Retrieve all reviewed proteins from a list of species names

Question

[Francesco]

hi, i have to retrieve all reviewed proteins from a list of species names (in a csv file. 646 species) on uniprot. i tried to use uniprot api service and unipressed (python library). This is che script i wrote:

from unipressed import UniprotkbClient
import pandas as pd


data_df = pd.read_csv('organisms.csv', header=0, sep=',')

species_names = (data_df['Species'])

species_names = (species_names.dropna())

for record in UniprotkbClient.search(
    query = {

        'organism_name' : s for s in species_names

}).each_record():
   display(record)

unfortunately, the for loop is unable to retrieve all proteins of all species (it downloads only proteins of the last specie). i tried to add an AND condition to download only reviewed proteins but i get an error message. please help me :')

[GenoMax]

Have you seen the examples that UniProt has for Python queries : https://www.uniprot.org/help/api_queries

If you are trying to download a large amount of data from public resources you will want to put some pauses between the species to prevent overloading the servers/getting your IP banned.

[Francesco]

thank you!

[Kevin Blighe]

I have a script here, which you can modify: Need help to retrive sequences

You just need to change the tax ID encoded in the script. Currently it is set to txid9606 (Homo sapiens)

Kevin