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NamoonaNamoona
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final update
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‎1.1-Data-Engineering-Explore.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "b8e4608a",
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"metadata": {},
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"source": [
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"### Data Engineering"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "8ff0ab9d",
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"metadata": {},
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"outputs": [],
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"source": [
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"import pandas as pd\n",
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"import json as json"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "fa9d1a84",
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"metadata": {},
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"outputs": [],
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"source": [
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"# read in the data\n",
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"with open(\"data/aac-data/data/9_5.json\", 'r') as f:\n",
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" data = json.load(f)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "04edfa92",
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"metadata": {},
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"outputs": [],
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"source": [
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"df = pd.DataFrame(data)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "96741da9",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>Organism</th>\n",
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" <th>Uniprot_AC</th>\n",
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" <th>position</th>\n",
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" <th>standard_seq</th>\n",
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" <th>PTM_Catalogy</th>\n",
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" <th>PTM_Type</th>\n",
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" <th>ref</th>\n",
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" <th>cell_line</th>\n",
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" <th>Identification_Strategy</th>\n",
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" <th>Identification_Technique</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9Y6C9</td>\n",
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" <td>79</td>\n",
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" <td>LFSYAQHIASIDGRRGLFTGLTPRLCSGVLGTVVHGKVLQHYQESD...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>28355876</td>\n",
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" <td>RKO cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>Dyn-2, TD, PYD, PRD and BTD</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9Y5M8</td>\n",
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" <td>100</td>\n",
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" <td>SGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPG...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>25175731</td>\n",
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" <td>RKO and A431 cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>Dyn-2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9Y5M8</td>\n",
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" <td>73</td>\n",
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" <td>LLTLVFWKLIRSRRSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQ...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>25175731</td>\n",
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" <td>RKO and A431 cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>Dyn-2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9Y5M8</td>\n",
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" <td>179</td>\n",
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" <td>DVAEFLYQVLIDSMGLKNTPSFLIACNKQDIAMAKSAKLIQQQLEK...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>28355876</td>\n",
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" <td>RKO cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>Dyn-2, TD, PYD, PRD and BTD</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9Y277</td>\n",
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" <td>36</td>\n",
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" <td>GKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASG...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>25175731</td>\n",
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" <td>RKO and A431 cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>Dyn-2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>...</th>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3433</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q9UJW0</td>\n",
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" <td>258</td>\n",
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" <td>YTRPVNLTEVTTLQQRLLQPDFQPVCASQLYPRHKHLLIKRSLRCR...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>31246462</td>\n",
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" <td>HEK293T cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>SAM-TCO</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3434</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>P52564</td>\n",
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" <td>38</td>\n",
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" <td>LKIPKEAFEQPQTSSTPPRDLDSKACISIGNQNFEVKADDLEPIME...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>31246462</td>\n",
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" <td>HEK293T cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>SAM-TCO</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3435</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q6PRD1</td>\n",
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" <td>1536</td>\n",
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" <td>KGSFGEMGEQTVKAVQKLSQQQESVCPRESTVPGHSSPCLDNSSSK...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>31246462</td>\n",
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" <td>HEK293T cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>SAM-TCO</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3436</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q01658</td>\n",
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" <td>94</td>\n",
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" <td>EHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIP...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>31246462</td>\n",
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" <td>HEK293T cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>SAM-TCO</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3437</th>\n",
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" <td>Homo sapiens</td>\n",
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" <td>Q96H55</td>\n",
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" <td>275</td>\n",
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" <td>RLQWHLPEGAAFSWLPNPERSLEEDCFEVTREAMLHLGIDTPTQNN...</td>\n",
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" <td>Oxidation PTM</td>\n",
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" <td>S-sulfenylation</td>\n",
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" <td>31246462</td>\n",
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" <td>HEK293T cells</td>\n",
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" <td>Direct capture</td>\n",
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" <td>SAM-TCO</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"<p>3438 rows × 10 columns</p>\n",
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"</div>"
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],
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"text/plain": [
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" Organism Uniprot_AC position \\\n",
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"0 Homo sapiens Q9Y6C9 79 \n",
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"1 Homo sapiens Q9Y5M8 100 \n",
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"2 Homo sapiens Q9Y5M8 73 \n",
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"3 Homo sapiens Q9Y5M8 179 \n",
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"4 Homo sapiens Q9Y277 36 \n",
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"... ... ... ... \n",
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"3433 Homo sapiens Q9UJW0 258 \n",
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"3434 Homo sapiens P52564 38 \n",
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"3435 Homo sapiens Q6PRD1 1536 \n",
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"3436 Homo sapiens Q01658 94 \n",
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"3437 Homo sapiens Q96H55 275 \n",
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"\n",
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" standard_seq PTM_Catalogy \\\n",
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"0 LFSYAQHIASIDGRRGLFTGLTPRLCSGVLGTVVHGKVLQHYQESD... Oxidation PTM \n",
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"1 SGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPG... Oxidation PTM \n",
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"2 LLTLVFWKLIRSRRSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQ... Oxidation PTM \n",
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"3 DVAEFLYQVLIDSMGLKNTPSFLIACNKQDIAMAKSAKLIQQQLEK... Oxidation PTM \n",
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"4 GKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASG... Oxidation PTM \n",
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"... ... ... \n",
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"3433 YTRPVNLTEVTTLQQRLLQPDFQPVCASQLYPRHKHLLIKRSLRCR... Oxidation PTM \n",
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"3434 LKIPKEAFEQPQTSSTPPRDLDSKACISIGNQNFEVKADDLEPIME... Oxidation PTM \n",
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"3435 KGSFGEMGEQTVKAVQKLSQQQESVCPRESTVPGHSSPCLDNSSSK... Oxidation PTM \n",
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"3436 EHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIP... Oxidation PTM \n",
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"3437 RLQWHLPEGAAFSWLPNPERSLEEDCFEVTREAMLHLGIDTPTQNN... Oxidation PTM \n",
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"\n",
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" PTM_Type ref cell_line Identification_Strategy \\\n",
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"0 S-sulfenylation 28355876 RKO cells Direct capture \n",
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"1 S-sulfenylation 25175731 RKO and A431 cells Direct capture \n",
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"2 S-sulfenylation 25175731 RKO and A431 cells Direct capture \n",
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"3 S-sulfenylation 28355876 RKO cells Direct capture \n",
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"4 S-sulfenylation 25175731 RKO and A431 cells Direct capture \n",
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"... ... ... ... ... \n",
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"3433 S-sulfenylation 31246462 HEK293T cells Direct capture \n",
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"3434 S-sulfenylation 31246462 HEK293T cells Direct capture \n",
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"3435 S-sulfenylation 31246462 HEK293T cells Direct capture \n",
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"3436 S-sulfenylation 31246462 HEK293T cells Direct capture \n",
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"3437 S-sulfenylation 31246462 HEK293T cells Direct capture \n",
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"\n",
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" Identification_Technique \n",
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"0 Dyn-2, TD, PYD, PRD and BTD \n",
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"1 Dyn-2 \n",
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"2 Dyn-2 \n",
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"3 Dyn-2, TD, PYD, PRD and BTD \n",
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"4 Dyn-2 \n",
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"... ... \n",
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"3433 SAM-TCO \n",
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"3434 SAM-TCO \n",
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"3435 SAM-TCO \n",
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"3436 SAM-TCO \n",
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"3437 SAM-TCO \n",
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"\n",
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"[3438 rows x 10 columns]"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"df"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "e4791db8",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"(3438, 10)"
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"execution_count": 5,
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}
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],
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"source": [
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]
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},
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{
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"display_name": "Python 3 (ipykernel)",
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