1.2 Patterns DREBIOP - Disease 2 (Pathway-based treated disease).ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "from sqlalchemy import create_engine\n",
    "from sklearn import preprocessing\n",
    "import mysql.connector\n",
    "from pandas import DataFrame"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "triplets_total = pd.read_excel('./Data/Input/DISNET/triples_drebiop_final_dos.xlsx',engine='openpyxl')\n",
    "triplets_total = triplets_total.drop(columns=['Unnamed: 0'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "triplets_total = triplets_total.drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "disease_two = triplets_total[[\"disease_id\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "genes = pd.read_excel((\"./Data/Input/DISNET/dis_gen.xlsx\"),engine='openpyxl')\n",
    "genes = gen.drop([\"Unnamed: 0\"],axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gene = disease_two.merge(genes, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gen_num_gen = dis_gen.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gen_num_gen = dis_gen_num_gen.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "count      6.000000\n",
       "mean     423.666667\n",
       "std      372.215350\n",
       "min        3.000000\n",
       "25%      104.500000\n",
       "50%      428.500000\n",
       "75%      687.250000\n",
       "max      912.000000\n",
       "Name: gene_id, dtype: float64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_gen_num_gen[\"gene_id\"].describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "#### pw via gene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pw_gene = pd.read_csv('./Data/Input/DISNET/pathways_genes.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = disease_two.merge(pw_gene, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = dis_pw_gen.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = dis_gen_pw.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "count       6.000000\n",
       "mean     1568.000000\n",
       "std      1344.291337\n",
       "min         3.000000\n",
       "25%       415.000000\n",
       "50%      1745.500000\n",
       "75%      2380.000000\n",
       "max      3351.000000\n",
       "Name: pathway_id, dtype: float64"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_gen_pw[\"pathway_id\"].describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "#### pw direct"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = disease_two.merge(dis_path_direct,on=\"disease_id\",how= \"inner\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = dr_pw.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = dr_pw.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "25.833333333333332"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dr_pw[\"pathway_id\"].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "### drug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "drug = pd.read_csv('./Data/Input/DISNET/drugs.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = disease_two.merge(drug, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = dis_drug.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = dis_drug.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "657.3333333333334"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_drug[\"drug_id\"].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "### symptom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sint = pd.read_csv('./Data/Input/DISNET/sint_all.tsv', sep='\\t')\n",
    "sint = sint.drop([\"Unnamed: 0\"],axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = disease_two.merge(sint, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = dis_sint.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = dis_sint.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "106.66666666666667"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_sint[\"symptom\"].mean()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Pathways_type"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "drebiop_repodb = pd.read_excel((\"./Data/Input/DISNET/debriop_repodb_pws_info.xlsx\"),engine='openpyxl')\n",
    "drebiop_repodb = drebiop_repodb.drop(columns=['Unnamed: 0'])\n",
    "drebiop_repodb = drebiop_repodb.drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "drebiop_repodb_flip = pd.read_excel((\"./Data/Input/DISNET/debriop_repodb_flip_pws_info.xlsx\"),engine='openpyxl')\n",
    "drebiop_repodb_flip = drebiop_repodb_flip.drop(columns=['Unnamed: 0'])\n",
    "drebiop_repodb_flip = drebiop_repodb_flip.drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "drebiop_repodb_flip = drebiop_repodb_flip.rename(columns={\"disease2\": \"disease1\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "drebiop_csbj = pd.read_excel((\"./Data/Input/DISNET/debriop_csbj_pws_info.xlsx\"),engine='openpyxl')\n",
    "drebiop_csbj = drebiop_csbj.drop(columns=['Unnamed: 0'])\n",
    "drebiop_csbj = drebiop_csbj.drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "drebiop_csbj = drebiop_csbj.rename(columns={\"Original Condition CUI\": \"disease1\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "pws_all_triples_drebiop = pd.concat([drebiop_repodb,drebiop_repodb_flip,drebiop_csbj])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "60"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(pws_all_triples_drebiop)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "WP554     18\n",
       "WP1531    18\n",
       "WP4756     9\n",
       "WP2371     6\n",
       "WP3303     6\n",
       "WP1533     3\n",
       "Name: pathway_id, dtype: int64"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pws_all_triples_drebiop[\"pathway_id\"].value_counts()"
   ]
  }
 ],
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