PPAR_LiverInjury_id_test.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "077092a9",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Parameter inputs\n",
    "aragorn_submit_url = \"https://aragorn-u24.apps.renci.org/robokop/query\"\n",
    "input_search_string = 'ppara'\n",
    "output_search_string = 'liver fibrosis'\n",
    "\n",
    "# Initializing directory to write\n",
    "from datetime import datetime\n",
    "from pathlib import Path\n",
    "\n",
    "now = datetime.now()\n",
    "dt_string = now.strftime(\"%Y-%m-%d_%H%M%S\")\n",
    "write_dir = Path(\"output/TRAPI\",str(dt_string))\n",
    "write_dir.mkdir(parents=True, exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "cf672bb7",
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "import json\n",
    "import pprint\n",
    "pp = pprint.PrettyPrinter(indent=5)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8b32ecc6",
   "metadata": {},
   "source": [
    "This notebook provides a deeper dive into the TRAPI options for querying the ROBOKOP KG using the ARA functionality. It assumes you are familiar with the concepts covered in `HelloRobokop.ipynb`.  This follows the same format and process as in `HelloRobokop_TRAPI.ipynb` except using the API based upon Automomous Relay Agent (ARA) methodology developed as part of the NIH Biomedical Data Translator to query the ROBOKOP knowledgegraph, which returns a score for each result.\n",
    "\n",
    "TRAPI Documentation: https://github.com/NCATSTranslator/ReasonerAPI\n",
    "\n",
    "Most TRAPI documents contain a `message` key.  Within that `message` are a `query_graph` denoting the user query,\n",
    "a `knowledge_graph` consisting of the union of all nodes and edges that match the `query_graph` pattern, and a list of `results` that bind `query_graph` elements to `knowledge_graph` elements.\n",
    "\n",
    "The following message contains only a `query_graph`.  This query graph consists of 3 nodes connected together in a line.   Two of the nodes (`n00` and `n02`) have specified identifiers, while the middle node of the line does not.  Rather the middle node has a list of `categories` that are acceptable.\n",
    "\n",
    "For a researcher who is starting from a `name` who wants to use TRAPI, they can use the Name Resolver tool to get the identifers for the nodes.  This is illustrated in the `HelloRobokop_TRAPI_multiple_IDs.ipynb` notebook. \n",
    "\n",
    "This query asks \"Find me a Biological Process or Activity, or a Gene, or a Pathway that is related to both `PUBCHEM.COMPOUND:644073` (Buprenorphine) and `HP:0001337` (Tremor)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "72295614",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['UniProtKB:P37230', 'UniProtKB:Q07869', 'UniProtKB:Q95N78', 'PR:000013056', 'UniProtKB:P23204', 'NCBIGene:19013', 'NCBIGene:25747', 'NCBIGene:5465', 'NCBIGene:557714', 'NCBIGene:30755']\n"
     ]
    }
   ],
   "source": [
    "results = requests.post(f'https://name-resolution-sri.renci.org/lookup?string={input_search_string}&offset=0&limit=10')\n",
    "results_json = results.json()\n",
    "#print(json.dumps(results_json,indent=4))\n",
    "input_node_id_list = list(results_json.keys())\n",
    "print(input_node_id_list)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "602e6891",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['HP:0001395', 'UMLS:C4227681', 'UMLS:C4034373', 'UMLS:C5189427', 'UMLS:C0544816', 'MONDO:0100430', 'MONDO:0018840', 'UMLS:C1397317', 'UMLS:C4068302', 'UMLS:C4481250']\n"
     ]
    }
   ],
   "source": [
    "results = requests.post(f'https://name-resolution-sri.renci.org/lookup?string={output_search_string}&offset=0&limit=10')\n",
    "results_json = results.json()\n",
    "#print(json.dumps(results_json,indent=4))\n",
    "output_node_id_list = list(results_json.keys())\n",
    "print(output_node_id_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4d896f3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "query={\n",
    "    \"message\": {\n",
    "      \"query_graph\": {\n",
    "        \"edges\": {\n",
    "          \"e00\": {\n",
    "            \"subject\": \"n00\",\n",
    "              \"object\": \"n01\",\n",
    "          \"predicates\":[\"biolink:related_to\"]\n",
    "          },\n",
    "          \"e01\": {\n",
    "            \"subject\": \"n01\",\n",
    "              \"object\": \"n02\",\n",
    "          \"predicates\":[\"biolink:related_to\"]\n",
    "          }\n",
    "        },\n",
    "        \"nodes\": {\n",
    "          \"n00\": {\n",
    "            \"ids\": ['NCBIGene:5465'], #\n",
    "            \"categories\": [\"biolink:GeneOrGeneProduct\"]\n",
    "          },\n",
    "          \"n01\": {\n",
    "              \"categories\": [\"biolink:BiologicalEntity\"]\n",
    "          },\n",
    "          \"n02\": {\n",
    "            \"ids\": [\"HP:0001395\"],\n",
    "            \"categories\": [\"biolink:DiseaseOrPhenotypicFeature\"]\n",
    "          }\n",
    "        }\n",
    "      }\n",
    "    }\n",
    "  }\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e8e479b2",
   "metadata": {},
   "source": [
    "This query can be sent directly to the ROBOKOP KG hosted in the Automat system like this:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "bb8540f3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "57\n"
     ]
    }
   ],
   "source": [
    "response = requests.post(aragorn_submit_url,json=query)\n",
    "print(response.status_code)\n",
    "number_pathway_results = len(response.json()['message']['results'])\n",
    "print(len(response.json()['message']['results']))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8ed6ff38",
   "metadata": {},
   "source": [
    "The response in JSON form is a python dictionary with three main keys, the `message`, `log_level`, and `workflow`.  The `message` property contains the `query_graph`, `knowledge_graph`, and `results` from the query."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "1f30838e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['message', 'logs', 'status', 'pid'])\n",
      "dict_keys(['query_graph', 'knowledge_graph', 'results'])\n"
     ]
    }
   ],
   "source": [
    "print(response.json().keys())\n",
    "print(response.json()['message'].keys())\n",
    "\n",
    "query_out = response.json()['message']['query_graph']\n",
    "kg = response.json()['message']['knowledge_graph']\n",
    "results = response.json()['message']['results']"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "07adaad3",
   "metadata": {},
   "source": [
    "The original, submitted query graph with additional fields is returned with the `message` property in the `query_graph` property.\n",
    "\n",
    "The code below shows the changes between the submitted query graph and the results query graph. The results includes additional attributes such as `knowledge_type`, `attribute_constraints`, and `qualifier_constraints`.  These attributes can be explicitly defined when submitting to automat such that further filtering can be done.  Because nothing was specified for these attributes in the submitted query graph, their values in the returned query graph are blank."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "a952df0b",
   "metadata": {},
   "outputs": [],
   "source": [
    "edges = [\"e00\", \"e01\"]\n",
    "nodes = [\"n00\", \"n01\", \"n02\"]\n",
    "\n",
    "#print(nodes)\n",
    "#print(edges)\n",
    "#pp.pprint(query)\n",
    "#pp.pprint(query_out)\n",
    "#pp.pprint(results)\n",
    "#pp.pprint(kg.keys())\n",
    "#next(iter( kg['nodes'].items() ))\n",
    "#next(iter( kg['edges'].items() ))\n",
    "#pp.pprint(results[0])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "12b30325",
   "metadata": {},
   "source": [
    "The `results` property contains pathways resulting from the query message. Each pathway is organized into edge_bindings and node bindings and contains results for the edges and nodes specified in the query message.  Results are defined using the node and edge identifiers. The attributes for those nodes and edges (including the names) are available via the `knowledge_graph` component of the `message` section of the response."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4c3a6bd3",
   "metadata": {},
   "source": [
    "The code below writes out nodes from our `results`, but NOT the edges connecting the nodes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "bf0f2139",
   "metadata": {},
   "outputs": [
    {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n00</th>\n",
       "      <th>n00_name</th>\n",
       "      <th>n01</th>\n",
       "      <th>n01_name</th>\n",
       "      <th>n02</th>\n",
       "      <th>n02_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:4088</td>\n",
       "      <td>SMAD3</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7040</td>\n",
       "      <td>TGFB1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:6347</td>\n",
       "      <td>CCL2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:213</td>\n",
       "      <td>ALB</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:3082</td>\n",
       "      <td>HGF</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0005154</td>\n",
       "      <td>liver disorder</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:4313</td>\n",
       "      <td>MMP2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:3569</td>\n",
       "      <td>IL6</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0005154</td>\n",
       "      <td>liver disorder</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1490</td>\n",
       "      <td>CCN2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:2147</td>\n",
       "      <td>F2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0005154</td>\n",
       "      <td>liver disorder</td>\n",
       "      <td>HP:0001405</td>\n",
       "      <td>Periportal fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:6772</td>\n",
       "      <td>STAT1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:4780</td>\n",
       "      <td>NFE2L2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0005155</td>\n",
       "      <td>cirrhosis of liver</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1356</td>\n",
       "      <td>CP</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:5972</td>\n",
       "      <td>REN</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1277</td>\n",
       "      <td>COL1A1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:6696</td>\n",
       "      <td>SPP1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7422</td>\n",
       "      <td>VEGFA</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:183</td>\n",
       "      <td>AGT</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:183</td>\n",
       "      <td>AGT</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7040</td>\n",
       "      <td>TGFB1</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7046</td>\n",
       "      <td>TGFBR1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1499</td>\n",
       "      <td>CTNNB1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7057</td>\n",
       "      <td>THBS1</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:5972</td>\n",
       "      <td>REN</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:5314</td>\n",
       "      <td>PKHD1</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7057</td>\n",
       "      <td>THBS1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:5244</td>\n",
       "      <td>ABCB4</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:6347</td>\n",
       "      <td>CCL2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:2147</td>\n",
       "      <td>F2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1278</td>\n",
       "      <td>COL1A2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:5328</td>\n",
       "      <td>PLAU</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:2149</td>\n",
       "      <td>F2R</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:408</td>\n",
       "      <td>ARRB1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:2321</td>\n",
       "      <td>FLT1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:2247</td>\n",
       "      <td>FGF2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:405</td>\n",
       "      <td>ARNT</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:3956</td>\n",
       "      <td>LGALS1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:1356</td>\n",
       "      <td>CP</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:4864</td>\n",
       "      <td>NPC1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:1269</td>\n",
       "      <td>CNR2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:9104</td>\n",
       "      <td>RGN</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:6927</td>\n",
       "      <td>HNF1A</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:4763</td>\n",
       "      <td>NF1</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:183</td>\n",
       "      <td>AGT</td>\n",
       "      <td>MONDO:0018840</td>\n",
       "      <td>isolated congenital hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>NCBIGene:7431</td>\n",
       "      <td>VIM</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:4015</td>\n",
       "      <td>LOX</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NCBIGene:5465</td>\n",
       "      <td>PPARA</td>\n",
       "      <td>MONDO:0005154</td>\n",
       "      <td>liver disorder</td>\n",
       "      <td>HP:0012852</td>\n",
       "      <td>Hepatic bridging fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:183</td>\n",
       "      <td>AGT</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:1593</td>\n",
       "      <td>CYP27A1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:120227</td>\n",
       "      <td>CYP2R1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:3875</td>\n",
       "      <td>KRT18</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:3484</td>\n",
       "      <td>IGFBP1</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:1269</td>\n",
       "      <td>CNR2</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:Q07869-1</td>\n",
       "      <td>peroxisome proliferator-activated receptor alp...</td>\n",
       "      <td>NCBIGene:866</td>\n",
       "      <td>SERPINA6</td>\n",
       "      <td>HP:0001395</td>\n",
       "      <td>Hepatic fibrosis</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  n00                                           n00_name  \\\n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0       NCBIGene:5465                                              PPARA   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "0  UniProtKB:Q07869-1  peroxisome proliferator-activated receptor alp...   \n",
       "\n",
       "               n01            n01_name            n02  \\\n",
       "0    NCBIGene:4088               SMAD3     HP:0001395   \n",
       "0    NCBIGene:7040               TGFB1     HP:0001395   \n",
       "0    NCBIGene:6347                CCL2     HP:0001395   \n",
       "0     NCBIGene:213                 ALB     HP:0001395   \n",
       "0    NCBIGene:3082                 HGF     HP:0001395   \n",
       "0    MONDO:0005154      liver disorder     HP:0001395   \n",
       "0    NCBIGene:4313                MMP2     HP:0001395   \n",
       "0    NCBIGene:3569                 IL6     HP:0001395   \n",
       "0    MONDO:0005154      liver disorder  MONDO:0018840   \n",
       "0    NCBIGene:1490                CCN2     HP:0001395   \n",
       "0    NCBIGene:2147                  F2     HP:0001395   \n",
       "0    MONDO:0005154      liver disorder     HP:0001405   \n",
       "0    NCBIGene:6772               STAT1     HP:0001395   \n",
       "0    NCBIGene:4780              NFE2L2     HP:0001395   \n",
       "0    MONDO:0005155  cirrhosis of liver  MONDO:0018840   \n",
       "0    NCBIGene:1356                  CP     HP:0001395   \n",
       "0    NCBIGene:5972                 REN     HP:0001395   \n",
       "0    NCBIGene:1277              COL1A1     HP:0001395   \n",
       "0    NCBIGene:6696                SPP1     HP:0001395   \n",
       "0    NCBIGene:7422               VEGFA     HP:0001395   \n",
       "0     NCBIGene:183                 AGT     HP:0001395   \n",
       "0     NCBIGene:183                 AGT  MONDO:0018840   \n",
       "0    NCBIGene:7040               TGFB1  MONDO:0018840   \n",
       "0    NCBIGene:7046              TGFBR1     HP:0001395   \n",
       "0    NCBIGene:1499              CTNNB1     HP:0001395   \n",
       "0    NCBIGene:7057               THBS1  MONDO:0018840   \n",
       "0    NCBIGene:5972                 REN  MONDO:0018840   \n",
       "0    NCBIGene:5314               PKHD1  MONDO:0018840   \n",
       "0    NCBIGene:7057               THBS1     HP:0001395   \n",
       "0    NCBIGene:5244               ABCB4     HP:0001395   \n",
       "0    NCBIGene:6347                CCL2     HP:0001395   \n",
       "0    NCBIGene:2147                  F2     HP:0001395   \n",
       "0    NCBIGene:1278              COL1A2     HP:0001395   \n",
       "0    NCBIGene:5328                PLAU     HP:0001395   \n",
       "0    NCBIGene:2149                 F2R     HP:0001395   \n",
       "0     NCBIGene:408               ARRB1     HP:0001395   \n",
       "0    NCBIGene:2321                FLT1     HP:0001395   \n",
       "0    NCBIGene:2247                FGF2     HP:0001395   \n",
       "0     NCBIGene:405                ARNT     HP:0001395   \n",
       "0    NCBIGene:3956              LGALS1     HP:0001395   \n",
       "0    NCBIGene:1356                  CP     HP:0001395   \n",
       "0    NCBIGene:4864                NPC1     HP:0001395   \n",
       "0    NCBIGene:1269                CNR2     HP:0001395   \n",
       "0    NCBIGene:9104                 RGN     HP:0001395   \n",
       "0    NCBIGene:6927               HNF1A  MONDO:0018840   \n",
       "0    NCBIGene:4763                 NF1  MONDO:0018840   \n",
       "0     NCBIGene:183                 AGT  MONDO:0018840   \n",
       "0    NCBIGene:7431                 VIM     HP:0001395   \n",
       "0    NCBIGene:4015                 LOX     HP:0001395   \n",
       "0    MONDO:0005154      liver disorder     HP:0012852   \n",
       "0     NCBIGene:183                 AGT     HP:0001395   \n",
       "0    NCBIGene:1593             CYP27A1     HP:0001395   \n",
       "0  NCBIGene:120227              CYP2R1     HP:0001395   \n",
       "0    NCBIGene:3875               KRT18     HP:0001395   \n",
       "0    NCBIGene:3484              IGFBP1     HP:0001395   \n",
       "0    NCBIGene:1269                CNR2     HP:0001395   \n",
       "0     NCBIGene:866            SERPINA6     HP:0001395   \n",
       "\n",
       "                               n02_name  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                   Periportal fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0  isolated congenital hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0             Hepatic bridging fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  \n",
       "0                      Hepatic fibrosis  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[    'PPARA_SMAD3_Hepatic_fibrosis',\n",
      "     'PPARA_TGFB1_Hepatic_fibrosis',\n",
      "     'PPARA_CCL2_Hepatic_fibrosis',\n",
      "     'PPARA_ALB_Hepatic_fibrosis',\n",
      "     'PPARA_HGF_Hepatic_fibrosis',\n",
      "     'PPARA_liver_disorder_Hepatic_fibrosis',\n",
      "     'PPARA_MMP2_Hepatic_fibrosis',\n",
      "     'PPARA_IL6_Hepatic_fibrosis',\n",
      "     'PPARA_liver_disorder_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_CCN2_Hepatic_fibrosis',\n",
      "     'PPARA_F2_Hepatic_fibrosis',\n",
      "     'PPARA_liver_disorder_Periportal_fibrosis',\n",
      "     'PPARA_STAT1_Hepatic_fibrosis',\n",
      "     'PPARA_NFE2L2_Hepatic_fibrosis',\n",
      "     'PPARA_cirrhosis_of_liver_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_CP_Hepatic_fibrosis',\n",
      "     'PPARA_REN_Hepatic_fibrosis',\n",
      "     'PPARA_COL1A1_Hepatic_fibrosis',\n",
      "     'PPARA_SPP1_Hepatic_fibrosis',\n",
      "     'PPARA_VEGFA_Hepatic_fibrosis',\n",
      "     'PPARA_AGT_Hepatic_fibrosis',\n",
      "     'PPARA_AGT_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_TGFB1_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_TGFBR1_Hepatic_fibrosis',\n",
      "     'PPARA_CTNNB1_Hepatic_fibrosis',\n",
      "     'PPARA_THBS1_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_REN_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_PKHD1_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_THBS1_Hepatic_fibrosis',\n",
      "     'PPARA_ABCB4_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CCL2_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_F2_Hepatic_fibrosis',\n",
      "     'PPARA_COL1A2_Hepatic_fibrosis',\n",
      "     'PPARA_PLAU_Hepatic_fibrosis',\n",
      "     'PPARA_F2R_Hepatic_fibrosis',\n",
      "     'PPARA_ARRB1_Hepatic_fibrosis',\n",
      "     'PPARA_FLT1_Hepatic_fibrosis',\n",
      "     'PPARA_FGF2_Hepatic_fibrosis',\n",
      "     'PPARA_ARNT_Hepatic_fibrosis',\n",
      "     'PPARA_LGALS1_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CP_Hepatic_fibrosis',\n",
      "     'PPARA_NPC1_Hepatic_fibrosis',\n",
      "     'PPARA_CNR2_Hepatic_fibrosis',\n",
      "     'PPARA_RGN_Hepatic_fibrosis',\n",
      "     'PPARA_HNF1A_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_NF1_isolated_congenital_hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_AGT_isolated_congenital_hepatic_fibrosis',\n",
      "     'PPARA_VIM_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_LOX_Hepatic_fibrosis',\n",
      "     'PPARA_liver_disorder_Hepatic_bridging_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_AGT_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CYP27A1_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CYP2R1_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_KRT18_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_IGFBP1_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CNR2_Hepatic_fibrosis',\n",
      "     'peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_SERPINA6_Hepatic_fibrosis']\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import os\n",
    "\n",
    "cols = []\n",
    "for node in sorted(results[0]['node_bindings'].keys()):\n",
    "    cols.append(node)\n",
    "    cols.append(node + '_name')\n",
    "results_df = pd.DataFrame(columns = cols)\n",
    "\n",
    "results_list = []\n",
    "for result in results:\n",
    "    result_dict = {}\n",
    "    for node in sorted(result['node_bindings'].keys()):\n",
    "        node_id = result['node_bindings'][node][0]['id']\n",
    "        result_dict[node] = node_id\n",
    "        result_dict[node + '_name'] = kg['nodes'][node_id]['name']\n",
    "\n",
    "    results_list.append(pd.DataFrame([result_dict]))\n",
    "results_df = pd.concat(results_list)\n",
    "display(results_df)\n",
    "results_df.to_csv(os.path.join(write_dir,'results_TRAPI.csv'), index=False)\n",
    "\n",
    "combined_node_list = [\"_\".join([row[1].replace(\" \", \"_\"), row[3].replace(\" \", \"_\"), row[5].replace(\" \", \"_\")]) for row in results_df[cols].to_numpy()]\n",
    "pp.pprint(combined_node_list)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6fa0ed0d",
   "metadata": {},
   "source": [
    "The edge IDs are then retrieved from the `results` and used to find the corresponding `predicate` label in the `knowledge_graph`. Two nodes can have more than one edge connecting them because each edge represents a distinct type of association derived from a single data source. Because of this, the number of rows in this report may differ from the set of results above. For an answer with three nodes such as this one, there will be at least one edge between nodes 1 and 2 as well as nodes 2 and 3. The direction of the edge connecting two nodes can differ as well, such as for \"Buprenorphine\" and \"CYP2D6\" below. Sometimes a single association type will be derived from multiple data sources. In the code below, we print a single edge for each association type and include the count of the number of data sources where that association was found. The following writes out all unique edges for each of the results in the format of `subject` -> `predicate` -> `object` and exports the information into a single file per `result`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "d514536b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Pathway result: PPARA_SMAD3_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> SMAD3': 1,\n",
      "     'PPARA -> biolink:regulates -> SMAD3': 1,\n",
      "     'SMAD3 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'SMAD3 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'SMAD3 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_TGFB1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> TGFB1': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> TGFB1': 1,\n",
      "     'PPARA -> biolink:regulates -> TGFB1': 1,\n",
      "     'TGFB1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'TGFB1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_CCL2_Hepatic_fibrosis\n",
      "{    'CCL2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'CCL2 -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CCL2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> CCL2': 1,\n",
      "     'PPARA -> biolink:regulates -> CCL2': 1}\n",
      "\n",
      "Pathway result: PPARA_ALB_Hepatic_fibrosis\n",
      "{    'ALB -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'ALB -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'ALB -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> ALB': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:directly_physically_interacts_with -> ALB': 1,\n",
      "     'PPARA -> biolink:regulates -> ALB': 1}\n",
      "\n",
      "Pathway result: PPARA_HGF_Hepatic_fibrosis\n",
      "{    'HGF -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'HGF -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'HGF -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> HGF': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> HGF': 1}\n",
      "\n",
      "Pathway result: PPARA_liver_disorder_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> liver disorder': 1,\n",
      "     'Hepatic fibrosis -> biolink:subclass_of -> liver disorder': 1,\n",
      "     'PPARA -> biolink:contributes_to -> liver disorder': 1,\n",
      "     'PPARA -> biolink:genetic_association -> liver disorder': 1,\n",
      "     'liver disorder -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_MMP2_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> MMP2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'MMP2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'MMP2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'MMP2 -> biolink:regulates -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> MMP2': 1}\n",
      "\n",
      "Pathway result: PPARA_IL6_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> IL6': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'IL6 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'IL6 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'IL6 -> biolink:regulates -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> IL6': 1}\n",
      "\n",
      "Pathway result: PPARA_liver_disorder_isolated_congenital_hepatic_fibrosis\n",
      "{    'PPARA -> biolink:contributes_to -> liver disorder': 1,\n",
      "     'PPARA -> biolink:genetic_association -> liver disorder': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:subclass_of -> liver disorder': 1,\n",
      "     'liver disorder -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'liver disorder -> biolink:occurs_together_in_literature_with -> isolated congenital hepatic fibrosis': 1}\n",
      "\n",
      "Pathway result: PPARA_CCN2_Hepatic_fibrosis\n",
      "{    'CCN2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'CCN2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'CCN2 -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CCN2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> CCN2': 1}\n",
      "\n",
      "Pathway result: PPARA_F2_Hepatic_fibrosis\n",
      "{    'F2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'F2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> F2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:interacts_with -> F2': 1,\n",
      "     'PPARA -> biolink:regulates -> F2': 1}\n",
      "\n",
      "Pathway result: PPARA_liver_disorder_Periportal_fibrosis\n",
      "{    'PPARA -> biolink:contributes_to -> liver disorder': 1,\n",
      "     'PPARA -> biolink:genetic_association -> liver disorder': 1,\n",
      "     'Periportal fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Periportal fibrosis -> biolink:occurs_together_in_literature_with -> liver disorder': 1,\n",
      "     'Periportal fibrosis -> biolink:subclass_of -> liver disorder': 1,\n",
      "     'liver disorder -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_STAT1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> STAT1': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> STAT1': 1,\n",
      "     'PPARA -> biolink:regulates -> STAT1': 1,\n",
      "     'STAT1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'STAT1 -> biolink:interacts_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_NFE2L2_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> NFE2L2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'NFE2L2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'NFE2L2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'NFE2L2 -> biolink:regulates -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> NFE2L2': 1}\n",
      "\n",
      "Pathway result: PPARA_cirrhosis_of_liver_isolated_congenital_hepatic_fibrosis\n",
      "{    'PPARA -> biolink:contributes_to -> cirrhosis of liver': 1,\n",
      "     'cirrhosis of liver -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'cirrhosis of liver -> biolink:occurs_together_in_literature_with -> isolated congenital hepatic fibrosis': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:subclass_of -> cirrhosis of liver': 1}\n",
      "\n",
      "Pathway result: PPARA_CP_Hepatic_fibrosis\n",
      "{    'CP -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'CP -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'CP -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CP': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> CP': 1}\n",
      "\n",
      "Pathway result: PPARA_REN_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> REN': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> REN': 1,\n",
      "     'PPARA -> biolink:regulates -> REN': 1,\n",
      "     'REN -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'REN -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_COL1A1_Hepatic_fibrosis\n",
      "{    'COL1A1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'COL1A1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> COL1A1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> COL1A1': 1}\n",
      "\n",
      "Pathway result: PPARA_SPP1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> SPP1': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> SPP1': 1,\n",
      "     'PPARA -> biolink:regulates -> SPP1': 2,\n",
      "     'SPP1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'SPP1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_VEGFA_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> VEGFA': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> VEGFA': 1,\n",
      "     'PPARA -> biolink:regulates -> VEGFA': 1,\n",
      "     'VEGFA -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'VEGFA -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_AGT_Hepatic_fibrosis\n",
      "{    'AGT -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'AGT -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'AGT -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> AGT': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:interacts_with -> AGT': 1,\n",
      "     'PPARA -> biolink:regulates -> AGT': 1}\n",
      "\n",
      "Pathway result: PPARA_AGT_isolated_congenital_hepatic_fibrosis\n",
      "{    'AGT -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'AGT -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'AGT -> biolink:regulates -> PPARA': 1,\n",
      "     'PPARA -> biolink:interacts_with -> AGT': 1,\n",
      "     'PPARA -> biolink:regulates -> AGT': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> AGT': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_TGFB1_isolated_congenital_hepatic_fibrosis\n",
      "{    'PPARA -> biolink:occurs_together_in_literature_with -> TGFB1': 1,\n",
      "     'PPARA -> biolink:regulates -> TGFB1': 1,\n",
      "     'TGFB1 -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'TGFB1 -> biolink:regulates -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> TGFB1': 1}\n",
      "\n",
      "Pathway result: PPARA_TGFBR1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> TGFBR1': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> TGFBR1': 1,\n",
      "     'PPARA -> biolink:regulates -> TGFBR1': 1,\n",
      "     'TGFBR1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'TGFBR1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_CTNNB1_Hepatic_fibrosis\n",
      "{    'CTNNB1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'CTNNB1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'CTNNB1 -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CTNNB1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> CTNNB1': 1}\n",
      "\n",
      "Pathway result: PPARA_THBS1_isolated_congenital_hepatic_fibrosis\n",
      "{    'PPARA -> biolink:occurs_together_in_literature_with -> THBS1': 1,\n",
      "     'PPARA -> biolink:regulates -> THBS1': 1,\n",
      "     'THBS1 -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'THBS1 -> biolink:regulates -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> THBS1': 1}\n",
      "\n",
      "Pathway result: PPARA_REN_isolated_congenital_hepatic_fibrosis\n",
      "{    'PPARA -> biolink:occurs_together_in_literature_with -> REN': 1,\n",
      "     'PPARA -> biolink:regulates -> REN': 1,\n",
      "     'REN -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'REN -> biolink:regulates -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> REN': 1}\n",
      "\n",
      "Pathway result: PPARA_PKHD1_isolated_congenital_hepatic_fibrosis\n",
      "{    'PKHD1 -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'PKHD1 -> biolink:genetic_association -> isolated congenital hepatic fibrosis': 1,\n",
      "     'PKHD1 -> biolink:regulates -> PPARA': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PKHD1': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_THBS1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> THBS1': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> THBS1': 1,\n",
      "     'PPARA -> biolink:regulates -> THBS1': 1,\n",
      "     'THBS1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'THBS1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_ABCB4_Hepatic_fibrosis\n",
      "{    'ABCB4 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'ABCB4 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> ABCB4': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:interacts_with -> ABCB4': 1,\n",
      "     'PPARA -> biolink:regulates -> ABCB4': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CCL2_Hepatic_fibrosis\n",
      "{    'CCL2 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'CCL2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CCL2': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> CCL2': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_F2_Hepatic_fibrosis\n",
      "{    'F2 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'F2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> F2': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> F2': 1}\n",
      "\n",
      "Pathway result: PPARA_COL1A2_Hepatic_fibrosis\n",
      "{    'COL1A2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'COL1A2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> COL1A2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> COL1A2': 1}\n",
      "\n",
      "Pathway result: PPARA_PLAU_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PLAU': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PLAU -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'PLAU -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PLAU -> biolink:regulates -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> PLAU': 1}\n",
      "\n",
      "Pathway result: PPARA_F2R_Hepatic_fibrosis\n",
      "{    'F2R -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'F2R -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> F2R': 1}\n",
      "\n",
      "Pathway result: PPARA_ARRB1_Hepatic_fibrosis\n",
      "{    'ARRB1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'ARRB1 -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> ARRB1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_FLT1_Hepatic_fibrosis\n",
      "{    'FLT1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'FLT1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> FLT1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> FLT1': 1}\n",
      "\n",
      "Pathway result: PPARA_FGF2_Hepatic_fibrosis\n",
      "{    'FGF2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'FGF2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> FGF2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> FGF2': 1}\n",
      "\n",
      "Pathway result: PPARA_ARNT_Hepatic_fibrosis\n",
      "{    'ARNT -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'ARNT -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'ARNT -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> ARNT': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_LGALS1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> LGALS1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'LGALS1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'LGALS1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'LGALS1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CP_Hepatic_fibrosis\n",
      "{    'CP -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'CP -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CP': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> CP': 1}\n",
      "\n",
      "Pathway result: PPARA_NPC1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> NPC1': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'NPC1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'NPC1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'NPC1 -> biolink:regulates -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_CNR2_Hepatic_fibrosis\n",
      "{    'CNR2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'CNR2 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'CNR2 -> biolink:regulates -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CNR2': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_RGN_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> RGN': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> RGN': 1,\n",
      "     'PPARA -> biolink:regulates -> RGN': 1,\n",
      "     'RGN -> biolink:genetic_association -> Hepatic fibrosis': 1}\n",
      "\n",
      "Pathway result: PPARA_HNF1A_isolated_congenital_hepatic_fibrosis\n",
      "{    'HNF1A -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> HNF1A': 1,\n",
      "     'PPARA -> biolink:regulates -> HNF1A': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: PPARA_NF1_isolated_congenital_hepatic_fibrosis\n",
      "{    'NF1 -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'NF1 -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'PPARA -> biolink:regulates -> NF1': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> NF1': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_AGT_isolated_congenital_hepatic_fibrosis\n",
      "{    'AGT -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'AGT -> biolink:contributes_to -> isolated congenital hepatic fibrosis': 1,\n",
      "     'isolated congenital hepatic fibrosis -> biolink:occurs_together_in_literature_with -> AGT': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> AGT': 1}\n",
      "\n",
      "Pathway result: PPARA_VIM_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> PPARA': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> VIM': 1,\n",
      "     'PPARA -> biolink:occurs_together_in_literature_with -> VIM': 1,\n",
      "     'PPARA -> biolink:regulates -> VIM': 1,\n",
      "     'VIM -> biolink:genetic_association -> Hepatic fibrosis': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_LOX_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> LOX': 1,\n",
      "     'LOX -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'LOX -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> LOX': 1}\n",
      "\n",
      "Pathway result: PPARA_liver_disorder_Hepatic_bridging_fibrosis\n",
      "{    'Hepatic bridging fibrosis -> biolink:occurs_together_in_literature_with -> liver disorder': 1,\n",
      "     'Hepatic bridging fibrosis -> biolink:subclass_of -> liver disorder': 1,\n",
      "     'PPARA -> biolink:contributes_to -> liver disorder': 1,\n",
      "     'PPARA -> biolink:genetic_association -> liver disorder': 1,\n",
      "     'liver disorder -> biolink:occurs_together_in_literature_with -> PPARA': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_AGT_Hepatic_fibrosis\n",
      "{    'AGT -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'AGT -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> AGT': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> AGT': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CYP27A1_Hepatic_fibrosis\n",
      "{    'CYP27A1 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'CYP27A1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CYP27A1': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> CYP27A1': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CYP2R1_Hepatic_fibrosis\n",
      "{    'CYP2R1 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'CYP2R1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CYP2R1': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> CYP2R1': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_KRT18_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> KRT18': 1,\n",
      "     'KRT18 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'KRT18 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> KRT18': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_IGFBP1_Hepatic_fibrosis\n",
      "{    'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> IGFBP1': 1,\n",
      "     'IGFBP1 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'IGFBP1 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> IGFBP1': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_CNR2_Hepatic_fibrosis\n",
      "{    'CNR2 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'CNR2 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'Hepatic fibrosis -> biolink:occurs_together_in_literature_with -> CNR2': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> CNR2': 1}\n",
      "\n",
      "Pathway result: peroxisome_proliferator-activated_receptor_alpha_isoform_1_(human)_SERPINA6_Hepatic_fibrosis\n",
      "{    'SERPINA6 -> biolink:coexpressed_with -> peroxisome proliferator-activated receptor alpha isoform 1 (human)': 1,\n",
      "     'SERPINA6 -> biolink:genetic_association -> Hepatic fibrosis': 1,\n",
      "     'peroxisome proliferator-activated receptor alpha isoform 1 (human) -> biolink:coexpressed_with -> SERPINA6': 1}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from collections import Counter\n",
    "import json\n",
    "import pprint\n",
    "pp = pprint.PrettyPrinter(indent=5)\n",
    "\n",
    "for i in range(number_pathway_results):\n",
    "    print(f\"Pathway result: {combined_node_list[i]}\")\n",
    "    edge_bindings = results[i]['edge_bindings']\n",
    "\n",
    "    edge_ids = []\n",
    "    for edge_name, edge_list in edge_bindings.items():\n",
    "        edge_ids.append({edge_name: [x['id'] for x in edge_list]})\n",
    "\n",
    "    string_out_list = []\n",
    "    for edge_dict in edge_ids:\n",
    "        for edge_name, edge_list in edge_dict.items():\n",
    "            for edge_id in edge_list:\n",
    "                subject_id = kg['edges'][edge_id]['subject']\n",
    "                subject = kg['nodes'][subject_id]['name']\n",
    "                predicate = kg['edges'][edge_id]['predicate']\n",
    "                object_id = kg['edges'][edge_id]['object']\n",
    "                object = kg['nodes'][object_id]['name']\n",
    "                string_out = f\"{subject} -> {predicate} -> {object}\"\n",
    "                string_out_list.append(string_out)\n",
    "    string_out_dict = dict(Counter(string_out_list).items())\n",
    "    pp.pprint(string_out_dict)\n",
    "    print(\"\")\n",
    "    \n",
    "    with open(os.path.join(write_dir,combined_node_list[i]+\".txt\"), 'w') as convert_file:\n",
    "        convert_file.write(json.dumps(string_out_dict))\n",
    "        "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "71bfe186",
   "metadata": {},
   "source": [
    "We see that the connection between Buprenorphine and CYP2D6 consists of two edge types `biolink:affects` and `biolink:directly_physically_interacts_with`. The `biolink:affects` relationship is bidirectional with one edge starting with Buprenorphine (`Buprenorphine -> biolink:affects -> CYP2D6`) and one starting with CYP2D6 (`CYP2D6 -> biolink:affects -> Buprenorphine`). These three edges are repeated for all results that include Buprenorphine and CYP2D6 as the first two nodes. Those results differ in the type of tremor found for the third node. There are three edges connecting Buprenorphine and OPRM1 (`biolink:affects`, `biolink:directly_physically_interacts_with`, `biolink:related_to`). Of note, the `biolink:affects` was identified in 4 different knowledge sources as indicated by the count reported after the colon."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "25bd5305",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['node_bindings', 'edge_bindings', 'score'])\n",
      "dict_keys(['n02', 'n01', 'n00'])\n",
      "dict_keys(['e00', 'e01', 's20', 's50', 's51'])\n",
      "0.4262633578538942\n"
     ]
    }
   ],
   "source": [
    "pp.pprint(results[0].keys())\n",
    "pp.pprint(results[0]['node_bindings'].keys())\n",
    "pp.pprint(results[0]['edge_bindings'].keys())\n",
    "pp.pprint(results[0]['score'])\n",
    "#pp.pprint(kg['edges'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "f994aa91",
   "metadata": {},
   "outputs": [],
   "source": [
    "aragorn_result_summaries = []\n",
    "for r in results:\n",
    "    rs = f\"Score={round(r['score'], 3)}: \"\n",
    "    j = 0\n",
    "    while j < len(nodes):\n",
    "        node_id = r['node_bindings'][nodes[j]][0]['id']\n",
    "        node_name = kg['nodes'][node_id]['name']\n",
    "        rs = rs + f\"{node_name} ({node_id})\"\n",
    "        if j < len(edges):\n",
    "            edge_id = r['edge_bindings'][edges[j]][0]['id']\n",
    "            edge_name = kg['edges'][edge_id]['predicate']\n",
    "            rs = rs + f\"--{edge_name}-->\"\n",
    "        j = j + 1\n",
    "    aragorn_result_summaries.append(rs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "38405e49",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Score=0.426: PPARA (NCBIGene:5465)--biolink:regulates-->SMAD3 (NCBIGene:4088)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.422: PPARA (NCBIGene:5465)--biolink:regulates-->TGFB1 (NCBIGene:7040)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.415: PPARA (NCBIGene:5465)--biolink:regulates-->CCL2 (NCBIGene:6347)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.406: PPARA (NCBIGene:5465)--biolink:regulates-->ALB (NCBIGene:213)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.395: PPARA (NCBIGene:5465)--biolink:regulates-->HGF (NCBIGene:3082)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.383: PPARA (NCBIGene:5465)--biolink:genetic_association-->liver disorder (MONDO:0005154)--biolink:subclass_of-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.36: PPARA (NCBIGene:5465)--biolink:regulates-->MMP2 (NCBIGene:4313)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.355: PPARA (NCBIGene:5465)--biolink:regulates-->IL6 (NCBIGene:3569)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.326: PPARA (NCBIGene:5465)--biolink:genetic_association-->liver disorder (MONDO:0005154)--biolink:subclass_of-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.319: PPARA (NCBIGene:5465)--biolink:regulates-->CCN2 (NCBIGene:1490)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.314: PPARA (NCBIGene:5465)--biolink:interacts_with-->F2 (NCBIGene:2147)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.314: PPARA (NCBIGene:5465)--biolink:genetic_association-->liver disorder (MONDO:0005154)--biolink:subclass_of-->Periportal fibrosis (HP:0001405)\n",
      "Score=0.308: PPARA (NCBIGene:5465)--biolink:interacts_with-->STAT1 (NCBIGene:6772)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.303: PPARA (NCBIGene:5465)--biolink:regulates-->NFE2L2 (NCBIGene:4780)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.295: PPARA (NCBIGene:5465)--biolink:contributes_to-->cirrhosis of liver (MONDO:0005155)--biolink:subclass_of-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.256: PPARA (NCBIGene:5465)--biolink:regulates-->CP (NCBIGene:1356)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.246: PPARA (NCBIGene:5465)--biolink:regulates-->REN (NCBIGene:5972)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.239: PPARA (NCBIGene:5465)--biolink:regulates-->COL1A1 (NCBIGene:1277)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.239: PPARA (NCBIGene:5465)--biolink:regulates-->SPP1 (NCBIGene:6696)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.236: PPARA (NCBIGene:5465)--biolink:regulates-->VEGFA (NCBIGene:7422)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.235: PPARA (NCBIGene:5465)--biolink:regulates-->AGT (NCBIGene:183)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.231: PPARA (NCBIGene:5465)--biolink:regulates-->AGT (NCBIGene:183)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.222: PPARA (NCBIGene:5465)--biolink:regulates-->TGFB1 (NCBIGene:7040)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.22: PPARA (NCBIGene:5465)--biolink:regulates-->TGFBR1 (NCBIGene:7046)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.22: PPARA (NCBIGene:5465)--biolink:regulates-->CTNNB1 (NCBIGene:1499)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.216: PPARA (NCBIGene:5465)--biolink:regulates-->THBS1 (NCBIGene:7057)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.211: PPARA (NCBIGene:5465)--biolink:regulates-->REN (NCBIGene:5972)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.204: PPARA (NCBIGene:5465)--biolink:regulates-->PKHD1 (NCBIGene:5314)--biolink:genetic_association-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.198: PPARA (NCBIGene:5465)--biolink:regulates-->THBS1 (NCBIGene:7057)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.192: PPARA (NCBIGene:5465)--biolink:regulates-->ABCB4 (NCBIGene:5244)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.191: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->CCL2 (NCBIGene:6347)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.191: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->F2 (NCBIGene:2147)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.182: PPARA (NCBIGene:5465)--biolink:regulates-->COL1A2 (NCBIGene:1278)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.176: PPARA (NCBIGene:5465)--biolink:regulates-->PLAU (NCBIGene:5328)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.172: PPARA (NCBIGene:5465)--biolink:regulates-->F2R (NCBIGene:2149)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.171: PPARA (NCBIGene:5465)--biolink:regulates-->ARRB1 (NCBIGene:408)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.166: PPARA (NCBIGene:5465)--biolink:regulates-->FLT1 (NCBIGene:2321)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.165: PPARA (NCBIGene:5465)--biolink:regulates-->FGF2 (NCBIGene:2247)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.161: PPARA (NCBIGene:5465)--biolink:regulates-->ARNT (NCBIGene:405)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.159: PPARA (NCBIGene:5465)--biolink:regulates-->LGALS1 (NCBIGene:3956)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.154: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->CP (NCBIGene:1356)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.153: PPARA (NCBIGene:5465)--biolink:regulates-->NPC1 (NCBIGene:4864)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.147: PPARA (NCBIGene:5465)--biolink:regulates-->CNR2 (NCBIGene:1269)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.146: PPARA (NCBIGene:5465)--biolink:regulates-->RGN (NCBIGene:9104)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.146: PPARA (NCBIGene:5465)--biolink:regulates-->HNF1A (NCBIGene:6927)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.144: PPARA (NCBIGene:5465)--biolink:regulates-->NF1 (NCBIGene:4763)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.142: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->AGT (NCBIGene:183)--biolink:contributes_to-->isolated congenital hepatic fibrosis (MONDO:0018840)\n",
      "Score=0.141: PPARA (NCBIGene:5465)--biolink:regulates-->VIM (NCBIGene:7431)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.134: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->LOX (NCBIGene:4015)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.125: PPARA (NCBIGene:5465)--biolink:genetic_association-->liver disorder (MONDO:0005154)--biolink:subclass_of-->Hepatic bridging fibrosis (HP:0012852)\n",
      "Score=0.123: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->AGT (NCBIGene:183)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.118: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->CYP27A1 (NCBIGene:1593)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.115: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->CYP2R1 (NCBIGene:120227)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.113: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->KRT18 (NCBIGene:3875)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.106: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->IGFBP1 (NCBIGene:3484)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.105: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->CNR2 (NCBIGene:1269)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n",
      "Score=0.099: peroxisome proliferator-activated receptor alpha isoform 1 (human) (UniProtKB:Q07869-1)--biolink:coexpressed_with-->SERPINA6 (NCBIGene:866)--biolink:genetic_association-->Hepatic fibrosis (HP:0001395)\n"
     ]
    }
   ],
   "source": [
    "for rs in aragorn_result_summaries:\n",
    "    print(rs)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e05efcd7",
   "metadata": {},
   "source": [
    "The following assumes that the node names will sort in the correct order, which is the case with the default naming conventions. This exports the results showing the nodes and the score assigned to each result."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "41393fa4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(57, 7)\n"
     ]
    }
   ],
   "source": [
    "cols = []\n",
    "for node in sorted(results[0]['node_bindings'].keys()):\n",
    "    cols.append(node)\n",
    "    cols.append(node + '_name')\n",
    "results_df = pd.DataFrame(columns = cols)\n",
    "\n",
    "results_dict_list = []\n",
    "for result in results:\n",
    "    result_dict = {}\n",
    "    for node in result['node_bindings'].keys():\n",
    "        node_id = result['node_bindings'][node][0]['id']\n",
    "        result_dict[node] = node_id\n",
    "        result_dict[node + '_name'] = kg['nodes'][node_id]['name']\n",
    "    result_dict['score'] = result['score']\n",
    "    #print(result_dict)\n",
    "\n",
    "    results_dict_list.append(result_dict)\n",
    "    # results_df = results_df.append(result_dict, ignore_index=True)\n",
    "results_df = pd.concat([results_df,pd.DataFrame.from_records(results_dict_list)])\n",
    "print(results_df.shape)\n",
    "results_df.to_csv(os.path.join(write_dir,'results_TRAPI_aragorn.csv'))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ed37017-f4f4-4ebe-854c-3c0740379ca3",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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