src/extract_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "cf642eb2",
   "metadata": {},
   "outputs": [],
   "source": [
    "from neo4j import GraphDatabase\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import random"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "901e211d",
   "metadata": {},
   "source": [
    "## Extracting connected nodes and their relationships"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "b040748d",
   "metadata": {},
   "outputs": [],
   "source": [
    "host = \"neo4j+s://neo4j.alzkb.ai\"\n",
    "driver = GraphDatabase.driver(host, auth=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0f46291b",
   "metadata": {},
   "outputs": [],
   "source": [
    "def run_query(query, params={}):\n",
    "    with driver.session() as session:\n",
    "        result = session.run(query, params)\n",
    "        return pd.DataFrame([r.values() for r in result], columns=result.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a2d090fa",
   "metadata": {},
   "outputs": [],
   "source": [
    "def remove_key_value(row, key_to_remove):\n",
    "    try:\n",
    "        row.pop(key_to_remove)\n",
    "    except: \n",
    "        return row\n",
    "    return row"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "589efdfe",
   "metadata": {},
   "outputs": [],
   "source": [
    "df = run_query(\"\"\"\n",
    "MATCH (s)-[r]->(t)\n",
    "RETURN labels(s)[0] as source_label, properties(s) as source, type(r) as relationship_type, labels(t)[0] as target_label, properties(t) AS target\n",
    "\"\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "59a6ac0d",
   "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>source_label</th>\n",
       "      <th>source</th>\n",
       "      <th>relationship_type</th>\n",
       "      <th>target_label</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Droperidol', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALBINDSGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Raloxifene', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Anagrelide', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Amodiaquine', 'xrefDrugbank': ...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...</td>\n",
       "      <td>CHEMICALDECREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1309461</th>\n",
       "      <td>Disease</td>\n",
       "      <td>{'commonName': 'Familial Alzheimer Disease (FA...</td>\n",
       "      <td>DISEASELOCALIZESTOANATOMY</td>\n",
       "      <td>BodyPart</td>\n",
       "      <td>{'commonName': 'dura mater', 'uri': 'http://jd...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1309462</th>\n",
       "      <td>Disease</td>\n",
       "      <td>{'commonName': 'Alzheimer's Disease', 'xrefUml...</td>\n",
       "      <td>DISEASELOCALIZESTOANATOMY</td>\n",
       "      <td>BodyPart</td>\n",
       "      <td>{'commonName': 'forebrain', 'uri': 'http://jdr...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1309463</th>\n",
       "      <td>Disease</td>\n",
       "      <td>{'commonName': 'Familial Alzheimer Disease (FA...</td>\n",
       "      <td>DISEASELOCALIZESTOANATOMY</td>\n",
       "      <td>BodyPart</td>\n",
       "      <td>{'commonName': 'spinal cord', 'uri': 'http://j...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1309464</th>\n",
       "      <td>Disease</td>\n",
       "      <td>{'commonName': 'Alzheimer's Disease', 'xrefUml...</td>\n",
       "      <td>DISEASELOCALIZESTOANATOMY</td>\n",
       "      <td>BodyPart</td>\n",
       "      <td>{'commonName': 'olfactory nerve', 'uri': 'http...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1309465</th>\n",
       "      <td>Disease</td>\n",
       "      <td>{'commonName': 'Alzheimer's Disease', 'xrefUml...</td>\n",
       "      <td>DISEASELOCALIZESTOANATOMY</td>\n",
       "      <td>BodyPart</td>\n",
       "      <td>{'commonName': 'brain', 'uri': 'http://jdr.bio...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1309466 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        source_label                                             source  \\\n",
       "0               Drug  {'commonName': 'Droperidol', 'xrefDrugbank': '...   \n",
       "1               Drug  {'commonName': 'Raloxifene', 'xrefDrugbank': '...   \n",
       "2               Drug  {'commonName': 'Anagrelide', 'xrefDrugbank': '...   \n",
       "3               Drug  {'commonName': 'Amodiaquine', 'xrefDrugbank': ...   \n",
       "4               Drug  {'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...   \n",
       "...              ...                                                ...   \n",
       "1309461      Disease  {'commonName': 'Familial Alzheimer Disease (FA...   \n",
       "1309462      Disease  {'commonName': 'Alzheimer's Disease', 'xrefUml...   \n",
       "1309463      Disease  {'commonName': 'Familial Alzheimer Disease (FA...   \n",
       "1309464      Disease  {'commonName': 'Alzheimer's Disease', 'xrefUml...   \n",
       "1309465      Disease  {'commonName': 'Alzheimer's Disease', 'xrefUml...   \n",
       "\n",
       "                   relationship_type target_label  \\\n",
       "0                  CHEMICALBINDSGENE         Gene   \n",
       "1        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "2        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "3        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "4        CHEMICALDECREASESEXPRESSION         Gene   \n",
       "...                              ...          ...   \n",
       "1309461    DISEASELOCALIZESTOANATOMY     BodyPart   \n",
       "1309462    DISEASELOCALIZESTOANATOMY     BodyPart   \n",
       "1309463    DISEASELOCALIZESTOANATOMY     BodyPart   \n",
       "1309464    DISEASELOCALIZESTOANATOMY     BodyPart   \n",
       "1309465    DISEASELOCALIZESTOANATOMY     BodyPart   \n",
       "\n",
       "                                                    target  \n",
       "0        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "2        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "3        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "4        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "...                                                    ...  \n",
       "1309461  {'commonName': 'dura mater', 'uri': 'http://jd...  \n",
       "1309462  {'commonName': 'forebrain', 'uri': 'http://jdr...  \n",
       "1309463  {'commonName': 'spinal cord', 'uri': 'http://j...  \n",
       "1309464  {'commonName': 'olfactory nerve', 'uri': 'http...  \n",
       "1309465  {'commonName': 'brain', 'uri': 'http://jdr.bio...  \n",
       "\n",
       "[1309466 rows x 5 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "2e99fcbc",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Getting inverse relationship for gene-gene interactions - not sure if this needs to be explicitly extracted\n",
    "gene_gene_df = run_query(\"\"\"\n",
    "MATCH (s)-[r:GENEINTERACTSWITHGENE]->(t)\n",
    "RETURN labels(t)[0] as source_label, properties(t) as source, type(r) as relationship_type, labels(s)[0] as target_label, properties(s) AS target\n",
    "\"\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "4deb90ee",
   "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>source_label</th>\n",
       "      <th>source</th>\n",
       "      <th>relationship_type</th>\n",
       "      <th>target_label</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146996</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146997</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146998</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146999</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>147000</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>147001 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       source_label                                             source  \\\n",
       "0              Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1              Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "2              Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "3              Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "4              Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "...             ...                                                ...   \n",
       "146996         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "146997         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "146998         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "146999         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "147000         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "\n",
       "            relationship_type target_label  \\\n",
       "0       GENEINTERACTSWITHGENE         Gene   \n",
       "1       GENEINTERACTSWITHGENE         Gene   \n",
       "2       GENEINTERACTSWITHGENE         Gene   \n",
       "3       GENEINTERACTSWITHGENE         Gene   \n",
       "4       GENEINTERACTSWITHGENE         Gene   \n",
       "...                       ...          ...   \n",
       "146996  GENEINTERACTSWITHGENE         Gene   \n",
       "146997  GENEINTERACTSWITHGENE         Gene   \n",
       "146998  GENEINTERACTSWITHGENE         Gene   \n",
       "146999  GENEINTERACTSWITHGENE         Gene   \n",
       "147000  GENEINTERACTSWITHGENE         Gene   \n",
       "\n",
       "                                                   target  \n",
       "0       {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1       {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "2       {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "3       {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "4       {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "...                                                   ...  \n",
       "146996  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "146997  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "146998  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "146999  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "147000  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "\n",
       "[147001 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gene_gene_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c838b499",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_df = pd.concat([df, gene_gene_df], ignore_index=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "1a6215a9",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Apply the function to the column\n",
    "combined_df['source'] = combined_df['source'].apply(lambda row: remove_key_value(row, key_to_remove='uri'))\n",
    "combined_df['target'] = combined_df['target'].apply(lambda row: remove_key_value(row, key_to_remove='uri'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "c9a9d4d6",
   "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>source_label</th>\n",
       "      <th>source</th>\n",
       "      <th>relationship_type</th>\n",
       "      <th>target_label</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Droperidol', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALBINDSGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Raloxifene', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Anagrelide', 'xrefDrugbank': '...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Amodiaquine', 'xrefDrugbank': ...</td>\n",
       "      <td>CHEMICALINCREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...</td>\n",
       "      <td>CHEMICALDECREASESEXPRESSION</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456462</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456463</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456464</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456465</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456466</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>GENEINTERACTSWITHGENE</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1456467 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        source_label                                             source  \\\n",
       "0               Drug  {'commonName': 'Droperidol', 'xrefDrugbank': '...   \n",
       "1               Drug  {'commonName': 'Raloxifene', 'xrefDrugbank': '...   \n",
       "2               Drug  {'commonName': 'Anagrelide', 'xrefDrugbank': '...   \n",
       "3               Drug  {'commonName': 'Amodiaquine', 'xrefDrugbank': ...   \n",
       "4               Drug  {'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...   \n",
       "...              ...                                                ...   \n",
       "1456462         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456463         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456464         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456465         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456466         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "\n",
       "                   relationship_type target_label  \\\n",
       "0                  CHEMICALBINDSGENE         Gene   \n",
       "1        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "2        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "3        CHEMICALINCREASESEXPRESSION         Gene   \n",
       "4        CHEMICALDECREASESEXPRESSION         Gene   \n",
       "...                              ...          ...   \n",
       "1456462        GENEINTERACTSWITHGENE         Gene   \n",
       "1456463        GENEINTERACTSWITHGENE         Gene   \n",
       "1456464        GENEINTERACTSWITHGENE         Gene   \n",
       "1456465        GENEINTERACTSWITHGENE         Gene   \n",
       "1456466        GENEINTERACTSWITHGENE         Gene   \n",
       "\n",
       "                                                    target  \n",
       "0        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "2        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "3        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "4        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "...                                                    ...  \n",
       "1456462  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456463  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456464  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456465  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456466  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "\n",
       "[1456467 rows x 5 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "c822d80c",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['CHEMICALBINDSGENE', 'CHEMICALINCREASESEXPRESSION',\n",
       "       'CHEMICALDECREASESEXPRESSION', 'DRUGINCLASS', 'DRUGTREATSDISEASE',\n",
       "       'DRUGCAUSESEFFECT', 'GENEPARTICIPATESINBIOLOGICALPROCESS',\n",
       "       'GENEINPATHWAY', 'GENEINTERACTSWITHGENE',\n",
       "       'GENEHASMOLECULARFUNCTION', 'GENEASSOCIATEDWITHCELLULARCOMPONENT',\n",
       "       'GENEASSOCIATESWITHDISEASE', 'BODYPARTOVEREXPRESSESGENE',\n",
       "       'BODYPARTUNDEREXPRESSESGENE', 'SYMPTOMMANIFESTATIONOFDISEASE',\n",
       "       'DISEASELOCALIZESTOANATOMY', 'DISEASEASSOCIATESWITHDISEASE'],\n",
       "      dtype=object)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_df['relationship_type'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "aec98013",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Rewrite relationship type in Natural language\n",
    "rels_type = {'GENEINPATHWAY': 'gene in the pathway', 'GENEINTERACTSWITHGENE': 'gene interacts with the gene', \\\n",
    "             'GENEPARTICIPATESINBIOLOGICALPROCESS': 'gene participates in the biological process', \\\n",
    "             'GENEASSOCIATEDWITHCELLULARCOMPONENT': 'gene associated with the cellular component', \\\n",
    "             'GENEHASMOLECULARFUNCTION': 'gene has a molecular function', \\\n",
    "             'GENEASSOCIATESWITHDISEASE': 'gene associates with the disease', \\\n",
    "             'CHEMICALBINDSGENE': 'chemical or drug binds the gene', \\\n",
    "             'CHEMICALINCREASESEXPRESSION': 'chemical or drug increases the gene expression', \\\n",
    "             'CHEMICALDECREASESEXPRESSION': 'chemical or drug decreases the gene expression', \\\n",
    "             'DRUGINCLASS': 'chemical or drug in the drug class', \\\n",
    "             'DISEASELOCALIZESTOANATOMY': 'disease localizes to anatomy or body part', \\\n",
    "             'DISEASEASSOCIATESWITHDISEASE': 'disease associates with another disease', \\\n",
    "             'DRUGCAUSESEFFECT': 'chemical or drug causes effect to the disease', \\\n",
    "             'DRUGTREATSDISEASE': 'chemical or drug treats the disease', \\\n",
    "             'SYMPTOMMANIFESTATIONOFDISEASE': 'symptom manifestation of the disease', \\\n",
    "             'BODYPARTOVEREXPRESSESGENE': 'body part over-expresses the gene', \\\n",
    "             'BODYPARTUNDEREXPRESSESGENE': 'body part under-expresses the gene'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "d30b0009",
   "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>source_label</th>\n",
       "      <th>source</th>\n",
       "      <th>relationship_type</th>\n",
       "      <th>target_label</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Droperidol', 'xrefDrugbank': '...</td>\n",
       "      <td>chemical or drug binds the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Raloxifene', 'xrefDrugbank': '...</td>\n",
       "      <td>chemical or drug increases the gene expression</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Anagrelide', 'xrefDrugbank': '...</td>\n",
       "      <td>chemical or drug increases the gene expression</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Amodiaquine', 'xrefDrugbank': ...</td>\n",
       "      <td>chemical or drug increases the gene expression</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Drug</td>\n",
       "      <td>{'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...</td>\n",
       "      <td>chemical or drug decreases the gene expression</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456462</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>gene interacts with the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456463</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>gene interacts with the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456464</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>gene interacts with the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456465</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>gene interacts with the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1456466</th>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "      <td>gene interacts with the gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>{'typeOfGene': 'protein-coding', 'commonName':...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1456467 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        source_label                                             source  \\\n",
       "0               Drug  {'commonName': 'Droperidol', 'xrefDrugbank': '...   \n",
       "1               Drug  {'commonName': 'Raloxifene', 'xrefDrugbank': '...   \n",
       "2               Drug  {'commonName': 'Anagrelide', 'xrefDrugbank': '...   \n",
       "3               Drug  {'commonName': 'Amodiaquine', 'xrefDrugbank': ...   \n",
       "4               Drug  {'commonName': 'Digoxin', 'xrefDrugbank': 'DB0...   \n",
       "...              ...                                                ...   \n",
       "1456462         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456463         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456464         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456465         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "1456466         Gene  {'typeOfGene': 'protein-coding', 'commonName':...   \n",
       "\n",
       "                                      relationship_type target_label  \\\n",
       "0                       chemical or drug binds the gene         Gene   \n",
       "1        chemical or drug increases the gene expression         Gene   \n",
       "2        chemical or drug increases the gene expression         Gene   \n",
       "3        chemical or drug increases the gene expression         Gene   \n",
       "4        chemical or drug decreases the gene expression         Gene   \n",
       "...                                                 ...          ...   \n",
       "1456462                    gene interacts with the gene         Gene   \n",
       "1456463                    gene interacts with the gene         Gene   \n",
       "1456464                    gene interacts with the gene         Gene   \n",
       "1456465                    gene interacts with the gene         Gene   \n",
       "1456466                    gene interacts with the gene         Gene   \n",
       "\n",
       "                                                    target  \n",
       "0        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "2        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "3        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "4        {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "...                                                    ...  \n",
       "1456462  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456463  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456464  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456465  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "1456466  {'typeOfGene': 'protein-coding', 'commonName':...  \n",
       "\n",
       "[1456467 rows x 5 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_df['relationship_type'] = combined_df['relationship_type'].replace(rels_type)\n",
    "combined_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "8a9a4f48",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_df.to_csv('alzkb_relationships_v2.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "74fcdedb",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_df.to_json('alzkb_relationships.json')"
   ]
  }
 ],
 "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": "3.9.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}