KG_Generator_Prototype-Copy1.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "95894b68",
   "metadata": {},
   "source": [
    "# KG Generator Tool"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e6cd5418",
   "metadata": {},
   "source": [
    "## Let's get started by importing relevant libraries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "35a63bc0",
   "metadata": {},
   "outputs": [],
   "source": [
    "#pip install -r requirements.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "b41fb83b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "import json\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import os\n",
    "from tqdm.auto import tqdm\n",
    "\n",
    "import pybel\n",
    "from pybel.io.jupyter import to_jupyter\n",
    "from utils import *\n",
    "from kg_gen_2 import *\n",
    "\n",
    "from IPython.display import Markdown, display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2036d66a",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 216x216 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "text/markdown": [
       "<span style='color:blue'>**Welcome to the KG Generator tool. In the following steps, we will need some inputs from your side.**</span>"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Please enter the disease you are interested in and we will try to find the best matches for you.\n",
      "\n",
      "Input: fdld\n",
      "Ooops!! Did you have a typo in the name. Please try again!\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 216x216 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "text/markdown": [
       "<span style='color:blue'>**Welcome to the KG Generator tool. In the following steps, we will need some inputs from your side.**</span>"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Please enter the disease you are interested in and we will try to find the best matches for you.\n",
      "\n",
      "Input: covid\n"
     ]
    }
   ],
   "source": [
    "kg = createKG()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eb82d4c6",
   "metadata": {},
   "outputs": [],
   "source": [
    "to_jupyter(kg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8b36d40f",
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "kg.summarize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9cbd4014",
   "metadata": {},
   "outputs": [],
   "source": [
    "KG_namespace_plot(kg)"
   ]
  }
 ],
 "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
}