Create_Drug_Cooccurance_Graph.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Creating Co-Occurence Graph of Drugs-Chemicals-PMIDs\n",
    "This notebook creates a graph database storing the relation of drugs and \n",
    "chemicals related to oxidative stress and their occurance in PubMed abstracts\n",
    "\n",
    "Nodes are created for drugs, chemicals, articles, and MeSH terms."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [],
   "source": [
    "import neo4j_functions.driver as neo4j_driver\n",
    "import pandas as pd\n",
    "import importlib"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "outputs": [],
   "source": [
    "drug_list_df = pd.read_csv('lib/Drug list total 04.05.19   - Overview Drug list.csv')\n",
    "drug_occurance_df = pd.read_csv('lib/Drug_PMID_occurances.csv')\n",
    "\n",
    "chemical_list_df = pd.read_csv('lib/Oxidative Stress Text Mining Targets 4.1 - Summary of Oxidative Stress.csv')\n",
    "chemical_occurance_df = pd.read_csv('lib/Chemical_PMID_occurances.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Merging Drug List with Drug Occurance Data Sets\n",
    "\n",
    "1. Duplicate drug names in the lab provided list are merged, the drug with an associated category is kept if possible\n",
    "2. Deduplicated list of drug names is merged with a dataframe for drug occurance generated on the CaseOLAP cloud instance\n",
    "    - Notebook used to generate drug occurance list located at `/home/ubuntu/RotationStd/elasticsearch/chemical_drug_elastic_occurance.ipynb`\n",
    "3. Final merged dataframe saved in to `import` folder of neo4j instance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Removing Duplicate drug names, keeping version with a drug category if possible\n",
    "deduped_drug_list = drug_list_df.sort_values(by='Drug Category').drop_duplicates(subset=['Name'], keep='first')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Merging drug list with drug occurance list\n",
    "drug_occurance_df['MeSH'] = drug_occurance_df['MeSH'].str.replace('[', '').str.replace(']', '').str.replace(\"'\", '')\n",
    "\n",
    "drug_list_occurance_df = drug_occurance_df.merge(\n",
    "    deduped_drug_list.rename(columns={\n",
    "        'Name': 'drug',\n",
    "        'Drug Category': 'category',\n",
    "        'MeSH Descriptor': 'drug_mesh',\n",
    "    }),\n",
    "    how='inner',\n",
    "    validate='m:1'\n",
    ")\n",
    "# Values with NaN for category or synonym replaced\n",
    "# NaN for synonym replaced with drug name, category replaced with 'None'\n",
    "drug_list_occurance_df['drug']  = drug_list_occurance_df['drug'].str.strip()\n",
    "drug_list_occurance_df.loc[drug_list_occurance_df.MeSH == '', 'MeSH'] = 'None'\n",
    "\n",
    "drug_list_occurance_df.loc[drug_list_occurance_df.category.isnull(), 'category']  = 'None'\n",
    "drug_list_occurance_df.loc[drug_list_occurance_df.drug_mesh.isnull(), 'drug_mesh']  = 'None'\n",
    "drug_list_occurance_df.loc[drug_list_occurance_df.Synonyms.isnull(), 'Synonyms']  = drug_list_occurance_df[drug_list_occurance_df.Synonyms.isnull()].drug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>MeSH</th>\n",
       "      <th>PMID</th>\n",
       "      <th>abstract</th>\n",
       "      <th>title</th>\n",
       "      <th>drug</th>\n",
       "      <th>category</th>\n",
       "      <th>#</th>\n",
       "      <th>Synonyms</th>\n",
       "      <th>drug_mesh</th>\n",
       "      <th>MeSH tree(s)</th>\n",
       "      <th>Common adverse effects</th>\n",
       "      <th>Dosage (freq/amount/time/delivery)</th>\n",
       "      <th>Duration (time)</th>\n",
       "      <th>Pham Action</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Actinomycetales, chemistry, enzymology, Adenos...</td>\n",
       "      <td>8784428</td>\n",
       "      <td>a phosphotransferase which modifies the alpha ...</td>\n",
       "      <td>Acarbose 7-phosphotransferase from Actinoplane...</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>Alpha-glucosidase Inhibitors</td>\n",
       "      <td>54</td>\n",
       "      <td>Acarbosa, Acarbose, Acarbosum</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>D09.698.629.802.100</td>\n",
       "      <td>Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...</td>\n",
       "      <td>3/25-50-100mg/day/po</td>\n",
       "      <td>4-8 weeks intervals</td>\n",
       "      <td>Glycoside \\nHydrolase Inhibitors</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Acarbose, Adult, Blood Glucose, metabolism, Cl...</td>\n",
       "      <td>6350115</td>\n",
       "      <td>in a double blind study we have compared the e...</td>\n",
       "      <td>Effect of acarbose, pectin, a combination of a...</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>Alpha-glucosidase Inhibitors</td>\n",
       "      <td>54</td>\n",
       "      <td>Acarbosa, Acarbose, Acarbosum</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>D09.698.629.802.100</td>\n",
       "      <td>Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...</td>\n",
       "      <td>3/25-50-100mg/day/po</td>\n",
       "      <td>4-8 weeks intervals</td>\n",
       "      <td>Glycoside \\nHydrolase Inhibitors</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>Acarbose, Adult, Aged, Blood Glucose, metaboli...</td>\n",
       "      <td>9663365</td>\n",
       "      <td>acarbose is an alpha glucosidase inhibitor app...</td>\n",
       "      <td>Effects of beano on the tolerability and pharm...</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>Alpha-glucosidase Inhibitors</td>\n",
       "      <td>54</td>\n",
       "      <td>Acarbosa, Acarbose, Acarbosum</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>D09.698.629.802.100</td>\n",
       "      <td>Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...</td>\n",
       "      <td>3/25-50-100mg/day/po</td>\n",
       "      <td>4-8 weeks intervals</td>\n",
       "      <td>Glycoside \\nHydrolase Inhibitors</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>Acarbose, administration &amp; dosage, Animals, Bo...</td>\n",
       "      <td>11779583</td>\n",
       "      <td>as alpha glucosidase inhibitor, the antidiabet...</td>\n",
       "      <td>Chronic acarbose-feeding increases GLUT1 prote...</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>Alpha-glucosidase Inhibitors</td>\n",
       "      <td>54</td>\n",
       "      <td>Acarbosa, Acarbose, Acarbosum</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>D09.698.629.802.100</td>\n",
       "      <td>Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...</td>\n",
       "      <td>3/25-50-100mg/day/po</td>\n",
       "      <td>4-8 weeks intervals</td>\n",
       "      <td>Glycoside \\nHydrolase Inhibitors</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>Acarbose, Aged, Blood Glucose, metabolism, Dia...</td>\n",
       "      <td>9428831</td>\n",
       "      <td>to compare the therapeutic potential of acarbo...</td>\n",
       "      <td>Efficacy of 24-week monotherapy with acarbose,...</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>Alpha-glucosidase Inhibitors</td>\n",
       "      <td>54</td>\n",
       "      <td>Acarbosa, Acarbose, Acarbosum</td>\n",
       "      <td>Acarbose</td>\n",
       "      <td>D09.698.629.802.100</td>\n",
       "      <td>Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...</td>\n",
       "      <td>3/25-50-100mg/day/po</td>\n",
       "      <td>4-8 weeks intervals</td>\n",
       "      <td>Glycoside \\nHydrolase Inhibitors</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                MeSH      PMID  \\\n",
       "0  Actinomycetales, chemistry, enzymology, Adenos...   8784428   \n",
       "1  Acarbose, Adult, Blood Glucose, metabolism, Cl...   6350115   \n",
       "2  Acarbose, Adult, Aged, Blood Glucose, metaboli...   9663365   \n",
       "3  Acarbose, administration & dosage, Animals, Bo...  11779583   \n",
       "4  Acarbose, Aged, Blood Glucose, metabolism, Dia...   9428831   \n",
       "\n",
       "                                            abstract  \\\n",
       "0  a phosphotransferase which modifies the alpha ...   \n",
       "1  in a double blind study we have compared the e...   \n",
       "2  acarbose is an alpha glucosidase inhibitor app...   \n",
       "3  as alpha glucosidase inhibitor, the antidiabet...   \n",
       "4  to compare the therapeutic potential of acarbo...   \n",
       "\n",
       "                                               title      drug  \\\n",
       "0  Acarbose 7-phosphotransferase from Actinoplane...  Acarbose   \n",
       "1  Effect of acarbose, pectin, a combination of a...  Acarbose   \n",
       "2  Effects of beano on the tolerability and pharm...  Acarbose   \n",
       "3  Chronic acarbose-feeding increases GLUT1 prote...  Acarbose   \n",
       "4  Efficacy of 24-week monotherapy with acarbose,...  Acarbose   \n",
       "\n",
       "                       category   #                       Synonyms drug_mesh  \\\n",
       "0  Alpha-glucosidase Inhibitors  54  Acarbosa, Acarbose, Acarbosum  Acarbose   \n",
       "1  Alpha-glucosidase Inhibitors  54  Acarbosa, Acarbose, Acarbosum  Acarbose   \n",
       "2  Alpha-glucosidase Inhibitors  54  Acarbosa, Acarbose, Acarbosum  Acarbose   \n",
       "3  Alpha-glucosidase Inhibitors  54  Acarbosa, Acarbose, Acarbosum  Acarbose   \n",
       "4  Alpha-glucosidase Inhibitors  54  Acarbosa, Acarbose, Acarbosum  Acarbose   \n",
       "\n",
       "          MeSH tree(s)                             Common adverse effects  \\\n",
       "0  D09.698.629.802.100  Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...   \n",
       "1  D09.698.629.802.100  Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...   \n",
       "2  D09.698.629.802.100  Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...   \n",
       "3  D09.698.629.802.100  Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...   \n",
       "4  D09.698.629.802.100  Hypoglycaemia, Hypoglycaemic \\ncoma, pneumatos...   \n",
       "\n",
       "  Dosage (freq/amount/time/delivery)      Duration (time)  \\\n",
       "0               3/25-50-100mg/day/po  4-8 weeks intervals   \n",
       "1               3/25-50-100mg/day/po  4-8 weeks intervals   \n",
       "2               3/25-50-100mg/day/po  4-8 weeks intervals   \n",
       "3               3/25-50-100mg/day/po  4-8 weeks intervals   \n",
       "4               3/25-50-100mg/day/po  4-8 weeks intervals   \n",
       "\n",
       "                        Pham Action  \n",
       "0  Glycoside \\nHydrolase Inhibitors  \n",
       "1  Glycoside \\nHydrolase Inhibitors  \n",
       "2  Glycoside \\nHydrolase Inhibitors  \n",
       "3  Glycoside \\nHydrolase Inhibitors  \n",
       "4  Glycoside \\nHydrolase Inhibitors  "
      ]
     },
     "execution_count": 108,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Saving file to import area of local neo4j instance\n",
    "drug_list_occurance_file = '/Users/akre96/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-dc2bbd3b-84e9-421e-8594-9fe29be9bb02/installation-3.5.6/import/drug_list_occurance.csv'\n",
    "drug_list_occurance_df.to_csv(drug_list_occurance_file, index=False)\n",
    "drug_list_occurance_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating Neo4J Graph Database for Drug occurance in PMIDs\n",
    "1. Neo4J Driver initialized\n",
    "2. Query formed to import data from list generated in previous section of this notebook\n",
    "    - Loading csv\n",
    "    - Creating drug entities with name, category, and synonym fields\n",
    "    - Creating article entities with PMID, abstract, title, and MeSH fields\n",
    "    - Creating edges labeled OCCURANCE for connecting drugs referenced by a PMID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 109,
   "metadata": {},
   "outputs": [],
   "source": [
    "importlib.reload(neo4j_driver)\n",
    "driver = neo4j_driver.driver(uri = \"bolt://localhost:7687\", user = \"neo4j\", password = \"drug1234\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Query:\n",
      "\t LOAD CSV WITH HEADERS FROM \"file:///drug_list_occurance.csv\" AS row MERGE (drug:Drug {name: row.drug, category: row.category, synonyms: row.Synonyms}) MERGE (article:Article {PMID: row.PMID, abstract: row.abstract, title: row.title, MeSH: split(row.MeSH, ', ')}) MERGE (drug)-[:OCCURANCE]->(article) MERGE (drugmesh:MeSH {name: row.drug_mesh}) MERGE (drug)-[:OCCURANCE]->(article) MERGE (drug)-[:HAS_MESH]->(drugmesh)\n"
     ]
    }
   ],
   "source": [
    "import_data_query = (\n",
    "    \"LOAD CSV WITH HEADERS FROM %s AS row\"\n",
    "    \" MERGE (drug:Drug {name: row.drug, category: row.category, synonyms: row.Synonyms})\"\n",
    "    \" MERGE (article:Article {PMID: row.PMID, abstract: row.abstract, title: row.title, MeSH: split(row.MeSH, %s)})\"\n",
    "    \" MERGE (drug)-[:OCCURANCE]->(article)\"\n",
    "    \" MERGE (drugmesh:MeSH {name: row.drug_mesh})\"\n",
    "    \" MERGE (drug)-[:OCCURANCE]->(article)\"\n",
    "    \" MERGE (drug)-[:HAS_MESH]->(drugmesh)\"\n",
    "    % ('\"file:///' + 'drug_list_occurance.csv' + '\"', \"', '\")\n",
    ")\n",
    "print('Query:\\n\\t', import_data_query)\n",
    "with driver.driver.session() as session:\n",
    "    result = session.run(import_data_query)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Merging Chemical List with Chemical Occurance Data Sets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {},
   "outputs": [],
   "source": [
    "deduped_chem_list = chemical_list_df\\\n",
    "    .dropna(subset=['Molecule/Enzyme/Protein'])\\\n",
    "    .sort_values(by='Molecular and Functional Categories')\\\n",
    "    .drop_duplicates(subset=['Molecule/Enzyme/Protein'], keep='first')\\\n",
    "    .fillna('None')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>MeSH</th>\n",
       "      <th>PMID</th>\n",
       "      <th>abstract</th>\n",
       "      <th>title</th>\n",
       "      <th>chemical</th>\n",
       "      <th>GO_Oxidative_Stress</th>\n",
       "      <th>GO_MF</th>\n",
       "      <th>chemical_mesh</th>\n",
       "      <th>MeSH Supplementary</th>\n",
       "      <th>MeSH tree numbers</th>\n",
       "      <th>formula</th>\n",
       "      <th>Examples</th>\n",
       "      <th>Pharm Actions</th>\n",
       "      <th>Tree Numbers</th>\n",
       "      <th>References</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>31368101</td>\n",
       "      <td>coronary spasm plays an important role in the ...</td>\n",
       "      <td>Association of East Asian Variant Aldehyde Deh...</td>\n",
       "      <td>4-hydroxy-2-nonenal (4-HNE)</td>\n",
       "      <td>135</td>\n",
       "      <td>Lipid Peroxidation Products</td>\n",
       "      <td>Aldehydes</td>\n",
       "      <td>4-hydroxy-2-nonenal</td>\n",
       "      <td>D02.047</td>\n",
       "      <td>C9H16O2</td>\n",
       "      <td>4-HNE, MDA</td>\n",
       "      <td>Cross-Linking Reagents</td>\n",
       "      <td>D27.720.470.410.210</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Acetylcholinesterase, metabolism, Aldehydes, m...</td>\n",
       "      <td>10463393</td>\n",
       "      <td>we have investigated the effect of soman induc...</td>\n",
       "      <td>Increased levels of nitrogen oxides and lipid ...</td>\n",
       "      <td>4-hydroxy-2-nonenal (4-HNE)</td>\n",
       "      <td>135</td>\n",
       "      <td>Lipid Peroxidation Products</td>\n",
       "      <td>Aldehydes</td>\n",
       "      <td>4-hydroxy-2-nonenal</td>\n",
       "      <td>D02.047</td>\n",
       "      <td>C9H16O2</td>\n",
       "      <td>4-HNE, MDA</td>\n",
       "      <td>Cross-Linking Reagents</td>\n",
       "      <td>D27.720.470.410.210</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>Aldehydes, chemistry, Amines, chemistry, Benzy...</td>\n",
       "      <td>8448343</td>\n",
       "      <td>the reaction of trans 4 hydroxy 2 nonenal (4 h...</td>\n",
       "      <td>Pyrrole formation from 4-hydroxynonenal and pr...</td>\n",
       "      <td>4-hydroxy-2-nonenal (4-HNE)</td>\n",
       "      <td>135</td>\n",
       "      <td>Lipid Peroxidation Products</td>\n",
       "      <td>Aldehydes</td>\n",
       "      <td>4-hydroxy-2-nonenal</td>\n",
       "      <td>D02.047</td>\n",
       "      <td>C9H16O2</td>\n",
       "      <td>4-HNE, MDA</td>\n",
       "      <td>Cross-Linking Reagents</td>\n",
       "      <td>D27.720.470.410.210</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>Animals, Blood-Brain Barrier, metabolism, path...</td>\n",
       "      <td>29775963</td>\n",
       "      <td>brain ischemic preconditioning (ipc) with mild...</td>\n",
       "      <td>Brain ischemic preconditioning protects agains...</td>\n",
       "      <td>4-hydroxy-2-nonenal (4-HNE)</td>\n",
       "      <td>135</td>\n",
       "      <td>Lipid Peroxidation Products</td>\n",
       "      <td>Aldehydes</td>\n",
       "      <td>4-hydroxy-2-nonenal</td>\n",
       "      <td>D02.047</td>\n",
       "      <td>C9H16O2</td>\n",
       "      <td>4-HNE, MDA</td>\n",
       "      <td>Cross-Linking Reagents</td>\n",
       "      <td>D27.720.470.410.210</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>Alzheimer Disease, drug therapy, enzymology, p...</td>\n",
       "      <td>30218858</td>\n",
       "      <td>excessive production of amyloid β (aβ) induced...</td>\n",
       "      <td>Neuro-protective effects of aloperine in an Al...</td>\n",
       "      <td>4-hydroxy-2-nonenal (4-HNE)</td>\n",
       "      <td>135</td>\n",
       "      <td>Lipid Peroxidation Products</td>\n",
       "      <td>Aldehydes</td>\n",
       "      <td>4-hydroxy-2-nonenal</td>\n",
       "      <td>D02.047</td>\n",
       "      <td>C9H16O2</td>\n",
       "      <td>4-HNE, MDA</td>\n",
       "      <td>Cross-Linking Reagents</td>\n",
       "      <td>D27.720.470.410.210</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                MeSH      PMID  \\\n",
       "0                                               None  31368101   \n",
       "1  Acetylcholinesterase, metabolism, Aldehydes, m...  10463393   \n",
       "2  Aldehydes, chemistry, Amines, chemistry, Benzy...   8448343   \n",
       "3  Animals, Blood-Brain Barrier, metabolism, path...  29775963   \n",
       "4  Alzheimer Disease, drug therapy, enzymology, p...  30218858   \n",
       "\n",
       "                                            abstract  \\\n",
       "0  coronary spasm plays an important role in the ...   \n",
       "1  we have investigated the effect of soman induc...   \n",
       "2  the reaction of trans 4 hydroxy 2 nonenal (4 h...   \n",
       "3  brain ischemic preconditioning (ipc) with mild...   \n",
       "4  excessive production of amyloid β (aβ) induced...   \n",
       "\n",
       "                                               title  \\\n",
       "0  Association of East Asian Variant Aldehyde Deh...   \n",
       "1  Increased levels of nitrogen oxides and lipid ...   \n",
       "2  Pyrrole formation from 4-hydroxynonenal and pr...   \n",
       "3  Brain ischemic preconditioning protects agains...   \n",
       "4  Neuro-protective effects of aloperine in an Al...   \n",
       "\n",
       "                      chemical GO_Oxidative_Stress  \\\n",
       "0  4-hydroxy-2-nonenal (4-HNE)                 135   \n",
       "1  4-hydroxy-2-nonenal (4-HNE)                 135   \n",
       "2  4-hydroxy-2-nonenal (4-HNE)                 135   \n",
       "3  4-hydroxy-2-nonenal (4-HNE)                 135   \n",
       "4  4-hydroxy-2-nonenal (4-HNE)                 135   \n",
       "\n",
       "                         GO_MF chemical_mesh   MeSH Supplementary  \\\n",
       "0  Lipid Peroxidation Products     Aldehydes  4-hydroxy-2-nonenal   \n",
       "1  Lipid Peroxidation Products     Aldehydes  4-hydroxy-2-nonenal   \n",
       "2  Lipid Peroxidation Products     Aldehydes  4-hydroxy-2-nonenal   \n",
       "3  Lipid Peroxidation Products     Aldehydes  4-hydroxy-2-nonenal   \n",
       "4  Lipid Peroxidation Products     Aldehydes  4-hydroxy-2-nonenal   \n",
       "\n",
       "  MeSH tree numbers  formula    Examples           Pharm Actions  \\\n",
       "0           D02.047  C9H16O2  4-HNE, MDA  Cross-Linking Reagents   \n",
       "1           D02.047  C9H16O2  4-HNE, MDA  Cross-Linking Reagents   \n",
       "2           D02.047  C9H16O2  4-HNE, MDA  Cross-Linking Reagents   \n",
       "3           D02.047  C9H16O2  4-HNE, MDA  Cross-Linking Reagents   \n",
       "4           D02.047  C9H16O2  4-HNE, MDA  Cross-Linking Reagents   \n",
       "\n",
       "          Tree Numbers References  \n",
       "0  D27.720.470.410.210       None  \n",
       "1  D27.720.470.410.210       None  \n",
       "2  D27.720.470.410.210       None  \n",
       "3  D27.720.470.410.210       None  \n",
       "4  D27.720.470.410.210       None  "
      ]
     },
     "execution_count": 112,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chemical_occurance_df['MeSH'] = chemical_occurance_df['MeSH'].str.replace('[', '').str.replace(']', '').str.replace(\"'\", '')\n",
    "chem_list_occurance_df = chemical_occurance_df.merge(\n",
    "    deduped_chem_list.rename(columns={\n",
    "        'Molecule/Enzyme/Protein': 'chemical',\n",
    "        'Chemical Formula': 'formula',\n",
    "        'Molecular and Functional Categories': 'GO_MF',\n",
    "        'Biological Events of Oxidative Stress': 'GO_Oxidative_Stress',\n",
    "        'MeSH Heading': 'chemical_mesh'\n",
    "    }),\n",
    "    how='inner',\n",
    "    validate='m:1'\n",
    ").fillna('None')\n",
    "chem_list_occurance_df['chemical'] = chem_list_occurance_df.chemical.str.strip()\n",
    "chem_list_occurance_df.loc[chem_list_occurance_df.MeSH == '', 'MeSH'] = 'None'\n",
    "chem_list_occurance_df.head()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Saving file to import area of local neo4j instance\n",
    "chem_list_occurance_file = '/Users/akre96/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-dc2bbd3b-84e9-421e-8594-9fe29be9bb02/installation-3.5.6/import/chem_list_occurance.csv'\n",
    "chem_list_occurance_df.to_csv(chem_list_occurance_file, index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Adding to Neo4J Graph Database for Chemical occurance in PMIDs\n",
    "1. Query formed to import data from list generated in previous section of this notebook\n",
    "    - Loading csv\n",
    "    - Creating chemical entities with name, example, and formula fields\n",
    "    - Merges article entities with PMID, abstract, title, and MeSH fields\n",
    "    - Creating edges labeled OCCURANCE for connecting drugs referenced by a PMID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Query:\n",
      "\t LOAD CSV WITH HEADERS FROM \"file:///chem_list_occurance.csv\" AS row MERGE (chem:Chemical {name: row.chemical, example: row.Examples, formula: row.formula}) MERGE (article:Article {PMID: row.PMID, abstract: row.abstract, title: row.title, MeSH: split(row.MeSH, ', ')}) MERGE (mesh:MeSH {name: row.chemical_mesh}) MERGE (chem)-[:OCCURANCE]->(article) MERGE (chem)-[:HAS_MESH]->(mesh)\n"
     ]
    }
   ],
   "source": [
    "import_chemical_data_query = (\n",
    "    \"LOAD CSV WITH HEADERS FROM %s AS row\"\n",
    "    \" MERGE (chem:Chemical {name: row.chemical, example: row.Examples, formula: row.formula})\"\n",
    "    \" MERGE (article:Article {PMID: row.PMID, abstract: row.abstract, title: row.title, MeSH: split(row.MeSH, %s)})\"\n",
    "    \" MERGE (mesh:MeSH {name: row.chemical_mesh})\"\n",
    "    \" MERGE (chem)-[:OCCURANCE]->(article)\"\n",
    "    \" MERGE (chem)-[:HAS_MESH]->(mesh)\"\n",
    "    % ('\"file:///' + 'chem_list_occurance.csv' + '\"', \"', '\")\n",
    "\n",
    ")\n",
    "print('Query:\\n\\t', import_chemical_data_query)\n",
    "with driver.driver.session() as session:\n",
    "    result = session.run(import_chemical_data_query)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Adding MeSH descriptors from Articles as MeSH node\n",
    "1. Adds nodes from mesh descriptor list\n",
    "2. Deletes \"none\" node"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 115,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Query:\n",
      "\t MATCH (article:Article) UNWIND article.MeSH AS m MERGE (artMesh:MeSH {name: m}) MERGE (article)-[:HAS_MESH]->(artMesh)\n"
     ]
    }
   ],
   "source": [
    "article_mesh_descriptors_query = (\n",
    "    \"MATCH (article:Article)\"\n",
    "    \" UNWIND article.MeSH AS m\"\n",
    "    \" MERGE (artMesh:MeSH {name: m})\"\n",
    "    \" MERGE (article)-[:HAS_MESH]->(artMesh)\"\n",
    ")\n",
    "print('Query:\\n\\t', article_mesh_descriptors_query)\n",
    "with driver.driver.session() as session:\n",
    "    result = session.run(article_mesh_descriptors_query)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 116,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Query:\n",
      "\t MATCH (m:MeSH {name: 'None'}) DETACH DELETE m\n"
     ]
    }
   ],
   "source": [
    "delete_none_mesh_descriptors_query = (\n",
    "    \"MATCH (m:MeSH {name: 'None'})\"\n",
    "    \" DETACH DELETE m\"\n",
    ")\n",
    "print('Query:\\n\\t', delete_none_mesh_descriptors_query)\n",
    "with driver.driver.session() as session:\n",
    "    result = session.run(delete_none_mesh_descriptors_query)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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