notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb

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    "# Tutorial 2a) Retrieve identifier and identifier database name for a protein.\n",
    "Get the ID and name of the PTEN protein in the cytosol with identifier R-HSA-199420\n",
    "\n",
    "[**Reactome Tutorial**: Retrieving identifiers for proteins or chemicals](https://reactome.org/dev/graph-database/extract-participating-molecules#identifiers-proteins-or-chemicals)\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)"
   ]
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  {
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   "execution_count": 2,
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   "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 2) Query\n",
    " ###  Get the ID, ID database, and name of the PTEN protein in the cytosol with identifier R-HSA-199420\n",
    " An _EntityWithAccessionedSequence_ corresponds to a protein in Reactome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    P60484 UniProt PTEN [cytosol]\n"
     ]
    }
   ],
   "source": [
    "query = ('MATCH (ewas:EntityWithAccessionedSequence{stId:\"R-HSA-199420\"}),'\n",
    "         '(ewas)-[:referenceEntity]->(re:ReferenceEntity)-[:referenceDatabase]->(rd:ReferenceDatabase)'\n",
    "         'RETURN '\n",
    "         'ewas.displayName AS Name, '\n",
    "         're.identifier AS ID, '\n",
    "         'rd.displayName AS Database')\n",
    "\n",
    "with gdbdr.session() as session:\n",
    "    for rec in session.run(query).data():\n",
    "        print(\"    {ID} {Database} {Name}\".format(**rec))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Copyright (C) 2018-present, DV Klopfenstein. All rights reserved."
   ]
  }
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