UniProtKB - mapping gene name to ID (*_HUMAN ) using python2

Question

[jg]

Hello!

I have a large list of kinase (gene) names extracted from the UniProtKB modified residue section. (e.g. MAPK1, CDK1, SRC, ATM etc.)

I am trying to convert these names to their entry names (ID) to get:

MAPK1: MK01_HUMAN

CDK1: CDK1_HUMAN

SRC: SRC_HUMAN

etc...

The problem is that for ever gene name I get many IDs and I only want the official one (see below) which always seems to be the only one reviewed.

I tried adding 'columns': 'reviewed' and 'organism': 'human' in the params below but it has no effect. I am basically lost!

An example using MAPK1 kinase:

import urllib,urllib2

    url = 'https://www.uniprot.org/uploadlists/'

    params = {
    'from':'GENENAME',
    'to':'ID',
    'format':'tab',
    'query':'MAPK1',
    'columns': 'reviewed'
    }

    data = urllib.urlencode(params)
    request = urllib2.Request(url, data)
    contact = "[e-mail]" 
    request.add_header('User-Agent', 'Python %s' % contact)
    response = urllib2.urlopen(request)
    header = response.readline()
    entries=response.read()

    id_list=[]
    new_entries=entries.split("\n")
    for element in new_entries:
        if element=="":
            continue
        else:
            element=element.split("\t")
            if "_HUMAN" in element[1]:
                id_list.append(element[1])

The final id_list is: ['MK01_HUMAN', 'Q1HBJ4_HUMAN', 'Q499G7_HUMAN']

I am only interested in extracting the 'main' identifier; MK01_HUMAN. Please can anyone help?

Answer 1

[vkkodali_ncbi]

Try changing your url to https://www.uniprot.org/uniprot/ and params to:

{
    'query': 'gene_exact:mapk1 AND organism:homo_sapiens AND reviewed:yes', 
    'format': 'tab', 
    'columns': 'id,entry_name,genes'
}

[jg]

Thank you so much - it worked. Now I can sleep peacefully after hours of staring at this :)

[Learner]

@vkkodali I get error like

url = "https://www.uniprot.org/uniprot/" ^ IndentationError: unexpected indent

[vkkodali_ncbi]

Python seems to be complaining about indentation. If you have copy/pasted the code from above, you should make sure the indentation is correct. I don't think you need to indent the entire code block after the import statement.

[Learner]

@vkkodali I just correct the indent but it runs and does not give any output

[vkkodali_ncbi]

Without more detailed information from you, I cannot be of much help. What have you tried? How did you run the code? Did you run it as a script? Or did you run it at the python interpreter? Did you use the example posted here or did you use your own example? I am not sure what you mean by 'does not give any output'. What were you expecting? The code, as written in the first post, does not output anything. It populates a list called id_list. Did you see anything in that list?