237 entries long, so it fits the limit. :)

[Andrzej Zielezinski]

Great. I moved my comment to the answer. You can accept the answer if it has solved your issue.