06-neo4j.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "06-neo4j\n",
    " - reformat for neo4j import"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# make the file headers correct\n",
    "# https://neo4j.com/docs/operations-manual/current/tools/import/file-header-format/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pickle\n",
    "%matplotlib inline\n",
    "import pandas as pd\n",
    "import seaborn as sns\n",
    "import shelve\n",
    "import re\n",
    "from collections import defaultdict, Counter\n",
    "from tqdm import tqdm\n",
    "import requests\n",
    "from pyquery import PyQuery as pq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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>ID</th>\n",
       "      <th>LABEL</th>\n",
       "      <th>umls_type</th>\n",
       "      <th>umls_type_label</th>\n",
       "      <th>blm_type</th>\n",
       "      <th>xrefs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C0061133</td>\n",
       "      <td>gastrin releasing peptide (14-27)</td>\n",
       "      <td>T116</td>\n",
       "      <td>Amino Acid, Peptide, or Protein</td>\n",
       "      <td>protein</td>\n",
       "      <td>MESH:C041922</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C1523610</td>\n",
       "      <td>regulation of tube length, open tracheal system</td>\n",
       "      <td>T042</td>\n",
       "      <td>Organ or Tissue Function</td>\n",
       "      <td>biological_process_or_activity</td>\n",
       "      <td>GO:GO:0035159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>C0312636</td>\n",
       "      <td>Antibody to hepatitis E virus</td>\n",
       "      <td>T116|T129</td>\n",
       "      <td>Amino Acid, Peptide, or Protein|Immunologic Fa...</td>\n",
       "      <td>biological_entity</td>\n",
       "      <td>LNC:MTHU004056;SNMI:F-C2A90;MTH:NOCODE;SNOMEDC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>C0539817</td>\n",
       "      <td>cytochrome p30</td>\n",
       "      <td>T116|T126</td>\n",
       "      <td>Amino Acid, Peptide, or Protein|Enzyme</td>\n",
       "      <td>protein</td>\n",
       "      <td>MESH:C106367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C0406240</td>\n",
       "      <td>Photosensitive atopic dermatitis</td>\n",
       "      <td>T047</td>\n",
       "      <td>Disease or Syndrome</td>\n",
       "      <td>disease_or_phenotypic_feature</td>\n",
       "      <td>RCD:X505U;SNOMEDCT_US:238548006;SNOMEDCT_US:23...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         ID                                            LABEL  umls_type  \\\n",
       "0  C0061133                gastrin releasing peptide (14-27)       T116   \n",
       "1  C1523610  regulation of tube length, open tracheal system       T042   \n",
       "2  C0312636                    Antibody to hepatitis E virus  T116|T129   \n",
       "3  C0539817                                   cytochrome p30  T116|T126   \n",
       "4  C0406240                 Photosensitive atopic dermatitis       T047   \n",
       "\n",
       "                                     umls_type_label  \\\n",
       "0                    Amino Acid, Peptide, or Protein   \n",
       "1                           Organ or Tissue Function   \n",
       "2  Amino Acid, Peptide, or Protein|Immunologic Fa...   \n",
       "3             Amino Acid, Peptide, or Protein|Enzyme   \n",
       "4                                Disease or Syndrome   \n",
       "\n",
       "                         blm_type  \\\n",
       "0                         protein   \n",
       "1  biological_process_or_activity   \n",
       "2               biological_entity   \n",
       "3                         protein   \n",
       "4   disease_or_phenotypic_feature   \n",
       "\n",
       "                                               xrefs  \n",
       "0                                       MESH:C041922  \n",
       "1                                      GO:GO:0035159  \n",
       "2  LNC:MTHU004056;SNMI:F-C2A90;MTH:NOCODE;SNOMEDC...  \n",
       "3                                       MESH:C106367  \n",
       "4  RCD:X505U;SNOMEDCT_US:238548006;SNOMEDCT_US:23...  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# https://biolink.github.io/biolink-model/docs/NamedThing.html\n",
    "nodes = pd.read_csv(\"nodes_xref.csv\")\n",
    "nodes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "chemical_substance                58812\n",
       "disease_or_phenotypic_feature     36248\n",
       "gene                              20695\n",
       "biological_entity                 14905\n",
       "protein                           12644\n",
       "gross_anatomical_structure         8472\n",
       "biological_process_or_activity     6887\n",
       "anatomical_entity                  2750\n",
       "cell_component                     1644\n",
       "cell                               1099\n",
       "activity_and_behavior               935\n",
       "phenotypic_feature                  393\n",
       "genomic_entity                      174\n",
       "Name: blm_type, dtype: int64"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nodes.blm_type.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "nodes.ID = \"UMLS:\" + nodes.ID\n",
    "nodes['category:STRING'] = nodes.blm_type\n",
    "nodes['id:STRING'] = nodes.ID\n",
    "nodes.umls_type_label = nodes.umls_type_label.str.replace(\"|\", \";\")\n",
    "nodes.umls_type = nodes.umls_type.str.replace(\"|\", \";\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "nodes.rename(columns = {'ID': ':ID', \n",
    "                        'LABEL': 'name:STRING', \n",
    "                        'blm_type': ':LABEL',\n",
    "                        'umls_type_label': 'umls_type_label:STRING[]',\n",
    "                        'umls_type': 'umls_type:STRING[]',\n",
    "                        'xrefs': 'xrefs:STRING[]'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "    }\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>:ID</th>\n",
       "      <th>name:STRING</th>\n",
       "      <th>umls_type:STRING[]</th>\n",
       "      <th>umls_type_label:STRING[]</th>\n",
       "      <th>:LABEL</th>\n",
       "      <th>xrefs:STRING[]</th>\n",
       "      <th>category:STRING</th>\n",
       "      <th>id:STRING</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UMLS:C0061133</td>\n",
       "      <td>gastrin releasing peptide (14-27)</td>\n",
       "      <td>T116</td>\n",
       "      <td>Amino Acid, Peptide, or Protein</td>\n",
       "      <td>protein</td>\n",
       "      <td>MESH:C041922</td>\n",
       "      <td>protein</td>\n",
       "      <td>UMLS:C0061133</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UMLS:C1523610</td>\n",
       "      <td>regulation of tube length, open tracheal system</td>\n",
       "      <td>T042</td>\n",
       "      <td>Organ or Tissue Function</td>\n",
       "      <td>biological_process_or_activity</td>\n",
       "      <td>GO:GO:0035159</td>\n",
       "      <td>biological_process_or_activity</td>\n",
       "      <td>UMLS:C1523610</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UMLS:C0312636</td>\n",
       "      <td>Antibody to hepatitis E virus</td>\n",
       "      <td>T116;T129</td>\n",
       "      <td>Amino Acid, Peptide, or Protein;Immunologic Fa...</td>\n",
       "      <td>biological_entity</td>\n",
       "      <td>LNC:MTHU004056;SNMI:F-C2A90;MTH:NOCODE;SNOMEDC...</td>\n",
       "      <td>biological_entity</td>\n",
       "      <td>UMLS:C0312636</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UMLS:C0539817</td>\n",
       "      <td>cytochrome p30</td>\n",
       "      <td>T116;T126</td>\n",
       "      <td>Amino Acid, Peptide, or Protein;Enzyme</td>\n",
       "      <td>protein</td>\n",
       "      <td>MESH:C106367</td>\n",
       "      <td>protein</td>\n",
       "      <td>UMLS:C0539817</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UMLS:C0406240</td>\n",
       "      <td>Photosensitive atopic dermatitis</td>\n",
       "      <td>T047</td>\n",
       "      <td>Disease or Syndrome</td>\n",
       "      <td>disease_or_phenotypic_feature</td>\n",
       "      <td>RCD:X505U;SNOMEDCT_US:238548006;SNOMEDCT_US:23...</td>\n",
       "      <td>disease_or_phenotypic_feature</td>\n",
       "      <td>UMLS:C0406240</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             :ID                                      name:STRING  \\\n",
       "0  UMLS:C0061133                gastrin releasing peptide (14-27)   \n",
       "1  UMLS:C1523610  regulation of tube length, open tracheal system   \n",
       "2  UMLS:C0312636                    Antibody to hepatitis E virus   \n",
       "3  UMLS:C0539817                                   cytochrome p30   \n",
       "4  UMLS:C0406240                 Photosensitive atopic dermatitis   \n",
       "\n",
       "  umls_type:STRING[]                           umls_type_label:STRING[]  \\\n",
       "0               T116                    Amino Acid, Peptide, or Protein   \n",
       "1               T042                           Organ or Tissue Function   \n",
       "2          T116;T129  Amino Acid, Peptide, or Protein;Immunologic Fa...   \n",
       "3          T116;T126             Amino Acid, Peptide, or Protein;Enzyme   \n",
       "4               T047                                Disease or Syndrome   \n",
       "\n",
       "                           :LABEL  \\\n",
       "0                         protein   \n",
       "1  biological_process_or_activity   \n",
       "2               biological_entity   \n",
       "3                         protein   \n",
       "4   disease_or_phenotypic_feature   \n",
       "\n",
       "                                      xrefs:STRING[]  \\\n",
       "0                                       MESH:C041922   \n",
       "1                                      GO:GO:0035159   \n",
       "2  LNC:MTHU004056;SNMI:F-C2A90;MTH:NOCODE;SNOMEDC...   \n",
       "3                                       MESH:C106367   \n",
       "4  RCD:X505U;SNOMEDCT_US:238548006;SNOMEDCT_US:23...   \n",
       "\n",
       "                  category:STRING      id:STRING  \n",
       "0                         protein  UMLS:C0061133  \n",
       "1  biological_process_or_activity  UMLS:C1523610  \n",
       "2               biological_entity  UMLS:C0312636  \n",
       "3                         protein  UMLS:C0539817  \n",
       "4   disease_or_phenotypic_feature  UMLS:C0406240  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nodes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "nodes.to_csv(\"nodes_neo4j.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "###### EDGES"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# https://biolink.github.io/biolink-model/docs/Association.html\n",
    "edges = pd.read_csv('edges_biolink.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges['START_ID'] = \"UMLS:\" + edges.SUBJECT_CUI\n",
    "edges['END_ID'] = \"UMLS:\" + edges.OBJECT_CUI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges['n_pmids'] = edges.PMID.str.count(\";\")+1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SUBJECT_CUI</th>\n",
       "      <th>SEMMED_PRED</th>\n",
       "      <th>OBJECT_CUI</th>\n",
       "      <th>PMID</th>\n",
       "      <th>NEG</th>\n",
       "      <th>bl_pred</th>\n",
       "      <th>START_ID</th>\n",
       "      <th>END_ID</th>\n",
       "      <th>n_pmids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C1412045</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>C0023946</td>\n",
       "      <td>20801151</td>\n",
       "      <td>False</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0023946</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C1412045</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>C0028754</td>\n",
       "      <td>19789049</td>\n",
       "      <td>False</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0028754</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>C1412045</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>C0597304</td>\n",
       "      <td>1409557</td>\n",
       "      <td>False</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0597304</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>C1412045</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>C0599816</td>\n",
       "      <td>7617239</td>\n",
       "      <td>False</td>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0599816</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C1412045</td>\n",
       "      <td>ASSOCIATED_WITH</td>\n",
       "      <td>C0001807</td>\n",
       "      <td>8503828;8240219</td>\n",
       "      <td>False</td>\n",
       "      <td>RELATED_TO</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0001807</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  SUBJECT_CUI      SEMMED_PRED OBJECT_CUI             PMID    NEG     bl_pred  \\\n",
       "0    C1412045          AFFECTS   C0023946         20801151  False     AFFECTS   \n",
       "1    C1412045          AFFECTS   C0028754         19789049  False     AFFECTS   \n",
       "2    C1412045          AFFECTS   C0597304          1409557  False     AFFECTS   \n",
       "3    C1412045          AFFECTS   C0599816          7617239  False     AFFECTS   \n",
       "4    C1412045  ASSOCIATED_WITH   C0001807  8503828;8240219  False  RELATED_TO   \n",
       "\n",
       "        START_ID         END_ID  n_pmids  \n",
       "0  UMLS:C1412045  UMLS:C0023946        1  \n",
       "1  UMLS:C1412045  UMLS:C0028754        1  \n",
       "2  UMLS:C1412045  UMLS:C0597304        1  \n",
       "3  UMLS:C1412045  UMLS:C0599816        1  \n",
       "4  UMLS:C1412045  UMLS:C0001807        2  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "edges.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges.bl_pred = edges.bl_pred.str.lower()\n",
    "edges.rename(columns = {'START_ID': ':START_ID', 'END_ID': ':END_ID', \n",
    "                        'bl_pred': ':TYPE', 'NEG': 'negated',\n",
    "                       'PMID': 'pmids'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges['is_defined_by'] = \"semmeddb\"\n",
    "edges['relation'] = \"semmeddb:\" + edges[\":TYPE\"].str.lower()\n",
    "edges['provided_by'] = \"semmeddb_sulab\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "del edges['SUBJECT_CUI']\n",
    "del edges['OBJECT_CUI']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SEMMED_PRED</th>\n",
       "      <th>pmids</th>\n",
       "      <th>negated</th>\n",
       "      <th>:TYPE</th>\n",
       "      <th>:START_ID</th>\n",
       "      <th>:END_ID</th>\n",
       "      <th>n_pmids</th>\n",
       "      <th>is_defined_by</th>\n",
       "      <th>relation</th>\n",
       "      <th>provided_by</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>20801151</td>\n",
       "      <td>False</td>\n",
       "      <td>affects</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0023946</td>\n",
       "      <td>1</td>\n",
       "      <td>semmeddb</td>\n",
       "      <td>semmeddb:affects</td>\n",
       "      <td>semmeddb_sulab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>19789049</td>\n",
       "      <td>False</td>\n",
       "      <td>affects</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0028754</td>\n",
       "      <td>1</td>\n",
       "      <td>semmeddb</td>\n",
       "      <td>semmeddb:affects</td>\n",
       "      <td>semmeddb_sulab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>1409557</td>\n",
       "      <td>False</td>\n",
       "      <td>affects</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0597304</td>\n",
       "      <td>1</td>\n",
       "      <td>semmeddb</td>\n",
       "      <td>semmeddb:affects</td>\n",
       "      <td>semmeddb_sulab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AFFECTS</td>\n",
       "      <td>7617239</td>\n",
       "      <td>False</td>\n",
       "      <td>affects</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0599816</td>\n",
       "      <td>1</td>\n",
       "      <td>semmeddb</td>\n",
       "      <td>semmeddb:affects</td>\n",
       "      <td>semmeddb_sulab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ASSOCIATED_WITH</td>\n",
       "      <td>8503828;8240219</td>\n",
       "      <td>False</td>\n",
       "      <td>related_to</td>\n",
       "      <td>UMLS:C1412045</td>\n",
       "      <td>UMLS:C0001807</td>\n",
       "      <td>2</td>\n",
       "      <td>semmeddb</td>\n",
       "      <td>semmeddb:related_to</td>\n",
       "      <td>semmeddb_sulab</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       SEMMED_PRED            pmids  negated       :TYPE      :START_ID  \\\n",
       "0          AFFECTS         20801151    False     affects  UMLS:C1412045   \n",
       "1          AFFECTS         19789049    False     affects  UMLS:C1412045   \n",
       "2          AFFECTS          1409557    False     affects  UMLS:C1412045   \n",
       "3          AFFECTS          7617239    False     affects  UMLS:C1412045   \n",
       "4  ASSOCIATED_WITH  8503828;8240219    False  related_to  UMLS:C1412045   \n",
       "\n",
       "         :END_ID  n_pmids is_defined_by             relation     provided_by  \n",
       "0  UMLS:C0023946        1      semmeddb     semmeddb:affects  semmeddb_sulab  \n",
       "1  UMLS:C0028754        1      semmeddb     semmeddb:affects  semmeddb_sulab  \n",
       "2  UMLS:C0597304        1      semmeddb     semmeddb:affects  semmeddb_sulab  \n",
       "3  UMLS:C0599816        1      semmeddb     semmeddb:affects  semmeddb_sulab  \n",
       "4  UMLS:C0001807        2      semmeddb  semmeddb:related_to  semmeddb_sulab  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "edges.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges.to_csv(\"edges_neo4j.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "# notes to copy and set up neo4j\n",
    "\n",
    "scp -i ~/.ssh/Neo4j-AWSMarketplace-Key.pem nodes_neo4j.csv edges_neo4j.csv ubuntu@34.229.55.225:\n",
    "\n",
    "ssh -i ~/.ssh/Neo4j-AWSMarketplace-Key.pem ubuntu@34.229.55.225\n",
    "# on aws\n",
    "sudo su\n",
    "neo4j stop\n",
    "rm -rf /var/lib/neo4j/data/databases/graph.db\n",
    "cd /var/lib/neo4j/import/\n",
    "neo4j-admin import --nodes nodes_neo4j.csv --relationships edges_neo4j.csv\n",
    "neo4j start\n"
   ]
  }
 ],
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