notebooks/tutorial/s4b_pathway_superpathways.ipynb

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   "source": [
    "# Tutorial 4b) Retrieving pathways and superpathways\n",
    "What superpathways are above the pathway, R-HSA-983169, _Class I MHC mediated antigen processing & presentation_?\n",
    "\n",
    "[**Reactome Tutorial**: Retrieving pathways, subpathways and superpathways](https://reactome.org/dev/graph-database/extract-participating-molecules#retrieving-pathways)\n",
    "\n",
    "## Step 1) [Connect to Neo4j loaded with the Reactome Knowledgebase](https://github.com/dvklopfenstein/reactome_neo4j_py/blob/master/doc/md/README_gdbdr.md)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "from neo4j import GraphDatabase\n",
    "\n",
    "neo4j_url = 'bolt://localhost:7687'\n",
    "neo4j_usr = 'neo4j'\n",
    "neo4j_password = 'myneo4j_password'\n",
    "\n",
    "gdbdr = GraphDatabase.driver(neo4j_url, auth=(neo4j_usr, neo4j_password))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " ## Step 2a) Query Immediate Superpathways\n",
    " ### What superpathways are directly over pathway, R-HSA-983169, _Class I MHC mediated antigen processing & presentation_?"
   ]
  },
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   "cell_type": "code",
   "execution_count": 8,
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   "outputs": [],
   "source": [
    "query = ('MATCH (p:Pathway{stId:\"R-HSA-983169\"})<-[:hasEvent]-(sp:Pathway) '\n",
    "         'RETURN '\n",
    "         'p.stId AS Pathway, '\n",
    "         'sp.stId AS SuperPathway_ID, '\n",
    "         'sp.displayName as SuperPathway_Name')\n",
    "\n",
    "# Query and get the sub-pathways under R-HSA-983169\n",
    "def _get_data():\n",
    "    with gdbdr.session() as session:\n",
    "        return session.run(query).data()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 2b) Print Immediate Superpathways\n",
    "### Print sub-pathways under R-HSA-983169"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    Pathway      | SuperPathway ID | SuperPathway Name\n",
      "-----------------|-----------------|----------------\n",
      "    R-HSA-983169 | R-HSA-1280218   | Adaptive Immune System\n"
     ]
    }
   ],
   "source": [
    "print('    Pathway      | SuperPathway ID | SuperPathway Name')\n",
    "print('-----------------|-----------------|----------------')\n",
    "for data in _get_data():\n",
    "    print(\"    {Pathway} | {SuperPathway_ID:15} | {SuperPathway_Name}\".format(**data))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " ## Step 3a) Query All Superpathways\n",
    " ### Retrieve all superpathways directly over pathway, R-HSA-983169, _Class I MHC mediated antigen processing & presentation_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "query = ('MATCH (p:Pathway{stId:\"R-HSA-983169\"})<-[:hasEvent*]-(sp:Pathway) '\n",
    "         'RETURN '\n",
    "         'p.stId AS Pathway, '\n",
    "         'sp.stId AS SuperPathway_ID, '\n",
    "         'sp.displayName as SuperPathway_Name')\n",
    "\n",
    "# Query and get the sub-pathways under R-HSA-983169\n",
    "def _get_data():\n",
    "    with gdbdr.session() as session:\n",
    "        return session.run(query).data()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3b) Print All Superpathways"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    Pathway      | SuperPathway ID | SuperPathway Name\n",
      "-----------------|-----------------|----------------\n",
      "    R-HSA-983169 | R-HSA-1280218   | Adaptive Immune System\n",
      "    R-HSA-983169 | R-HSA-168256    | Immune System\n"
     ]
    }
   ],
   "source": [
    "# Print sub-pathways under R-HSA-983169\n",
    "print('    Pathway      | SuperPathway ID | SuperPathway Name')\n",
    "print('-----------------|-----------------|----------------')\n",
    "for data in sorted(_get_data(), key=lambda d:d['SuperPathway_ID']):\n",
    "    print(\"    {Pathway} | {SuperPathway_ID:15} | {SuperPathway_Name}\".format(**data))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Copyright (C) 2018-present, DV Klopfenstein. All rights reserved."
   ]
  }
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