HumanProteins_Jenslab.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 62,
   "id": "ad3fd6a7",
   "metadata": {},
   "outputs": [],
   "source": [
    "#jenslab\n",
    "import pandas as pd\n",
    "import os\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "id": "ccbf6813",
   "metadata": {},
   "outputs": [],
   "source": [
    "colnames = 'Gene HGNC doid disease z-score confidence url'.split(' ')\n",
    "mpox_human = pd.read_csv('C:/Users/reagon.karki/Documents/GitHub/mpox-kg/data/human_disease_textmining_filtered.tsv',\n",
    "                         sep='\\t',names=colnames,header=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "id": "8859ff40",
   "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>Gene</th>\n",
       "      <th>HGNC</th>\n",
       "      <th>doid</th>\n",
       "      <th>disease</th>\n",
       "      <th>z-score</th>\n",
       "      <th>confidence</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C15orf59-AS1</td>\n",
       "      <td>C15orf59-AS1</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.153</td>\n",
       "      <td>1.577</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSP00000011653</td>\n",
       "      <td>CD4</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.931</td>\n",
       "      <td>1.965</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSP00000240618</td>\n",
       "      <td>KLRK1</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.081</td>\n",
       "      <td>1.541</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSP00000276927</td>\n",
       "      <td>IFNA1</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.227</td>\n",
       "      <td>1.613</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSP00000282141</td>\n",
       "      <td>CRYGC</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.089</td>\n",
       "      <td>1.544</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ENSP00000285013</td>\n",
       "      <td>SLFN13</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.126</td>\n",
       "      <td>1.563</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ENSP00000304802</td>\n",
       "      <td>DTYMK</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.024</td>\n",
       "      <td>1.512</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ENSP00000313875</td>\n",
       "      <td>CD46</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.132</td>\n",
       "      <td>1.566</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ENSP00000354468</td>\n",
       "      <td>CYB5R3</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>4.429</td>\n",
       "      <td>2.215</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ENSP00000356030</td>\n",
       "      <td>CD55</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.328</td>\n",
       "      <td>1.664</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ENSP00000356530</td>\n",
       "      <td>RNASEL</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.079</td>\n",
       "      <td>1.539</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>ENSP00000369581</td>\n",
       "      <td>IFNB1</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.024</td>\n",
       "      <td>1.512</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>ENSP00000378063</td>\n",
       "      <td>SLFN12</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.354</td>\n",
       "      <td>1.677</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>ENSP00000378365</td>\n",
       "      <td>CCL26</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.315</td>\n",
       "      <td>1.658</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ENSP00000386559</td>\n",
       "      <td>CD8A</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>4.115</td>\n",
       "      <td>2.058</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>ENSP00000396688</td>\n",
       "      <td>C4A</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.206</td>\n",
       "      <td>1.603</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>ENSP00000415941</td>\n",
       "      <td>C4B</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.229</td>\n",
       "      <td>1.615</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>ENSP00000440396</td>\n",
       "      <td>ANKRD49</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.362</td>\n",
       "      <td>1.681</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>ENSP00000471896</td>\n",
       "      <td>IRF3</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.091</td>\n",
       "      <td>1.546</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>ENSP00000477445</td>\n",
       "      <td>OR10G6</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.513</td>\n",
       "      <td>1.757</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>ENSP00000480609</td>\n",
       "      <td>ENSP00000480609</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.083</td>\n",
       "      <td>1.541</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>GS1-600G8.3</td>\n",
       "      <td>GS1-600G8.3</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.259</td>\n",
       "      <td>1.629</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>LINC01285</td>\n",
       "      <td>LINC01285</td>\n",
       "      <td>DOID:3292</td>\n",
       "      <td>Monkeypox</td>\n",
       "      <td>3.259</td>\n",
       "      <td>1.629</td>\n",
       "      <td>https://diseases.jensenlab.org/Entity?document...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               Gene             HGNC       doid    disease  z-score  \\\n",
       "0      C15orf59-AS1     C15orf59-AS1  DOID:3292  Monkeypox    3.153   \n",
       "1   ENSP00000011653              CD4  DOID:3292  Monkeypox    3.931   \n",
       "2   ENSP00000240618            KLRK1  DOID:3292  Monkeypox    3.081   \n",
       "3   ENSP00000276927            IFNA1  DOID:3292  Monkeypox    3.227   \n",
       "4   ENSP00000282141            CRYGC  DOID:3292  Monkeypox    3.089   \n",
       "5   ENSP00000285013           SLFN13  DOID:3292  Monkeypox    3.126   \n",
       "6   ENSP00000304802            DTYMK  DOID:3292  Monkeypox    3.024   \n",
       "7   ENSP00000313875             CD46  DOID:3292  Monkeypox    3.132   \n",
       "8   ENSP00000354468           CYB5R3  DOID:3292  Monkeypox    4.429   \n",
       "9   ENSP00000356030             CD55  DOID:3292  Monkeypox    3.328   \n",
       "10  ENSP00000356530           RNASEL  DOID:3292  Monkeypox    3.079   \n",
       "11  ENSP00000369581            IFNB1  DOID:3292  Monkeypox    3.024   \n",
       "12  ENSP00000378063           SLFN12  DOID:3292  Monkeypox    3.354   \n",
       "13  ENSP00000378365            CCL26  DOID:3292  Monkeypox    3.315   \n",
       "14  ENSP00000386559             CD8A  DOID:3292  Monkeypox    4.115   \n",
       "15  ENSP00000396688              C4A  DOID:3292  Monkeypox    3.206   \n",
       "16  ENSP00000415941              C4B  DOID:3292  Monkeypox    3.229   \n",
       "17  ENSP00000440396          ANKRD49  DOID:3292  Monkeypox    3.362   \n",
       "18  ENSP00000471896             IRF3  DOID:3292  Monkeypox    3.091   \n",
       "19  ENSP00000477445           OR10G6  DOID:3292  Monkeypox    3.513   \n",
       "20  ENSP00000480609  ENSP00000480609  DOID:3292  Monkeypox    3.083   \n",
       "21      GS1-600G8.3      GS1-600G8.3  DOID:3292  Monkeypox    3.259   \n",
       "22        LINC01285        LINC01285  DOID:3292  Monkeypox    3.259   \n",
       "\n",
       "    confidence                                                url  \n",
       "0        1.577  https://diseases.jensenlab.org/Entity?document...  \n",
       "1        1.965  https://diseases.jensenlab.org/Entity?document...  \n",
       "2        1.541  https://diseases.jensenlab.org/Entity?document...  \n",
       "3        1.613  https://diseases.jensenlab.org/Entity?document...  \n",
       "4        1.544  https://diseases.jensenlab.org/Entity?document...  \n",
       "5        1.563  https://diseases.jensenlab.org/Entity?document...  \n",
       "6        1.512  https://diseases.jensenlab.org/Entity?document...  \n",
       "7        1.566  https://diseases.jensenlab.org/Entity?document...  \n",
       "8        2.215  https://diseases.jensenlab.org/Entity?document...  \n",
       "9        1.664  https://diseases.jensenlab.org/Entity?document...  \n",
       "10       1.539  https://diseases.jensenlab.org/Entity?document...  \n",
       "11       1.512  https://diseases.jensenlab.org/Entity?document...  \n",
       "12       1.677  https://diseases.jensenlab.org/Entity?document...  \n",
       "13       1.658  https://diseases.jensenlab.org/Entity?document...  \n",
       "14       2.058  https://diseases.jensenlab.org/Entity?document...  \n",
       "15       1.603  https://diseases.jensenlab.org/Entity?document...  \n",
       "16       1.615  https://diseases.jensenlab.org/Entity?document...  \n",
       "17       1.681  https://diseases.jensenlab.org/Entity?document...  \n",
       "18       1.546  https://diseases.jensenlab.org/Entity?document...  \n",
       "19       1.757  https://diseases.jensenlab.org/Entity?document...  \n",
       "20       1.541  https://diseases.jensenlab.org/Entity?document...  \n",
       "21       1.629  https://diseases.jensenlab.org/Entity?document...  \n",
       "22       1.629  https://diseases.jensenlab.org/Entity?document...  "
      ]
     },
     "execution_count": 72,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mpox_human = mpox_human.loc[mpox_human['doid'] == ('DOID:3292')]\n",
    "mpox_human = mpox_human.reset_index(drop=True)\n",
    "mpox_human"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "id": "a9bd052a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "23"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mpox_human = list(mpox_human['HGNC'])\n",
    "len(mpox_human)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "id": "dbe223ad",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['C15orf59-AS1',\n",
       " 'CD4',\n",
       " 'KLRK1',\n",
       " 'IFNA1',\n",
       " 'CRYGC',\n",
       " 'SLFN13',\n",
       " 'DTYMK',\n",
       " 'CD46',\n",
       " 'CYB5R3',\n",
       " 'CD55',\n",
       " 'RNASEL',\n",
       " 'IFNB1',\n",
       " 'SLFN12',\n",
       " 'CCL26',\n",
       " 'CD8A',\n",
       " 'C4A',\n",
       " 'C4B',\n",
       " 'ANKRD49',\n",
       " 'IRF3',\n",
       " 'OR10G6',\n",
       " 'ENSP00000480609',\n",
       " 'GS1-600G8.3',\n",
       " 'LINC01285']"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mpox_human"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "id": "8eec8ae9",
   "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>From</th>\n",
       "      <th>Entry</th>\n",
       "      <th>Reviewed</th>\n",
       "      <th>Entry Name</th>\n",
       "      <th>Gene Names</th>\n",
       "      <th>Organism</th>\n",
       "      <th>Length</th>\n",
       "      <th>Gene Names (primary)</th>\n",
       "      <th>Protein names</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>OR10G6</td>\n",
       "      <td>Q8NH81</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>O10G6_HUMAN</td>\n",
       "      <td>OR10G6 OR10G6P</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>332</td>\n",
       "      <td>OR10G6</td>\n",
       "      <td>Olfactory receptor 10G6 (Olfactory receptor OR...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SLFN13</td>\n",
       "      <td>Q68D06</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>SLN13_HUMAN</td>\n",
       "      <td>SLFN13</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>897</td>\n",
       "      <td>SLFN13</td>\n",
       "      <td>Schlafen family member 13, EC 3.1.-.- (Schlafe...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>IRF3</td>\n",
       "      <td>Q14653</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>IRF3_HUMAN</td>\n",
       "      <td>IRF3</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>427</td>\n",
       "      <td>IRF3</td>\n",
       "      <td>Interferon regulatory factor 3, IRF-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ANKRD49</td>\n",
       "      <td>Q8WVL7</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>ANR49_HUMAN</td>\n",
       "      <td>ANKRD49 FGIF</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>239</td>\n",
       "      <td>ANKRD49</td>\n",
       "      <td>Ankyrin repeat domain-containing protein 49 (F...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CCL26</td>\n",
       "      <td>Q9Y258</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CCL26_HUMAN</td>\n",
       "      <td>CCL26 SCYA26 UNQ216/PRO242</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>94</td>\n",
       "      <td>CCL26</td>\n",
       "      <td>C-C motif chemokine 26 (CC chemokine IMAC) (Eo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SLFN12</td>\n",
       "      <td>Q8IYM2</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>SLN12_HUMAN</td>\n",
       "      <td>SLFN12</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>578</td>\n",
       "      <td>SLFN12</td>\n",
       "      <td>Ribonuclease SLFN12, EC 3.1.-.- (Schlafen fami...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CD8A</td>\n",
       "      <td>P01732</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CD8A_HUMAN</td>\n",
       "      <td>CD8A MAL</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>235</td>\n",
       "      <td>CD8A</td>\n",
       "      <td>T-cell surface glycoprotein CD8 alpha chain (T...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CYB5R3</td>\n",
       "      <td>P00387</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>NB5R3_HUMAN</td>\n",
       "      <td>CYB5R3 DIA1</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>301</td>\n",
       "      <td>CYB5R3</td>\n",
       "      <td>NADH-cytochrome b5 reductase 3, B5R, Cytochrom...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>C4A</td>\n",
       "      <td>P0C0L4</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CO4A_HUMAN</td>\n",
       "      <td>C4A CO4 CPAMD2</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>1744</td>\n",
       "      <td>C4A</td>\n",
       "      <td>Complement C4-A (Acidic complement C4) (C3 and...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CD4</td>\n",
       "      <td>P01730</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CD4_HUMAN</td>\n",
       "      <td>CD4</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>458</td>\n",
       "      <td>CD4</td>\n",
       "      <td>T-cell surface glycoprotein CD4 (T-cell surfac...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>RNASEL</td>\n",
       "      <td>Q05823</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>RN5A_HUMAN</td>\n",
       "      <td>RNASEL RNS4</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>741</td>\n",
       "      <td>RNASEL</td>\n",
       "      <td>2-5A-dependent ribonuclease, 2-5A-dependent RN...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>C4B</td>\n",
       "      <td>P0C0L5</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CO4B_HUMAN</td>\n",
       "      <td>C4B CO4 CPAMD3; C4B_2</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>1744</td>\n",
       "      <td>C4B; C4B_2</td>\n",
       "      <td>Complement C4-B (Basic complement C4) (C3 and ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>IFNA1</td>\n",
       "      <td>P01562</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>IFNA1_HUMAN</td>\n",
       "      <td>IFNA1; IFNA13</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>189</td>\n",
       "      <td>IFNA1; IFNA13</td>\n",
       "      <td>Interferon alpha-1/13, IFN-alpha-1/13 (Interfe...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>CRYGC</td>\n",
       "      <td>P07315</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>CRGC_HUMAN</td>\n",
       "      <td>CRYGC CRYG3</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>174</td>\n",
       "      <td>CRYGC</td>\n",
       "      <td>Gamma-crystallin C (Gamma-C-crystallin) (Gamma...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>CD46</td>\n",
       "      <td>P15529</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>MCP_HUMAN</td>\n",
       "      <td>CD46 MCP MIC10</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>392</td>\n",
       "      <td>CD46</td>\n",
       "      <td>Membrane cofactor protein (TLX) (Trophoblast l...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>KLRK1</td>\n",
       "      <td>P26718</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>NKG2D_HUMAN</td>\n",
       "      <td>KLRK1 D12S2489E NKG2D</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>216</td>\n",
       "      <td>KLRK1</td>\n",
       "      <td>NKG2-D type II integral membrane protein (Kill...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>CD55</td>\n",
       "      <td>P08174</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>DAF_HUMAN</td>\n",
       "      <td>CD55 CR DAF</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>381</td>\n",
       "      <td>CD55</td>\n",
       "      <td>Complement decay-accelerating factor (CD antig...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>DTYMK</td>\n",
       "      <td>P23919</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>KTHY_HUMAN</td>\n",
       "      <td>DTYMK CDC8 TMPK TYMK</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>212</td>\n",
       "      <td>DTYMK</td>\n",
       "      <td>Thymidylate kinase, EC 2.7.4.9 (dTMP kinase)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>IFNB1</td>\n",
       "      <td>P01574</td>\n",
       "      <td>reviewed</td>\n",
       "      <td>IFNB_HUMAN</td>\n",
       "      <td>IFNB1 IFB IFNB</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>187</td>\n",
       "      <td>IFNB1</td>\n",
       "      <td>Interferon beta, IFN-beta (Fibroblast interferon)</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       From   Entry  Reviewed   Entry Name                  Gene Names  \\\n",
       "0    OR10G6  Q8NH81  reviewed  O10G6_HUMAN              OR10G6 OR10G6P   \n",
       "1    SLFN13  Q68D06  reviewed  SLN13_HUMAN                      SLFN13   \n",
       "2      IRF3  Q14653  reviewed   IRF3_HUMAN                        IRF3   \n",
       "3   ANKRD49  Q8WVL7  reviewed  ANR49_HUMAN                ANKRD49 FGIF   \n",
       "4     CCL26  Q9Y258  reviewed  CCL26_HUMAN  CCL26 SCYA26 UNQ216/PRO242   \n",
       "5    SLFN12  Q8IYM2  reviewed  SLN12_HUMAN                      SLFN12   \n",
       "6      CD8A  P01732  reviewed   CD8A_HUMAN                    CD8A MAL   \n",
       "7    CYB5R3  P00387  reviewed  NB5R3_HUMAN                 CYB5R3 DIA1   \n",
       "8       C4A  P0C0L4  reviewed   CO4A_HUMAN              C4A CO4 CPAMD2   \n",
       "9       CD4  P01730  reviewed    CD4_HUMAN                         CD4   \n",
       "10   RNASEL  Q05823  reviewed   RN5A_HUMAN                 RNASEL RNS4   \n",
       "11      C4B  P0C0L5  reviewed   CO4B_HUMAN       C4B CO4 CPAMD3; C4B_2   \n",
       "12    IFNA1  P01562  reviewed  IFNA1_HUMAN               IFNA1; IFNA13   \n",
       "13    CRYGC  P07315  reviewed   CRGC_HUMAN                 CRYGC CRYG3   \n",
       "14     CD46  P15529  reviewed    MCP_HUMAN              CD46 MCP MIC10   \n",
       "15    KLRK1  P26718  reviewed  NKG2D_HUMAN       KLRK1 D12S2489E NKG2D   \n",
       "16     CD55  P08174  reviewed    DAF_HUMAN                 CD55 CR DAF   \n",
       "17    DTYMK  P23919  reviewed   KTHY_HUMAN        DTYMK CDC8 TMPK TYMK   \n",
       "18    IFNB1  P01574  reviewed   IFNB_HUMAN              IFNB1 IFB IFNB   \n",
       "\n",
       "                Organism  Length Gene Names (primary)  \\\n",
       "0   Homo sapiens (Human)     332               OR10G6   \n",
       "1   Homo sapiens (Human)     897               SLFN13   \n",
       "2   Homo sapiens (Human)     427                 IRF3   \n",
       "3   Homo sapiens (Human)     239              ANKRD49   \n",
       "4   Homo sapiens (Human)      94                CCL26   \n",
       "5   Homo sapiens (Human)     578               SLFN12   \n",
       "6   Homo sapiens (Human)     235                 CD8A   \n",
       "7   Homo sapiens (Human)     301               CYB5R3   \n",
       "8   Homo sapiens (Human)    1744                  C4A   \n",
       "9   Homo sapiens (Human)     458                  CD4   \n",
       "10  Homo sapiens (Human)     741               RNASEL   \n",
       "11  Homo sapiens (Human)    1744           C4B; C4B_2   \n",
       "12  Homo sapiens (Human)     189        IFNA1; IFNA13   \n",
       "13  Homo sapiens (Human)     174                CRYGC   \n",
       "14  Homo sapiens (Human)     392                 CD46   \n",
       "15  Homo sapiens (Human)     216                KLRK1   \n",
       "16  Homo sapiens (Human)     381                 CD55   \n",
       "17  Homo sapiens (Human)     212                DTYMK   \n",
       "18  Homo sapiens (Human)     187                IFNB1   \n",
       "\n",
       "                                        Protein names  \n",
       "0   Olfactory receptor 10G6 (Olfactory receptor OR...  \n",
       "1   Schlafen family member 13, EC 3.1.-.- (Schlafe...  \n",
       "2               Interferon regulatory factor 3, IRF-3  \n",
       "3   Ankyrin repeat domain-containing protein 49 (F...  \n",
       "4   C-C motif chemokine 26 (CC chemokine IMAC) (Eo...  \n",
       "5   Ribonuclease SLFN12, EC 3.1.-.- (Schlafen fami...  \n",
       "6   T-cell surface glycoprotein CD8 alpha chain (T...  \n",
       "7   NADH-cytochrome b5 reductase 3, B5R, Cytochrom...  \n",
       "8   Complement C4-A (Acidic complement C4) (C3 and...  \n",
       "9   T-cell surface glycoprotein CD4 (T-cell surfac...  \n",
       "10  2-5A-dependent ribonuclease, 2-5A-dependent RN...  \n",
       "11  Complement C4-B (Basic complement C4) (C3 and ...  \n",
       "12  Interferon alpha-1/13, IFN-alpha-1/13 (Interfe...  \n",
       "13  Gamma-crystallin C (Gamma-C-crystallin) (Gamma...  \n",
       "14  Membrane cofactor protein (TLX) (Trophoblast l...  \n",
       "15  NKG2-D type II integral membrane protein (Kill...  \n",
       "16  Complement decay-accelerating factor (CD antig...  \n",
       "17       Thymidylate kinase, EC 2.7.4.9 (dTMP kinase)  \n",
       "18  Interferon beta, IFN-beta (Fibroblast interferon)  "
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mpox_human_uprot = pd.read_csv('C:/Users/reagon.karki/Documents/GitHub/mpox-kg/data/jenslab.tsv',sep='\\t')\n",
    "mpox_human_uprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "id": "d7377ab7",
   "metadata": {},
   "outputs": [],
   "source": [
    "mpox_human_uprot.to_csv('C:/Users/reagon.karki/Documents/GitHub/mpox-kg/data/mpox_humanProteins_Jenslab.csv',sep=',')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "013b9111",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}