1.1-Data-Engineering-Explore.ipynb

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