This example shows how to use external services to set up Cytoscape session with pathways
In [6]:
import requests
import json
import pandas as pd
import io
from IPython.display import Image
# Basic Setup
PORT_NUMBER = 1234
BASE = 'http://localhost:' + str(PORT_NUMBER) + '/v1/'
# KEGG API
KEGG_API_URL = 'http://rest.kegg.jp/'
# Header for posting data to the server as JSON
HEADERS = {'Content-Type': 'application/json'}
requests.get(BASE)
Out[6]:
<Response [200]>
In [2]:
# Find information about cancer from KEGG disease database.
query = 'cancer'
res = requests.get(KEGG_API_URL + '/find/disease/' + query)
pathway_list = res.content.decode('utf8')
disease_df = pd.read_csv(io.StringIO(pathway_list), delimiter='\t', header=None, names=['id', 'name'])
disease_df
Out[2]:
id
name
0
ds:H00013
Small cell lung cancer
1
ds:H00014
Non-small cell lung cancer
2
ds:H00016
Oral cancer
3
ds:H00017
Esophageal cancer
4
ds:H00018
Gastric cancer
5
ds:H00019
Pancreatic cancer
6
ds:H00020
Colorectal cancer
7
ds:H00022
Bladder cancer
8
ds:H00023
Testicular cancer
9
ds:H00024
Prostate cancer
10
ds:H00025
Penile cancer
11
ds:H00026
Endometrial Cancer
12
ds:H00027
Ovarian cancer
13
ds:H00029
Vulvar cancer
14
ds:H00030
Cervical cancer
15
ds:H00031
Breast cancer
16
ds:H00032
Thyroid cancer
17
ds:H00044
Cancer of the anal canal
18
ds:H00047
Gallbladder cancer
19
ds:H00054
Nasopharyngeal cancer
20
ds:H00055
Laryngeal cancer
21
ds:H00857
Oligodontia-colorectal cancer syndrome
22
ds:H00876
Mismatch repair deficiency, including: Heredit...
In [3]:
disease_ids = disease_df['id']
disease_urls = disease_ids.apply(lambda x: KEGG_API_URL + 'get/' + x)
def disease_parser(entry):
lines = entry.split('\n')
data = {}
last_key = None
for line in lines:
if '///' in line:
return data
parts = line.split(' ')
if parts[0] is not None and len(parts[0]) != 0:
last_key = parts[0]
data[parts[0]] = line.replace(parts[0], '').strip()
else:
last_val = data[last_key]
data[last_key] = last_val + '|' + line.strip()
return data
result = []
for url in disease_urls:
res = requests.get(url)
rows = disease_parser(res.content)
result.append(rows)
In [4]:
disease_df = pd.DataFrame(result)
pathways = disease_df['PATHWAY'].dropna().unique()
p_urls = []
for pathway in pathways:
entries = pathway.split('|')
for en in entries:
url = KEGG_API_URL + 'get/' + en.split(' ')[0].split('(')[0] + '/kgml'
p_urls.append(url)
In [5]:
def create_from_list(network_list):
server_res = requests.post(BASE + 'networks?source=url&collection=' + query, data=json.dumps(network_list), headers=HEADERS)
return json.loads(server_res.content)
requests.delete(BASE + 'networks')
url_list = list(set(p_urls))
pathway_suids = create_from_list(url_list)
In [17]:
# Check the result.
print(json.dumps(pathway_suids[0], indent=4))
Image(url=BASE+'networks/' + str(pathway_suids[0]['networkSUID'][0]) + '/views/first.png', embed=True)
{
"source": "http://rest.kegg.jp/get/hsa05200/kgml",
"networkSUID": [
35821
]
}
Out[17]:
In [74]:
# Find SUID for Cancer Overview Pathway
cancer_overview_pathway_suid = None
for result in pathway_suids:
if 'hsa05200' in result['source']:
cancer_overview_pathway_suid = result['networkSUID'][0]
break
rows_res = requests.get(BASE + 'networks/' + str(cancer_overview_pathway_suid) + '/tables/defaultnode/rows')
# Convert it to DataFrame
cancer_df = pd.read_json(rows_res.content)
genes = cancer_df[cancer_df['KEGG_NODE_TYPE'] == 'gene']
gene_set = set([])
count = 0
converted = ''
query_str = ''
for gene_list in genes['KEGG_ID']:
for gene in gene_list:
gene_set.add(gene)
query_str = query_str + gene + '+'
count = count + 1
if count == 99:
conversion = requests.get('http://rest.kegg.jp/conv/uniprot/' + query_str)
converted = converted + conversion.content
count = 0
query_str = ''
conversion = requests.get('http://rest.kegg.jp/conv/uniprot /' + query_str)
converted = converted + conversion.content
print(len(gene_set))
327
In [88]:
conversion_map = pd.read_csv(io.StringIO(converted.decode('utf8')), delimiter='\t', header=None, names=['KEGG_ID', 'uniprot_id'])
id_list = conversion_map.drop_duplicates()
type(id_list)
id_list['uniprot_id'] = id_list['uniprot_id'].apply(lambda x: x.split(':')[1])
print(json.dumps(json.loads(id_list.to_json(orient='records')), indent=4))
[
{
"KEGG_ID": "hsa:1630",
"uniprot_id": "P43146"
},
{
"KEGG_ID": "hsa:1630",
"uniprot_id": "Q49AK4"
},
{
"KEGG_ID": "hsa:836",
"uniprot_id": "P42574"
},
{
"KEGG_ID": "hsa:842",
"uniprot_id": "P55211"
},
{
"KEGG_ID": "hsa:999",
"uniprot_id": "P12830"
},
{
"KEGG_ID": "hsa:1499",
"uniprot_id": "B4DGU4"
},
{
"KEGG_ID": "hsa:1499",
"uniprot_id": "P35222"
},
{
"KEGG_ID": "hsa:51384",
"uniprot_id": "E9PH60"
},
{
"KEGG_ID": "hsa:51384",
"uniprot_id": "Q9UBV4"
},
{
"KEGG_ID": "hsa:54361",
"uniprot_id": "P56705"
},
{
"KEGG_ID": "hsa:7471",
"uniprot_id": "P04628"
},
{
"KEGG_ID": "hsa:7472",
"uniprot_id": "P09544"
},
{
"KEGG_ID": "hsa:7473",
"uniprot_id": "P56703"
},
{
"KEGG_ID": "hsa:7474",
"uniprot_id": "B3KQX9"
},
{
"KEGG_ID": "hsa:7474",
"uniprot_id": "P41221"
},
{
"KEGG_ID": "hsa:7475",
"uniprot_id": "Q8N2E5"
},
{
"KEGG_ID": "hsa:7475",
"uniprot_id": "Q9Y6F9"
},
{
"KEGG_ID": "hsa:7476",
"uniprot_id": "O00755"
},
{
"KEGG_ID": "hsa:7477",
"uniprot_id": "P56706"
},
{
"KEGG_ID": "hsa:7478",
"uniprot_id": "D6RF47"
},
{
"KEGG_ID": "hsa:7478",
"uniprot_id": "Q9H1J5"
},
{
"KEGG_ID": "hsa:7479",
"uniprot_id": "Q93098"
},
{
"KEGG_ID": "hsa:7480",
"uniprot_id": "O00744"
},
{
"KEGG_ID": "hsa:7481",
"uniprot_id": "O96014"
},
{
"KEGG_ID": "hsa:7482",
"uniprot_id": "Q5TEH8"
},
{
"KEGG_ID": "hsa:7482",
"uniprot_id": "Q5TEH9"
},
{
"KEGG_ID": "hsa:7482",
"uniprot_id": "Q93097"
},
{
"KEGG_ID": "hsa:7483",
"uniprot_id": "D9ZGG3"
},
{
"KEGG_ID": "hsa:7483",
"uniprot_id": "O14904"
},
{
"KEGG_ID": "hsa:7484",
"uniprot_id": "E7EPC3"
},
{
"KEGG_ID": "hsa:7484",
"uniprot_id": "O14905"
},
{
"KEGG_ID": "hsa:80326",
"uniprot_id": "Q9GZT5"
},
{
"KEGG_ID": "hsa:81029",
"uniprot_id": "Q9H1J7"
},
{
"KEGG_ID": "hsa:89780",
"uniprot_id": "P56704"
},
{
"KEGG_ID": "hsa:1495",
"uniprot_id": "B4DKT9"
},
{
"KEGG_ID": "hsa:1495",
"uniprot_id": "B4DU00"
},
{
"KEGG_ID": "hsa:1495",
"uniprot_id": "F8W845"
},
{
"KEGG_ID": "hsa:1495",
"uniprot_id": "G3XAM7"
},
{
"KEGG_ID": "hsa:1495",
"uniprot_id": "P35221"
},
{
"KEGG_ID": "hsa:1496",
"uniprot_id": "F6KRI5"
},
{
"KEGG_ID": "hsa:1496",
"uniprot_id": "P26232"
},
{
"KEGG_ID": "hsa:1496",
"uniprot_id": "Q49AD3"
},
{
"KEGG_ID": "hsa:29119",
"uniprot_id": "A8K141"
},
{
"KEGG_ID": "hsa:29119",
"uniprot_id": "Q8WW10"
},
{
"KEGG_ID": "hsa:29119",
"uniprot_id": "Q9UI47"
},
{
"KEGG_ID": "hsa:3688",
"uniprot_id": "P05556"
},
{
"KEGG_ID": "hsa:1855",
"uniprot_id": "O14640"
},
{
"KEGG_ID": "hsa:1856",
"uniprot_id": "O14641"
},
{
"KEGG_ID": "hsa:1857",
"uniprot_id": "Q92997"
},
{
"KEGG_ID": "hsa:10319",
"uniprot_id": "Q8N2D6"
},
{
"KEGG_ID": "hsa:10319",
"uniprot_id": "Q9Y6N6"
},
{
"KEGG_ID": "hsa:1282",
"uniprot_id": "P02462"
},
{
"KEGG_ID": "hsa:1284",
"uniprot_id": "P08572"
},
{
"KEGG_ID": "hsa:1285",
"uniprot_id": "Q01955"
},
{
"KEGG_ID": "hsa:1286",
"uniprot_id": "P53420"
},
{
"KEGG_ID": "hsa:1287",
"uniprot_id": "A7MBN3"
},
{
"KEGG_ID": "hsa:1287",
"uniprot_id": "P29400"
},
{
"KEGG_ID": "hsa:1287",
"uniprot_id": "Q49AM6"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "A8VPY0"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "B2RTX6"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "B7ZMM7"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "F5H3Q5"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "F5H851"
},
{
"KEGG_ID": "hsa:1288",
"uniprot_id": "Q14031"
},
{
"KEGG_ID": "hsa:22798",
"uniprot_id": "A4D0S4"
},
{
"KEGG_ID": "hsa:2335",
"uniprot_id": "P02751"
},
{
"KEGG_ID": "hsa:2335",
"uniprot_id": "Q6MZF4"
},
{
"KEGG_ID": "hsa:2335",
"uniprot_id": "Q6MZM7"
},
{
"KEGG_ID": "hsa:2335",
"uniprot_id": "Q6N084"
},
{
"KEGG_ID": "hsa:2335",
"uniprot_id": "Q9UQS6"
},
{
"KEGG_ID": "hsa:284217",
"uniprot_id": "P25391"
},
{
"KEGG_ID": "hsa:3908",
"uniprot_id": "P24043"
},
{
"KEGG_ID": "hsa:3908",
"uniprot_id": "Q59H37"
},
{
"KEGG_ID": "hsa:3909",
"uniprot_id": "B0YJ33"
},
{
"KEGG_ID": "hsa:3909",
"uniprot_id": "Q16787"
},
{
"KEGG_ID": "hsa:3910",
"uniprot_id": "Q16363"
},
{
"KEGG_ID": "hsa:3910",
"uniprot_id": "Q5D044"
},
{
"KEGG_ID": "hsa:3911",
"uniprot_id": "O15230"
},
{
"KEGG_ID": "hsa:3912",
"uniprot_id": "P07942"
},
{
"KEGG_ID": "hsa:3912",
"uniprot_id": "Q8TAS6"
},
{
"KEGG_ID": "hsa:3913",
"uniprot_id": "P55268"
},
{
"KEGG_ID": "hsa:3914",
"uniprot_id": "Q13751"
},
{
"KEGG_ID": "hsa:3915",
"uniprot_id": "P11047"
},
{
"KEGG_ID": "hsa:3915",
"uniprot_id": "Q6NVY8"
},
{
"KEGG_ID": "hsa:3918",
"uniprot_id": "Q13753"
},
{
"KEGG_ID": "hsa:3655",
"uniprot_id": "P23229"
},
{
"KEGG_ID": "hsa:3673",
"uniprot_id": "P17301"
},
{
"KEGG_ID": "hsa:3674",
"uniprot_id": "P08514"
},
{
"KEGG_ID": "hsa:3675",
"uniprot_id": "P26006"
},
{
"KEGG_ID": "hsa:3685",
"uniprot_id": "P06756"
},
{
"KEGG_ID": "hsa:5747",
"uniprot_id": "E7ESA6"
},
{
"KEGG_ID": "hsa:5747",
"uniprot_id": "Q05397"
},
{
"KEGG_ID": "hsa:5747",
"uniprot_id": "Q59GM6"
},
{
"KEGG_ID": "hsa:5747",
"uniprot_id": "Q658W2"
},
{
"KEGG_ID": "hsa:5728",
"uniprot_id": "F2YHV0"
},
{
"KEGG_ID": "hsa:5728",
"uniprot_id": "F6KD01"
},
{
"KEGG_ID": "hsa:5728",
"uniprot_id": "P60484"
},
{
"KEGG_ID": "hsa:11211",
"uniprot_id": "Q6NSL8"
},
{
"KEGG_ID": "hsa:11211",
"uniprot_id": "Q9ULW2"
},
{
"KEGG_ID": "hsa:2535",
"uniprot_id": "Q14332"
},
{
"KEGG_ID": "hsa:2535",
"uniprot_id": "Q86UZ8"
},
{
"KEGG_ID": "hsa:7855",
"uniprot_id": "Q13467"
},
{
"KEGG_ID": "hsa:7976",
"uniprot_id": "Q9NPG1"
},
{
"KEGG_ID": "hsa:8321",
"uniprot_id": "Q9UP38"
},
{
"KEGG_ID": "hsa:8322",
"uniprot_id": "Q9ULV1"
},
{
"KEGG_ID": "hsa:8323",
"uniprot_id": "B4E236"
},
{
"KEGG_ID": "hsa:8323",
"uniprot_id": "O60353"
},
{
"KEGG_ID": "hsa:8324",
"uniprot_id": "O75084"
},
{
"KEGG_ID": "hsa:8325",
"uniprot_id": "Q9H461"
},
{
"KEGG_ID": "hsa:8326",
"uniprot_id": "O00144"
},
{
"KEGG_ID": "hsa:26060",
"uniprot_id": "Q9UKG1"
},
{
"KEGG_ID": "hsa:25",
"uniprot_id": "P00519"
},
{
"KEGG_ID": "hsa:25",
"uniprot_id": "Q59FK4"
},
{
"KEGG_ID": "hsa:613",
"uniprot_id": "P11274"
},
{
"KEGG_ID": "hsa:1398",
"uniprot_id": "L7RT18"
},
{
"KEGG_ID": "hsa:1398",
"uniprot_id": "P46108"
},
{
"KEGG_ID": "hsa:1399",
"uniprot_id": "P46109"
},
{
"KEGG_ID": "hsa:23624",
"uniprot_id": "Q9ULV8"
},
{
"KEGG_ID": "hsa:867",
"uniprot_id": "P22681"
},
{
"KEGG_ID": "hsa:868",
"uniprot_id": "B3KSS7"
},
{
"KEGG_ID": "hsa:868",
"uniprot_id": "Q13191"
},
{
"KEGG_ID": "hsa:23533",
"uniprot_id": "J3KSW1"
},
{
"KEGG_ID": "hsa:23533",
"uniprot_id": "L7RT34"
},
{
"KEGG_ID": "hsa:23533",
"uniprot_id": "Q8WYR1"
},
{
"KEGG_ID": "hsa:5290",
"uniprot_id": "P42336"
},
{
"KEGG_ID": "hsa:5291",
"uniprot_id": "B4DER4"
},
{
"KEGG_ID": "hsa:5291",
"uniprot_id": "P42338"
},
{
"KEGG_ID": "hsa:5293",
"uniprot_id": "A7E2E0"
},
{
"KEGG_ID": "hsa:5293",
"uniprot_id": "B7ZM44"
},
{
"KEGG_ID": "hsa:5293",
"uniprot_id": "O00329"
},
{
"KEGG_ID": "hsa:5294",
"uniprot_id": "A8K9G9"
},
{
"KEGG_ID": "hsa:5294",
"uniprot_id": "P48736"
},
{
"KEGG_ID": "hsa:5295",
"uniprot_id": "P27986"
},
{
"KEGG_ID": "hsa:5296",
"uniprot_id": "O00459"
},
{
"KEGG_ID": "hsa:8503",
"uniprot_id": "Q8N381"
},
{
"KEGG_ID": "hsa:8503",
"uniprot_id": "Q92569"
},
{
"KEGG_ID": "hsa:6776",
"uniprot_id": "A8K6I5"
},
{
"KEGG_ID": "hsa:6776",
"uniprot_id": "K7EK35"
},
{
"KEGG_ID": "hsa:6776",
"uniprot_id": "P42229"
},
{
"KEGG_ID": "hsa:6776",
"uniprot_id": "Q59GY7"
},
{
"KEGG_ID": "hsa:6777",
"uniprot_id": "P51692"
},
{
"KEGG_ID": "hsa:3716",
"uniprot_id": "P23458"
},
{
"KEGG_ID": "hsa:1956",
"uniprot_id": "P00533"
},
{
"KEGG_ID": "hsa:2064",
"uniprot_id": "F5H1T4"
},
{
"KEGG_ID": "hsa:2064",
"uniprot_id": "J3QLU9"
},
{
"KEGG_ID": "hsa:2064",
"uniprot_id": "P04626"
},
{
"KEGG_ID": "hsa:2064",
"uniprot_id": "X5DNK3"
},
{
"KEGG_ID": "hsa:5156",
"uniprot_id": "P16234"
},
{
"KEGG_ID": "hsa:5159",
"uniprot_id": "P09619"
},
{
"KEGG_ID": "hsa:5159",
"uniprot_id": "Q59F04"
},
{
"KEGG_ID": "hsa:3480",
"uniprot_id": "C9J5X1"
},
{
"KEGG_ID": "hsa:3480",
"uniprot_id": "P08069"
},
{
"KEGG_ID": "hsa:3815",
"uniprot_id": "P10721"
},
{
"KEGG_ID": "hsa:2322",
"uniprot_id": "P36888"
},
{
"KEGG_ID": "hsa:4233",
"uniprot_id": "B4DLF5"
},
{
"KEGG_ID": "hsa:4233",
"uniprot_id": "P08581"
},
{
"KEGG_ID": "hsa:2260",
"uniprot_id": "P11362"
},
{
"KEGG_ID": "hsa:2261",
"uniprot_id": "P22607"
},
{
"KEGG_ID": "hsa:2261",
"uniprot_id": "Q0IJ44"
},
{
"KEGG_ID": "hsa:2261",
"uniprot_id": "X5D2G8"
},
{
"KEGG_ID": "hsa:2263",
"uniprot_id": "D2CGD1"
},
{
"KEGG_ID": "hsa:2263",
"uniprot_id": "D3DRD5"
},
{
"KEGG_ID": "hsa:2263",
"uniprot_id": "P21802"
},
{
"KEGG_ID": "hsa:10342",
"uniprot_id": "Q05BK6"
},
{
"KEGG_ID": "hsa:10342",
"uniprot_id": "Q92734"
},
{
"KEGG_ID": "hsa:4914",
"uniprot_id": "P04629"
},
{
"KEGG_ID": "hsa:4914",
"uniprot_id": "X5DR71"
},
{
"KEGG_ID": "hsa:7170",
"uniprot_id": "B4DQ80"
},
{
"KEGG_ID": "hsa:7170",
"uniprot_id": "J3KN67"
},
{
"KEGG_ID": "hsa:7170",
"uniprot_id": "P06753"
},
{
"KEGG_ID": "hsa:7175",
"uniprot_id": "P12270"
},
{
"KEGG_ID": "hsa:7039",
"uniprot_id": "F8VNR3"
},
{
"KEGG_ID": "hsa:7039",
"uniprot_id": "P01135"
},
{
"KEGG_ID": "hsa:1950",
"uniprot_id": "P01133"
},
{
"KEGG_ID": "hsa:3082",
"uniprot_id": "P14210"
},
{
"KEGG_ID": "hsa:5154",
"uniprot_id": "P04085"
},
{
"KEGG_ID": "hsa:5154",
"uniprot_id": "Q32M96"
},
{
"KEGG_ID": "hsa:5155",
"uniprot_id": "P01127"
},
{
"KEGG_ID": "hsa:3479",
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{
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"uniprot_id": "F1D8Q5"
},
{
"KEGG_ID": "hsa:6256",
"uniprot_id": "P19793"
},
{
"KEGG_ID": "hsa:6256",
"uniprot_id": "Q6P3U7"
},
{
"KEGG_ID": "hsa:6257",
"uniprot_id": "P28702"
},
{
"KEGG_ID": "hsa:6257",
"uniprot_id": "Q5STP9"
},
{
"KEGG_ID": "hsa:6258",
"uniprot_id": "F1D8Q7"
},
{
"KEGG_ID": "hsa:6258",
"uniprot_id": "F1T097"
},
{
"KEGG_ID": "hsa:6258",
"uniprot_id": "P48443"
},
{
"KEGG_ID": "hsa:5915",
"uniprot_id": "F1D8S6"
},
{
"KEGG_ID": "hsa:5915",
"uniprot_id": "P10826"
},
{
"KEGG_ID": "hsa:5915",
"uniprot_id": "Q3SB16"
},
{
"KEGG_ID": "hsa:5915",
"uniprot_id": "Q5QHG3"
},
{
"KEGG_ID": "hsa:5915",
"uniprot_id": "Q86UC5"
},
{
"KEGG_ID": "hsa:3728",
"uniprot_id": "P14923"
},
{
"KEGG_ID": "hsa:5914",
"uniprot_id": "A8K840"
},
{
"KEGG_ID": "hsa:5914",
"uniprot_id": "A8MUP8"
},
{
"KEGG_ID": "hsa:5914",
"uniprot_id": "F1D8N9"
},
{
"KEGG_ID": "hsa:5914",
"uniprot_id": "P10276"
},
{
"KEGG_ID": "hsa:5914",
"uniprot_id": "Q6I9R7"
},
{
"KEGG_ID": "hsa:7704",
"uniprot_id": "Q05516"
},
{
"KEGG_ID": "hsa:5371",
"uniprot_id": "P29590"
},
{
"KEGG_ID": "hsa:862",
"uniprot_id": "B2R6I9"
},
{
"KEGG_ID": "hsa:862",
"uniprot_id": "Q06455"
},
{
"KEGG_ID": "hsa:862",
"uniprot_id": "W8FW32"
},
{
"KEGG_ID": "hsa:6688",
"uniprot_id": "P17947"
},
{
"KEGG_ID": "hsa:1050",
"uniprot_id": "P49715"
},
{
"KEGG_ID": "hsa:4286",
"uniprot_id": "B4DNC7"
},
{
"KEGG_ID": "hsa:4286",
"uniprot_id": "O75030"
},
{
"KEGG_ID": "hsa:4286",
"uniprot_id": "Q8WYR3"
},
{
"KEGG_ID": "hsa:4149",
"uniprot_id": "P61244"
},
{
"KEGG_ID": "hsa:4149",
"uniprot_id": "Q8TAX8"
},
{
"KEGG_ID": "hsa:9063",
"uniprot_id": "O75928"
},
{
"KEGG_ID": "hsa:1026",
"uniprot_id": "J3KQV0"
},
{
"KEGG_ID": "hsa:1026",
"uniprot_id": "P38936"
},
{
"KEGG_ID": "hsa:1019",
"uniprot_id": "P11802"
},
{
"KEGG_ID": "hsa:1021",
"uniprot_id": "A4D1G0"
},
{
"KEGG_ID": "hsa:1021",
"uniprot_id": "Q00534"
},
{
"KEGG_ID": "hsa:5925",
"uniprot_id": "P06400"
},
{
"KEGG_ID": "hsa:1869",
"uniprot_id": "Q01094"
},
{
"KEGG_ID": "hsa:1869",
"uniprot_id": "Q9BSD8"
},
{
"KEGG_ID": "hsa:1870",
"uniprot_id": "Q14209"
},
{
"KEGG_ID": "hsa:1871",
"uniprot_id": "O00716"
},
{
"KEGG_ID": "hsa:1871",
"uniprot_id": "Q24JQ3"
},
{
"KEGG_ID": "hsa:1017",
"uniprot_id": "B4DDL9"
},
{
"KEGG_ID": "hsa:1017",
"uniprot_id": "E7ESI2"
},
{
"KEGG_ID": "hsa:1017",
"uniprot_id": "P24941"
},
{
"KEGG_ID": "hsa:898",
"uniprot_id": "P24864"
},
{
"KEGG_ID": "hsa:9134",
"uniprot_id": "O96020"
},
{
"KEGG_ID": "hsa:6502",
"uniprot_id": "Q13309"
},
{
"KEGG_ID": "hsa:1163",
"uniprot_id": "P61024"
},
{
"KEGG_ID": "hsa:1163",
"uniprot_id": "Q5T178"
},
{
"KEGG_ID": "hsa:1164",
"uniprot_id": "P33552"
},
{
"KEGG_ID": "hsa:8900",
"uniprot_id": "P78396"
},
{
"KEGG_ID": "hsa:1030",
"uniprot_id": "K7PPU3"
},
{
"KEGG_ID": "hsa:1030",
"uniprot_id": "P42772"
},
{
"KEGG_ID": "hsa:1029",
"uniprot_id": "G3XAG3"
},
{
"KEGG_ID": "hsa:1029",
"uniprot_id": "K7PML8"
},
{
"KEGG_ID": "hsa:1029",
"uniprot_id": "P42771"
},
{
"KEGG_ID": "hsa:1029",
"uniprot_id": "Q8N726"
},
{
"KEGG_ID": "hsa:355",
"uniprot_id": "P25445"
},
{
"KEGG_ID": "hsa:355",
"uniprot_id": "Q59FU8"
},
{
"KEGG_ID": "hsa:8772",
"uniprot_id": "Q13158"
},
{
"KEGG_ID": "hsa:841",
"uniprot_id": "Q14790"
},
{
"KEGG_ID": "hsa:637",
"uniprot_id": "A8ASI8"
},
{
"KEGG_ID": "hsa:637",
"uniprot_id": "B2ZP79"
},
{
"KEGG_ID": "hsa:637",
"uniprot_id": "B3KT21"
},
{
"KEGG_ID": "hsa:637",
"uniprot_id": "P55957"
},
{
"KEGG_ID": "hsa:650",
"uniprot_id": "C8C060"
},
{
"KEGG_ID": "hsa:650",
"uniprot_id": "P12643"
},
{
"KEGG_ID": "hsa:652",
"uniprot_id": "P12644"
},
{
"KEGG_ID": "hsa:652",
"uniprot_id": "Q53XC5"
},
{
"KEGG_ID": "hsa:2735",
"uniprot_id": "B4DNF7"
},
{
"KEGG_ID": "hsa:2735",
"uniprot_id": "P08151"
},
{
"KEGG_ID": "hsa:64399",
"uniprot_id": "Q96QV1"
},
{
"KEGG_ID": "hsa:8643",
"uniprot_id": "Q9Y6C5"
},
{
"KEGG_ID": "hsa:354",
"uniprot_id": "P07288"
},
{
"KEGG_ID": "hsa:354",
"uniprot_id": "Q546G3"
},
{
"KEGG_ID": "hsa:332",
"uniprot_id": "H3BLT4"
},
{
"KEGG_ID": "hsa:332",
"uniprot_id": "O15392"
},
{
"KEGG_ID": "hsa:5743",
"uniprot_id": "P35354"
},
{
"KEGG_ID": "hsa:4843",
"uniprot_id": "P35228"
},
{
"KEGG_ID": "hsa:596",
"uniprot_id": "P10415"
},
{
"KEGG_ID": "hsa:112401",
"uniprot_id": "Q6PIA0"
},
{
"KEGG_ID": "hsa:112401",
"uniprot_id": "Q96P09"
},
{
"KEGG_ID": "hsa:329",
"uniprot_id": "Q13490"
},
{
"KEGG_ID": "hsa:330",
"uniprot_id": "Q13489"
},
{
"KEGG_ID": "hsa:331",
"uniprot_id": "B2R9R2"
},
{
"KEGG_ID": "hsa:331",
"uniprot_id": "P98170"
},
{
"KEGG_ID": "hsa:79444",
"uniprot_id": "Q96CA5"
},
{
"KEGG_ID": "hsa:7185",
"uniprot_id": "Q13077"
},
{
"KEGG_ID": "hsa:7186",
"uniprot_id": "Q12933"
},
{
"KEGG_ID": "hsa:7187",
"uniprot_id": "A6NHG8"
},
{
"KEGG_ID": "hsa:7187",
"uniprot_id": "Q13114"
},
{
"KEGG_ID": "hsa:7188",
"uniprot_id": "D3DT93"
},
{
"KEGG_ID": "hsa:7188",
"uniprot_id": "O00463"
},
{
"KEGG_ID": "hsa:7189",
"uniprot_id": "Q9Y4K3"
},
{
"KEGG_ID": "hsa:9618",
"uniprot_id": "Q9BUZ4"
},
{
"KEGG_ID": "hsa:2277",
"uniprot_id": "O43915"
},
{
"KEGG_ID": "hsa:5228",
"uniprot_id": "G3XA84"
},
{
"KEGG_ID": "hsa:5228",
"uniprot_id": "P49763"
},
{
"KEGG_ID": "hsa:5228",
"uniprot_id": "Q53XY6"
},
{
"KEGG_ID": "hsa:5228",
"uniprot_id": "Q86TW6"
},
{
"KEGG_ID": "hsa:7422",
"uniprot_id": "A2A2V4"
},
{
"KEGG_ID": "hsa:7422",
"uniprot_id": "P15692"
},
{
"KEGG_ID": "hsa:7423",
"uniprot_id": "P49765"
},
{
"KEGG_ID": "hsa:7423",
"uniprot_id": "Q7LAP4"
},
{
"KEGG_ID": "hsa:7424",
"uniprot_id": "P49767"
},
{
"KEGG_ID": "hsa:6513",
"uniprot_id": "P11166"
},
{
"KEGG_ID": "hsa:6513",
"uniprot_id": "Q59GX2"
},
{
"KEGG_ID": "hsa:1612",
"uniprot_id": "B4DHI4"
},
{
"KEGG_ID": "hsa:1612",
"uniprot_id": "P53355"
},
{
"KEGG_ID": "hsa:1612",
"uniprot_id": "Q59H88"
},
{
"KEGG_ID": "hsa:1613",
"uniprot_id": "O43293"
},
{
"KEGG_ID": "hsa:23604",
"uniprot_id": "Q9UIK4"
},
{
"KEGG_ID": "hsa:2113",
"uniprot_id": "A8K725"
},
{
"KEGG_ID": "hsa:2113",
"uniprot_id": "B4DW78"
},
{
"KEGG_ID": "hsa:2113",
"uniprot_id": "P14921"
},
{
"KEGG_ID": "hsa:4312",
"uniprot_id": "B4DN15"
},
{
"KEGG_ID": "hsa:4312",
"uniprot_id": "P03956"
},
{
"KEGG_ID": "hsa:4312",
"uniprot_id": "Q53G95"
},
{
"KEGG_ID": "hsa:4313",
"uniprot_id": "P08253"
},
{
"KEGG_ID": "hsa:4318",
"uniprot_id": "P14780"
},
{
"KEGG_ID": "hsa:3576",
"uniprot_id": "P10145"
},
{
"KEGG_ID": "hsa:1438",
"uniprot_id": "P15509"
},
{
"KEGG_ID": "hsa:1441",
"uniprot_id": "Q99062"
},
{
"KEGG_ID": "hsa:1436",
"uniprot_id": "A2VDG3"
},
{
"KEGG_ID": "hsa:1436",
"uniprot_id": "P07333"
},
{
"KEGG_ID": "hsa:3569",
"uniprot_id": "B4DNQ5"
},
{
"KEGG_ID": "hsa:3569",
"uniprot_id": "B4DVM1"
},
{
"KEGG_ID": "hsa:3569",
"uniprot_id": "P05231"
},
{
"KEGG_ID": "hsa:3569",
"uniprot_id": "Q75MH2"
},
{
"KEGG_ID": "hsa:5467",
"uniprot_id": "F1D8S7"
},
{
"KEGG_ID": "hsa:5467",
"uniprot_id": "Q03181"
},
{
"KEGG_ID": "hsa:2308",
"uniprot_id": "Q12778"
},
{
"KEGG_ID": "hsa:4824",
"uniprot_id": "Q99801"
},
{
"KEGG_ID": "hsa:5594",
"uniprot_id": "P28482"
},
{
"KEGG_ID": "hsa:5594",
"uniprot_id": "Q1HBJ4"
},
{
"KEGG_ID": "hsa:5594",
"uniprot_id": "Q499G7"
},
{
"KEGG_ID": "hsa:5595",
"uniprot_id": "L7RXH5"
},
{
"KEGG_ID": "hsa:5595",
"uniprot_id": "P27361"
},
{
"KEGG_ID": "hsa:5595",
"uniprot_id": "Q9BWJ1"
},
{
"KEGG_ID": "hsa:10000",
"uniprot_id": "Q9Y243"
},
{
"KEGG_ID": "hsa:207",
"uniprot_id": "B0LPE5"
},
{
"KEGG_ID": "hsa:207",
"uniprot_id": "B3KVH4"
},
{
"KEGG_ID": "hsa:207",
"uniprot_id": "P31749"
},
{
"KEGG_ID": "hsa:208",
"uniprot_id": "B4DG79"
},
{
"KEGG_ID": "hsa:208",
"uniprot_id": "P31751"
},
{
"KEGG_ID": "hsa:2736",
"uniprot_id": "P10070"
},
{
"KEGG_ID": "hsa:2736",
"uniprot_id": "Q1PSW9"
},
{
"KEGG_ID": "hsa:2736",
"uniprot_id": "Q59FV5"
},
{
"KEGG_ID": "hsa:2737",
"uniprot_id": "P10071"
},
{
"KEGG_ID": "hsa:356",
"uniprot_id": "P48023"
},
{
"KEGG_ID": "hsa:356",
"uniprot_id": "Q53ZZ1"
},
{
"KEGG_ID": "hsa:4254",
"uniprot_id": "P21583"
},
{
"KEGG_ID": "hsa:2323",
"uniprot_id": "B7ZLY4"
},
{
"KEGG_ID": "hsa:2323",
"uniprot_id": "M0QYM9"
},
{
"KEGG_ID": "hsa:2323",
"uniprot_id": "P49771"
},
{
"KEGG_ID": "hsa:2246",
"uniprot_id": "A8K147"
},
{
"KEGG_ID": "hsa:2246",
"uniprot_id": "P05230"
},
{
"KEGG_ID": "hsa:2246",
"uniprot_id": "Q16089"
},
{
"KEGG_ID": "hsa:2247",
"uniprot_id": "P09038"
},
{
"KEGG_ID": "hsa:2248",
"uniprot_id": "P11487"
},
{
"KEGG_ID": "hsa:2249",
"uniprot_id": "P08620"
},
{
"KEGG_ID": "hsa:2250",
"uniprot_id": "P12034"
},
{
"KEGG_ID": "hsa:2250",
"uniprot_id": "Q8NBG6"
},
{
"KEGG_ID": "hsa:2251",
"uniprot_id": "P10767"
},
{
"KEGG_ID": "hsa:2252",
"uniprot_id": "P21781"
},
{
"KEGG_ID": "hsa:2252",
"uniprot_id": "Q6FGV5"
},
{
"KEGG_ID": "hsa:2253",
"uniprot_id": "A1A515"
},
{
"KEGG_ID": "hsa:2253",
"uniprot_id": "P55075"
},
{
"KEGG_ID": "hsa:2254",
"uniprot_id": "P31371"
},
{
"KEGG_ID": "hsa:2255",
"uniprot_id": "C7FDY0"
},
{
"KEGG_ID": "hsa:2255",
"uniprot_id": "O15520"
},
{
"KEGG_ID": "hsa:2256",
"uniprot_id": "Q92914"
},
{
"KEGG_ID": "hsa:2257",
"uniprot_id": "P61328"
},
{
"KEGG_ID": "hsa:2258",
"uniprot_id": "A8K1P5"
},
{
"KEGG_ID": "hsa:2258",
"uniprot_id": "Q92913"
},
{
"KEGG_ID": "hsa:2259",
"uniprot_id": "Q92915"
},
{
"KEGG_ID": "hsa:26281",
"uniprot_id": "Q9NP95"
},
{
"KEGG_ID": "hsa:26291",
"uniprot_id": "Q9NSA1"
},
{
"KEGG_ID": "hsa:27006",
"uniprot_id": "K7ELB9"
},
{
"KEGG_ID": "hsa:27006",
"uniprot_id": "Q9HCT0"
},
{
"KEGG_ID": "hsa:8074",
"uniprot_id": "Q9GZV9"
},
{
"KEGG_ID": "hsa:8817",
"uniprot_id": "O76093"
},
{
"KEGG_ID": "hsa:8822",
"uniprot_id": "O60258"
},
{
"KEGG_ID": "hsa:8823",
"uniprot_id": "O43320"
},
{
"KEGG_ID": "hsa:9965",
"uniprot_id": "O95750"
}
]
In [91]:
new_column = {
'name': 'KEGG_ID_TOP',
'type': 'String'
}
first_key_res = requests.post(BASE + 'networks/' + str(cancer_overview_pathway_suid) + '/tables/defaultnode/columns', data=json.dumps(new_column), headers=HEADERS)
In [ ]:
genes['KEGG_ID_TOP'] = genes.apply(lambda row: row['KEGG_ID'][0], axis=1)
In [118]:
sub_table= genes[['SUID', 'KEGG_ID_TOP']]
sub_table.columns = ['SUID', 'KEGG_ID']
208
In [128]:
merged = pd.merge(sub_table, id_list, on='KEGG_ID')
merged.columns = ['SUID', 'KEGG_ID_TOP', 'UNIPROT_ID']
table_data = json.loads(merged.to_json(orient='records'))
In [133]:
new_table_data = {
'data': table_data
}
# print(json.dumps(new_table_data, indent=4))
res = requests.put(BASE + 'networks/' + str(cancer_overview_pathway_suid) + '/tables/defaultnode', data=json.dumps(new_table_data), headers=HEADERS)
merged[['UNIPROT_ID']].to_clipboard(index=False, header=False)
Content source: muratcemkose/cy-rest-python
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