ExampleMECP2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Target Connections MECP2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pip._internal import main as pip\n",
    "try:\n",
    "    import csv\n",
    "except ImportError:\n",
    "    pip(['install', 'csv'])\n",
    "    import csv\n",
    "try:\n",
    "    from SPARQLWrapper import SPARQLWrapper, JSON\n",
    "except  ImportError:\n",
    "    pip(['install', 'sparqlwrapper'])\n",
    "    from SPARQLWrapper import SPARQLWrapper, JSON\n",
    "    \n",
    "import pandas\n",
    "\n",
    "sparql = SPARQLWrapper(\"http://sparql.wikipathways.org/sparql\")\n",
    "mecp2Conn = pandas.DataFrame(columns=['Source', 'Source Label', 'Target', 'Target Label', 'Pathway', 'Interaction'])\n",
    "\n",
    "pathwayQuery = '''\n",
    "SELECT DISTINCT (substr(str(?source),24 ) as ?source) (substr(str(?label),36 ) as ?sourceLabel ) \n",
    "(substr(str(?target),24 ) as ?target) ?label1 (substr(str(?pathway),37 ) as ?pathway) \n",
    "(substr(str(?interaction),54 ) as ?interaction)\n",
    "WHERE {\n",
    "    ?participant wp:bdbHgncSymbol    <http://identifiers.org/hgnc.symbol/MECP2> ;\n",
    "       dcterms:isPartOf ?pathway .\n",
    "    ?pathway a wp:Pathway .\n",
    "\n",
    "    ?interaction dcterms:isPartOf ?pathway ;\n",
    "       a wp:DirectedInteraction ;\n",
    "       wp:participants ?participant ;\n",
    "       wp:target ?target ;\n",
    "       wp:source ?source .\n",
    "\n",
    "    ?target rdfs:label ?label1 .\n",
    "    ?source dcterms:isPartOf ?pathway .\n",
    "    ?source a wp:GeneProduct .\n",
    "    ?source wp:bdbHgncSymbol ?label .  \n",
    " }\n",
    "    '''\n",
    "sparql.setQuery(pathwayQuery)\n",
    "sparql.setReturnFormat(JSON)\n",
    "results = sparql.query().convert()\n",
    "\n",
    "for result in results[\"results\"][\"bindings\"]:\n",
    "\tmecp2Conn = mecp2Conn.append({\n",
    "\t\t'Target': result[\"target\"][\"value\"],\n",
    "        'Target Label': result[\"label1\"][\"value\"],\n",
    "\t\t'Source': result[\"source\"][\"value\"],\n",
    "        'Source Label': result[\"sourceLabel\"][\"value\"],\n",
    "\t\t'Pathway': result[\"pathway\"][\"value\"],\n",
    "        'Interaction': result[\"interaction\"][\"value\"],        \n",
    "\t }, ignore_index=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<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</th>\n",
       "      <th>Source Label</th>\n",
       "      <th>Target</th>\n",
       "      <th>Target Label</th>\n",
       "      <th>Pathway</th>\n",
       "      <th>Interaction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>chebi/CHEBI:29987</td>\n",
       "      <td>glutamate</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id4f207df3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>chebi/CHEBI:29987</td>\n",
       "      <td>Glutamate</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id4f207df3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>ensembl/ENSG00000118260</td>\n",
       "      <td>CREB1</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/ida4a8b443</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>ensembl/ENSG00000118260</td>\n",
       "      <td>CREB</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/ida4a8b443</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>ensembl/ENSG00000176697</td>\n",
       "      <td>BDNF</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id4a259c62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>ensembl/ENSG00000155511</td>\n",
       "      <td>GRIA1</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id3bcd32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>ensembl/ENSG00000155511</td>\n",
       "      <td>AMPA</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id3bcd32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ensembl/ENSG00000169813</td>\n",
       "      <td>HNRNPF</td>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id1c3def3d</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ensembl/ENSG00000196132</td>\n",
       "      <td>MYT1</td>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/id8e7af5c</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ensembl/ENSG00000169045</td>\n",
       "      <td>HNRNPH1</td>\n",
       "      <td>ensembl/ENSG00000169057</td>\n",
       "      <td>MECP2</td>\n",
       "      <td>WP3584_r96364</td>\n",
       "      <td>Interaction/ida6a9fa9d</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Source Source Label                   Target Target Label  \\\n",
       "0  ensembl/ENSG00000169057        MECP2        chebi/CHEBI:29987    glutamate   \n",
       "1  ensembl/ENSG00000169057        MECP2        chebi/CHEBI:29987    Glutamate   \n",
       "2  ensembl/ENSG00000169057        MECP2  ensembl/ENSG00000118260        CREB1   \n",
       "3  ensembl/ENSG00000169057        MECP2  ensembl/ENSG00000118260         CREB   \n",
       "4  ensembl/ENSG00000169057        MECP2  ensembl/ENSG00000176697         BDNF   \n",
       "5  ensembl/ENSG00000169057        MECP2  ensembl/ENSG00000155511        GRIA1   \n",
       "6  ensembl/ENSG00000169057        MECP2  ensembl/ENSG00000155511         AMPA   \n",
       "7  ensembl/ENSG00000169813       HNRNPF  ensembl/ENSG00000169057        MECP2   \n",
       "8  ensembl/ENSG00000196132         MYT1  ensembl/ENSG00000169057        MECP2   \n",
       "9  ensembl/ENSG00000169045      HNRNPH1  ensembl/ENSG00000169057        MECP2   \n",
       "\n",
       "         Pathway             Interaction  \n",
       "0  WP3584_r96364  Interaction/id4f207df3  \n",
       "1  WP3584_r96364  Interaction/id4f207df3  \n",
       "2  WP3584_r96364  Interaction/ida4a8b443  \n",
       "3  WP3584_r96364  Interaction/ida4a8b443  \n",
       "4  WP3584_r96364  Interaction/id4a259c62  \n",
       "5  WP3584_r96364    Interaction/id3bcd32  \n",
       "6  WP3584_r96364    Interaction/id3bcd32  \n",
       "7  WP3584_r96364  Interaction/id1c3def3d  \n",
       "8  WP3584_r96364   Interaction/id8e7af5c  \n",
       "9  WP3584_r96364  Interaction/ida6a9fa9d  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mecp2Conn"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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