notebooks/get_lexicon.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Get Lexicon\n",
    "\n",
    "For the `20210515` run, we just used re-used the lexicon from `20200224`. Also, we didn't try filtering out non-human pathways this time, unlike the process we used for `20200224`, where we excluded figures from papers where PubTator had identified at least one species and none of those species were human or mouse.\n",
    "\n",
    "For the next run, it would be good to finish this notebook to get an updated lexicon and get species information for the papers. [The notes from our old codebook](https://github.com/wikipathways/pathway-figure-ocr/blob/76ae219e65bcc723bbeaa3b82744b4aec78fc9d7/codebook.md#generating-files-and-initial-tables) may be useful for how to do this."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext sql"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import csv\n",
    "import hashlib\n",
    "import io\n",
    "import json\n",
    "import os\n",
    "import re\n",
    "import subprocess\n",
    "import sys\n",
    "import warnings\n",
    "from itertools import zip_longest\n",
    "from pathlib import Path, PurePath\n",
    "from pprint import pprint\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import requests\n",
    "import requests_cache\n",
    "import seaborn as sns\n",
    "\n",
    "# from wand.image import Image\n",
    "from IPython.display import Image\n",
    "from nltk.metrics import edit_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "target_date = \"20210513\"\n",
    "images_dir = Path(f\"../data/images/{target_date}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Old Lexicon"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "%sql postgresql:///pfocr20200224"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " * postgresql:///pfocr20200224\n",
      "60244 rows affected.\n",
      "Returning data to local variable lexicon2020\n"
     ]
    }
   ],
   "source": [
    "%%sql lexicon2020 << SELECT symbol, xref as ncbigene_id, source\n",
    "FROM lexicon\n",
    "INNER JOIN xrefs ON lexicon.xref_id = xrefs.id\n",
    "INNER JOIN symbols ON lexicon.symbol_id = symbols.id;"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>symbol</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>source</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>S863-7</td>\n",
       "      <td>2</td>\n",
       "      <td>hgnc_alias_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>FWP007</td>\n",
       "      <td>2</td>\n",
       "      <td>hgnc_alias_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CPAMD5</td>\n",
       "      <td>2</td>\n",
       "      <td>hgnc_alias_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A2M</td>\n",
       "      <td>2</td>\n",
       "      <td>hgnc_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AAC2</td>\n",
       "      <td>10</td>\n",
       "      <td>hgnc_prev_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60239</th>\n",
       "      <td>C17orf113</td>\n",
       "      <td>110806298</td>\n",
       "      <td>hgnc_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60240</th>\n",
       "      <td>CSNKA2IP</td>\n",
       "      <td>111064647</td>\n",
       "      <td>hgnc_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60241</th>\n",
       "      <td>C19orf85</td>\n",
       "      <td>111064650</td>\n",
       "      <td>hgnc_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60242</th>\n",
       "      <td>IFITMD9</td>\n",
       "      <td>111216276</td>\n",
       "      <td>hgnc_alias_symbol</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60243</th>\n",
       "      <td>PMIS2</td>\n",
       "      <td>111216276</td>\n",
       "      <td>hgnc_symbol</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>60244 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          symbol ncbigene_id             source\n",
       "0         S863-7           2  hgnc_alias_symbol\n",
       "1         FWP007           2  hgnc_alias_symbol\n",
       "2         CPAMD5           2  hgnc_alias_symbol\n",
       "3            A2M           2        hgnc_symbol\n",
       "4           AAC2          10   hgnc_prev_symbol\n",
       "...          ...         ...                ...\n",
       "60239  C17orf113   110806298        hgnc_symbol\n",
       "60240   CSNKA2IP   111064647        hgnc_symbol\n",
       "60241   C19orf85   111064650        hgnc_symbol\n",
       "60242    IFITMD9   111216276  hgnc_alias_symbol\n",
       "60243      PMIS2   111216276        hgnc_symbol\n",
       "\n",
       "[60244 rows x 3 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lexicon2020_df = lexicon2020.DataFrame()\n",
    "lexicon2020_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(images_dir.joinpath(\"lexicon2020.json\"), \"w\") as f:\n",
    "    lexicon2020_df.to_json(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Updated Lexicon"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "I'm trying to translate [these steps](https://github.com/wikipathways/pathway-figure-ocr/blob/7b34d23982c7812ec98256ab1caf8c6ca3abccbb/codebook.md#generating-files-and-initial-tables) into Python in order to build a list of gene symbols to look for in the OCR text, but I haven't finished this yet. Status of the three main sources:\n",
    "\n",
    "- HGNC: done\n",
    "- bioentities: in progress\n",
    "- WikiPathways: not yet started\n",
    "\n",
    "For the bioentities file, it appears there are inconsistencies in mapping bioentities to NCBI Gene IDs. See that section below for more details."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/nix/store/ig1jyhw2kyjy1hb13zfzmkqqdmgi94mp-python3-3.8.8-env/lib/python3.8/site-packages/requests_cache/__init__.py\n"
     ]
    }
   ],
   "source": [
    "print(requests_cache.__file__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "requests_cache.install_cache(\"pfocr_cache\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext sql"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sns.set_style(\"dark\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import Levenshtein\n",
    "import Levenshtein_search\n",
    "import polyleven"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## HGNC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "hgnc_data_url = \"https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_aliases&col=gd_pub_acc_ids&col=gd_locus_type&col=gd_date_mod&col=family.id&col=gd_locus_group&col=gd_name_aliases&col=gd_date_sym_change&col=gd_pub_eg_id&col=family.name&col=gd_date_name_change&col=gd_prev_name&col=gd_date2app_or_res&status=Approved&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit\"\n",
    "hgnc_data = []\n",
    "r = requests.get(hgnc_data_url, stream=True)\n",
    "for record in csv.DictReader(\n",
    "    (line.decode(\"utf-8\") for line in r.iter_lines()), delimiter=\"\\t\"\n",
    "):\n",
    "    hgnc_data.append(record)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "42549\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[{'HGNC ID': 'HGNC:5',\n",
       "  'Approved symbol': 'A1BG',\n",
       "  'Approved name': 'alpha-1-B glycoprotein',\n",
       "  'Status': 'Approved',\n",
       "  'Previous symbols': '',\n",
       "  'Alias symbols': '',\n",
       "  'Accession numbers': '',\n",
       "  'Locus type': 'gene with protein product',\n",
       "  'Date modified': '2020-09-17',\n",
       "  'Gene group ID': '594',\n",
       "  'Locus group': 'protein-coding gene',\n",
       "  'Alias names': '',\n",
       "  'Date symbol changed': '',\n",
       "  'NCBI Gene ID': '1',\n",
       "  'Gene group name': 'Immunoglobulin like domain containing',\n",
       "  'Date name changed': '',\n",
       "  'Previous name': '',\n",
       "  'Date approved': '1989-06-30'},\n",
       " {'HGNC ID': 'HGNC:37133',\n",
       "  'Approved symbol': 'A1BG-AS1',\n",
       "  'Approved name': 'A1BG antisense RNA 1',\n",
       "  'Status': 'Approved',\n",
       "  'Previous symbols': 'NCRNA00181, A1BGAS, A1BG-AS',\n",
       "  'Alias symbols': 'FLJ23569',\n",
       "  'Accession numbers': 'BC040926',\n",
       "  'Locus type': 'RNA, long non-coding',\n",
       "  'Date modified': '2013-06-27',\n",
       "  'Gene group ID': '1987',\n",
       "  'Locus group': 'non-coding RNA',\n",
       "  'Alias names': '',\n",
       "  'Date symbol changed': '2010-11-25',\n",
       "  'NCBI Gene ID': '503538',\n",
       "  'Gene group name': 'Antisense RNAs',\n",
       "  'Date name changed': '2012-08-15',\n",
       "  'Previous name': 'non-protein coding RNA 181, \"A1BG antisense RNA (non-protein coding)\", \"A1BG antisense RNA 1 (non-protein coding)\"',\n",
       "  'Date approved': '2009-07-20'}]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(len(hgnc_data))\n",
    "hgnc_data[:2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "42549\n"
     ]
    }
   ],
   "source": [
    "raw_hgnc_df = (\n",
    "    pd.DataFrame(hgnc_data)[\n",
    "        [\n",
    "            \"HGNC ID\",\n",
    "            \"NCBI Gene ID\",\n",
    "            # \"Status\",\n",
    "            \"Approved symbol\",\n",
    "            \"Approved name\",\n",
    "            \"Alias symbols\",\n",
    "            \"Alias names\",\n",
    "            \"Previous symbols\",\n",
    "            \"Previous name\",\n",
    "        ]\n",
    "    ]\n",
    "    .rename(\n",
    "        columns={\n",
    "            \"HGNC ID\": \"hgnc_id\",\n",
    "            \"NCBI Gene ID\": \"ncbigene_id\",\n",
    "            \"Approved symbol\": \"approved_symbol\",\n",
    "            \"Approved name\": \"approved_name\",\n",
    "            \"Alias symbols\": \"alias_symbols\",\n",
    "            \"Alias names\": \"alias_names\",\n",
    "            \"Previous symbols\": \"previous_symbols\",\n",
    "            \"Previous name\": \"previous_name\",\n",
    "        }\n",
    "    )\n",
    "    .replace(\"\", np.nan)\n",
    ")\n",
    "print(len(raw_hgnc_df))\n",
    "# raw_hgnc_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\"ambiguous symbols\" are those that map to multiple ncbigene ids\n",
    "\n",
    "- `94436` when keeping first approved ambiguous symbol\n",
    "- `92535` when dropping all rows with ambiguous symbols"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hgnc_id</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>source</th>\n",
       "      <th>symbol</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC:5</td>\n",
       "      <td>1</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>A1BG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58949</th>\n",
       "      <td>HGNC:42824</td>\n",
       "      <td>100873287</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>RNA5SP48</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58950</th>\n",
       "      <td>HGNC:42825</td>\n",
       "      <td>100873288</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>RNA5SP49</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58951</th>\n",
       "      <td>HGNC:42827</td>\n",
       "      <td>106478992</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>RNA5SP50</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58952</th>\n",
       "      <td>HGNC:42828</td>\n",
       "      <td>100873289</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>RNA5SP51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>139992</th>\n",
       "      <td>HGNC:15864</td>\n",
       "      <td>10616</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>HOIL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>139993</th>\n",
       "      <td>HGNC:26120</td>\n",
       "      <td>79863</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>FLJ21172</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>139994</th>\n",
       "      <td>HGNC:26120</td>\n",
       "      <td>79863</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>HsT169</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>140024</th>\n",
       "      <td>HGNC:28842</td>\n",
       "      <td>83759</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>MGC10871</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98958</th>\n",
       "      <td>HGNC:32690</td>\n",
       "      <td>414918</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>AFI1B</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>94436 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           hgnc_id ncbigene_id           source    symbol\n",
       "0           HGNC:5           1  approved_symbol      A1BG\n",
       "58949   HGNC:42824   100873287  approved_symbol  RNA5SP48\n",
       "58950   HGNC:42825   100873288  approved_symbol  RNA5SP49\n",
       "58951   HGNC:42827   106478992  approved_symbol  RNA5SP50\n",
       "58952   HGNC:42828   100873289  approved_symbol  RNA5SP51\n",
       "...            ...         ...              ...       ...\n",
       "139992  HGNC:15864       10616     alias_symbol     HOIL1\n",
       "139993  HGNC:26120       79863     alias_symbol  FLJ21172\n",
       "139994  HGNC:26120       79863     alias_symbol    HsT169\n",
       "140024  HGNC:28842       83759     alias_symbol  MGC10871\n",
       "98958   HGNC:32690      414918     alias_symbol     AFI1B\n",
       "\n",
       "[94436 rows x 4 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hgnc_df = raw_hgnc_df[raw_hgnc_df[\"ncbigene_id\"].notnull()]\n",
    "\n",
    "name_columns = [\"approved_name\", \"previous_name\", \"alias_name\"]\n",
    "\n",
    "hgnc_df = (\n",
    "    hgnc_df.assign(\n",
    "        alias_symbol=hgnc_df[\"alias_symbols\"].str.split(\", \"),\n",
    "        alias_name=hgnc_df[\"alias_names\"].str.split(\", \"),\n",
    "        previous_symbol=hgnc_df[\"previous_symbols\"].str.split(\", \"),\n",
    "    )\n",
    "    .explode(\"alias_symbol\")\n",
    "    .explode(\"alias_name\")\n",
    "    .explode(\"previous_symbol\")\n",
    "    .drop(\n",
    "        columns=[\"alias_symbols\", \"alias_names\", \"previous_symbols\"]\n",
    "        + name_columns\n",
    "    )\n",
    "    .melt(\n",
    "        id_vars=[\"hgnc_id\", \"ncbigene_id\"],\n",
    "        value_vars=[\"approved_symbol\", \"alias_symbol\", \"previous_symbol\"],\n",
    "        var_name=\"source\",\n",
    "        value_name=\"symbol\",\n",
    "    )\n",
    "    .dropna()\n",
    "    # drop exact duplicates\n",
    "    .drop_duplicates()\n",
    ")\n",
    "\n",
    "hgnc_df = hgnc_df[\n",
    "    (hgnc_df[\"source\"] == \"approved_symbol\")\n",
    "    | (hgnc_df[\"symbol\"].str.len() >= 3)\n",
    "]\n",
    "\n",
    "variables_by_priority = {\n",
    "    \"approved_symbol\": 0,\n",
    "    \"previous_symbol\": 1,\n",
    "    \"alias_symbol\": 2,\n",
    "}\n",
    "\n",
    "hgnc_df[\"priority\"] = hgnc_df[\"source\"].apply(\n",
    "    lambda x: variables_by_priority[x]\n",
    ")\n",
    "\n",
    "# For rows with ambiguous symbols, keep the first for every symbol and drop the rest.\n",
    "# Note the sorting is approved before previous before alias.\n",
    "hgnc_df = (\n",
    "    hgnc_df.sort_values(by=[\"priority\"])\n",
    "    .drop_duplicates(subset=[\"symbol\"])\n",
    "    .drop(columns=[\"priority\"])\n",
    ")\n",
    "\n",
    "# we don't want this\n",
    "# drop all rows with ambiguous symbols\n",
    "# hgnc_df = hgnc_df.drop_duplicates(subset=[\"value\"], keep=False)\n",
    "\n",
    "hgnc_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Bioentities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP1</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP2</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA1</td>\n",
       "      <td>Actin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA2</td>\n",
       "      <td>Actin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2305</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2306</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2307</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2308</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2309</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2301 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentity\n",
       "0     HGNC  EIF4EBP1   EIF4EBP\n",
       "1     HGNC  EIF4EBP2   EIF4EBP\n",
       "2     HGNC  EIF4EBP3   EIF4EBP\n",
       "3     HGNC     ACTA1     Actin\n",
       "4     HGNC     ACTA2     Actin\n",
       "...    ...       ...       ...\n",
       "2305  HGNC     ITGB4  Integrin\n",
       "2306  HGNC     ITGB5  Integrin\n",
       "2307  HGNC     ITGB6  Integrin\n",
       "2308  HGNC     ITGB7  Integrin\n",
       "2309  HGNC     ITGB8  Integrin\n",
       "\n",
       "[2301 rows x 3 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_data_url = \"https://raw.githubusercontent.com/wikipathways/bioentities/master/relations.csv\"\n",
    "bioentities_data = []\n",
    "r = requests.get(bioentities_data_url, stream=True)\n",
    "for record in csv.DictReader(\n",
    "    (line.decode(\"utf-8\") for line in r.iter_lines()),\n",
    "    fieldnames=[\"type\", \"symbol\", \"isa\", \"type2\", \"bioentity\"],\n",
    "):\n",
    "    bioentities_data.append(record)\n",
    "\n",
    "bioentities_df = pd.DataFrame(bioentities_data)\n",
    "# There are 9 entries from UP (UniProt). They are duplicates the HGNC entries, so we ignore them.\n",
    "bioentities_df = (\n",
    "    bioentities_df[\n",
    "        bioentities_df[\"type\"].isin(\n",
    "            {\n",
    "                \"HGNC\",\n",
    "                \"BE\",\n",
    "            }\n",
    "        )\n",
    "    ]\n",
    ").drop(columns=[\"isa\", \"type2\"])\n",
    "bioentities_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are no missing values:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "type         False\n",
       "symbol       False\n",
       "bioentity    False\n",
       "dtype: bool"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(bioentities_df.replace(\"\", np.nan).isna().sum().sum())\n",
    "bioentities_df.replace(\"\", np.nan).isna().any()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP1</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1978</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP2</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>8637</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA1</td>\n",
       "      <td>Actin</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA2</td>\n",
       "      <td>Actin</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2296</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3691</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2297</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3694</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3695</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3696</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2301 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentity ncbigene_id\n",
       "0     HGNC  EIF4EBP1   EIF4EBP        1978\n",
       "1     HGNC  EIF4EBP2   EIF4EBP        1979\n",
       "2     HGNC  EIF4EBP3   EIF4EBP        8637\n",
       "3     HGNC     ACTA1     Actin          58\n",
       "4     HGNC     ACTA2     Actin          59\n",
       "...    ...       ...       ...         ...\n",
       "2296  HGNC     ITGB4  Integrin        3691\n",
       "2297  HGNC     ITGB5  Integrin        3693\n",
       "2298  HGNC     ITGB6  Integrin        3694\n",
       "2299  HGNC     ITGB7  Integrin        3695\n",
       "2300  HGNC     ITGB8  Integrin        3696\n",
       "\n",
       "[2301 rows x 4 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df = bioentities_df.merge(\n",
    "    hgnc_df[[\"ncbigene_id\", \"symbol\"]], how=\"left\", on=\"symbol\"\n",
    ")\n",
    "joined_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'BE', 'HGNC'}"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "set(joined_df[\"type\"].to_list())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2127</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_I</td>\n",
       "      <td>Troponin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2128</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_T</td>\n",
       "      <td>Troponin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2183</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>GRIN2A</td>\n",
       "      <td>NMDAR</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2240</th>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2280</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGA6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>96 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type      symbol bioentity ncbigene_id\n",
       "9       BE   Activin_A   Activin         NaN\n",
       "10      BE  Activin_AB   Activin         NaN\n",
       "11      BE   Activin_B   Activin         NaN\n",
       "12      BE   Inhibin_A   Inhibin         NaN\n",
       "13      BE   Inhibin_B   Inhibin         NaN\n",
       "...    ...         ...       ...         ...\n",
       "2127    BE  Troponin_I  Troponin         NaN\n",
       "2128    BE  Troponin_T  Troponin         NaN\n",
       "2183  HGNC      GRIN2A     NMDAR         NaN\n",
       "2240    BE       MAP2K     MAPKK         NaN\n",
       "2280  HGNC       ITGA6  Integrin         NaN\n",
       "\n",
       "[96 rows x 4 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"ncbigene_id\"].isnull()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>PRKAA1</td>\n",
       "      <td>AMPK_alpha</td>\n",
       "      <td>5562</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>PRKAA2</td>\n",
       "      <td>AMPK_alpha</td>\n",
       "      <td>5563</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    type  symbol   bioentity ncbigene_id\n",
       "28  HGNC  PRKAA1  AMPK_alpha        5562\n",
       "29  HGNC  PRKAA2  AMPK_alpha        5563"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"bioentity\"] == \"AMPK_alpha\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>231</th>\n",
       "      <td>BE</td>\n",
       "      <td>HSP90A</td>\n",
       "      <td>HSP90</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    type  symbol bioentity ncbigene_id\n",
       "231   BE  HSP90A     HSP90         NaN"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"symbol\"] == \"HSP90A\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>hierarchy_levels</th>\n",
       "      <th>hierarchy_apex</th>\n",
       "      <th>level_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP1</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1978</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP2</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1979</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>8637</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA1</td>\n",
       "      <td>Actin</td>\n",
       "      <td>58</td>\n",
       "      <td>[Actin]</td>\n",
       "      <td>Actin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA2</td>\n",
       "      <td>Actin</td>\n",
       "      <td>59</td>\n",
       "      <td>[Actin]</td>\n",
       "      <td>Actin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2296</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3691</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2297</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3693</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3694</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3695</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3696</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2301 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentity ncbigene_id hierarchy_levels hierarchy_apex  \\\n",
       "0     HGNC  EIF4EBP1   EIF4EBP        1978        [EIF4EBP]        EIF4EBP   \n",
       "1     HGNC  EIF4EBP2   EIF4EBP        1979        [EIF4EBP]        EIF4EBP   \n",
       "2     HGNC  EIF4EBP3   EIF4EBP        8637        [EIF4EBP]        EIF4EBP   \n",
       "3     HGNC     ACTA1     Actin          58          [Actin]          Actin   \n",
       "4     HGNC     ACTA2     Actin          59          [Actin]          Actin   \n",
       "...    ...       ...       ...         ...              ...            ...   \n",
       "2296  HGNC     ITGB4  Integrin        3691       [Integrin]       Integrin   \n",
       "2297  HGNC     ITGB5  Integrin        3693       [Integrin]       Integrin   \n",
       "2298  HGNC     ITGB6  Integrin        3694       [Integrin]       Integrin   \n",
       "2299  HGNC     ITGB7  Integrin        3695       [Integrin]       Integrin   \n",
       "2300  HGNC     ITGB8  Integrin        3696       [Integrin]       Integrin   \n",
       "\n",
       "      level_number  \n",
       "0                1  \n",
       "1                1  \n",
       "2                1  \n",
       "3                1  \n",
       "4                1  \n",
       "...            ...  \n",
       "2296             1  \n",
       "2297             1  \n",
       "2298             1  \n",
       "2299             1  \n",
       "2300             1  \n",
       "\n",
       "[2301 rows x 7 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def get_hierarchy_levels(bioentity, hierarchy_levels=None):\n",
    "    # ******\n",
    "    # The bioentities appear to be at least sometimes in a hierarchical\n",
    "    # relationship. This function traces the path up the hierarchy for\n",
    "    # a bioentity in joined_df.\n",
    "    # ******\n",
    "\n",
    "    if not hierarchy_levels:\n",
    "        # make the trace include the lowest (first) item\n",
    "        hierarchy_levels = bioentity\n",
    "\n",
    "    # We're trying to go one level up the hierarchy.\n",
    "    # If this bioentity has a parent bioentity, then this bioentity will be\n",
    "    # listed as a symbol in a row where the parent bioentity is listed in the\n",
    "    # bioentity column. I don't know whether we should expect multiple results.\n",
    "    match_column = joined_df[joined_df[\"symbol\"] == bioentity][\"bioentity\"]\n",
    "    if len(match_column) > 0:\n",
    "        ancestor = match_column.to_list()[0]\n",
    "\n",
    "        if ancestor in hierarchy_levels.split(\",\"):\n",
    "            return hierarchy_levels\n",
    "        # TODO: when I use a list for hierarchy_levels, the column values in the df end\n",
    "        # up all being the same, but when I use a string, they each properly\n",
    "        # show the different trace for their specific row. Why?\n",
    "        # if ancestor in hierarchy_levels:\n",
    "        #    return hierarchy_levels\n",
    "        # hierarchy_levels.insert(0, ancestor)\n",
    "\n",
    "        return get_hierarchy_levels(\n",
    "            ancestor, \",\".join([ancestor, hierarchy_levels])\n",
    "        )\n",
    "\n",
    "    return hierarchy_levels\n",
    "\n",
    "\n",
    "joined_df[\"hierarchy_levels\"] = joined_df[\"bioentity\"].apply(\n",
    "    # TODO: see comment in fn about str vs. list\n",
    "    lambda x: get_hierarchy_levels(x).split(\",\")\n",
    ")\n",
    "\n",
    "joined_df = joined_df.assign(\n",
    "    hierarchy_apex=joined_df[\"hierarchy_levels\"].apply(lambda x: x[0]),\n",
    "    level_number=joined_df[\"hierarchy_levels\"].apply(lambda x: len(x)),\n",
    ")\n",
    "\n",
    "joined_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\"level_number\"].max()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>hierarchy_levels</th>\n",
       "      <th>hierarchy_apex</th>\n",
       "      <th>level_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>233</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>HSP90AA1</td>\n",
       "      <td>HSP90AA</td>\n",
       "      <td>3320</td>\n",
       "      <td>[HSP90, HSP90A, HSP90AA]</td>\n",
       "      <td>HSP90</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>623</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K1</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5604</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>624</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K2</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5605</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1428</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>PIK3R1</td>\n",
       "      <td>PI3K_p85</td>\n",
       "      <td>5295</td>\n",
       "      <td>[PI3K, PIK3R_I, PI3K_p85]</td>\n",
       "      <td>PI3K</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1429</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>PIK3R2</td>\n",
       "      <td>PI3K_p85</td>\n",
       "      <td>5296</td>\n",
       "      <td>[PI3K, PIK3R_I, PI3K_p85]</td>\n",
       "      <td>PI3K</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentity ncbigene_id           hierarchy_levels  \\\n",
       "233   HGNC  HSP90AA1   HSP90AA        3320   [HSP90, HSP90A, HSP90AA]   \n",
       "623   HGNC    MAP2K1       MEK        5604        [MAPKK, MAP2K, MEK]   \n",
       "624   HGNC    MAP2K2       MEK        5605        [MAPKK, MAP2K, MEK]   \n",
       "1428  HGNC    PIK3R1  PI3K_p85        5295  [PI3K, PIK3R_I, PI3K_p85]   \n",
       "1429  HGNC    PIK3R2  PI3K_p85        5296  [PI3K, PIK3R_I, PI3K_p85]   \n",
       "\n",
       "     hierarchy_apex  level_number  \n",
       "233           HSP90             3  \n",
       "623           MAPKK             3  \n",
       "624           MAPKK             3  \n",
       "1428           PI3K             3  \n",
       "1429           PI3K             3  "
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"level_number\"] == 3]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I'm not sure how to interpret the following pattern in the bioentities, but it appears to be a mistake. As far as I can tell, `MAP2K`, `MAPKK` and `MEK` are synonyms, and every one of them each refers to the following collection of NCBI Gene IDs: `5604`, `5605`, `5606`, `5607`, `5608`, `5609`, `6416`. But `STAT` and `STAT5` are not synonyms. `STAT` refers to the NCBI Gene IDs `6772`, `6773`, `6774`, `6775`, `6776`, `6776`, `6777`, `6778`, but `STAT5` only refers to `6776` and `6777`.\n",
    "\n",
    "In the df, we have the following `BE` relationships for rows with hierarchy apex `MAPKK`:\n",
    "- `MAPKK` & `MAP2K`\n",
    "- `MAP2K` & `MEK`\n",
    "\n",
    "and for rows with hierarchy apex `STAT`:\n",
    "- `STAT` & `STAT5`\n",
    "\n",
    "If `BE` indicates synonyms, we get the correct results for `MAP2K`, `MAPKK` and `MEK` but the wrong results for `STAT` and `STAT5`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>hierarchy_levels</th>\n",
       "      <th>hierarchy_apex</th>\n",
       "      <th>level_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>623</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K1</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5604</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>624</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K2</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5605</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>625</th>\n",
       "      <td>BE</td>\n",
       "      <td>MEK</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>626</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K3</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5606</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>627</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K4</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>6416</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>628</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K5</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5607</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>629</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K6</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5608</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>630</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K7</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5609</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2240</th>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[MAPKK]</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type  symbol bioentity ncbigene_id     hierarchy_levels hierarchy_apex  \\\n",
       "623   HGNC  MAP2K1       MEK        5604  [MAPKK, MAP2K, MEK]          MAPKK   \n",
       "624   HGNC  MAP2K2       MEK        5605  [MAPKK, MAP2K, MEK]          MAPKK   \n",
       "625     BE     MEK     MAP2K         NaN       [MAPKK, MAP2K]          MAPKK   \n",
       "626   HGNC  MAP2K3     MAP2K        5606       [MAPKK, MAP2K]          MAPKK   \n",
       "627   HGNC  MAP2K4     MAP2K        6416       [MAPKK, MAP2K]          MAPKK   \n",
       "628   HGNC  MAP2K5     MAP2K        5607       [MAPKK, MAP2K]          MAPKK   \n",
       "629   HGNC  MAP2K6     MAP2K        5608       [MAPKK, MAP2K]          MAPKK   \n",
       "630   HGNC  MAP2K7     MAP2K        5609       [MAPKK, MAP2K]          MAPKK   \n",
       "2240    BE   MAP2K     MAPKK         NaN              [MAPKK]          MAPKK   \n",
       "\n",
       "      level_number  \n",
       "623              3  \n",
       "624              3  \n",
       "625              2  \n",
       "626              2  \n",
       "627              2  \n",
       "628              2  \n",
       "629              2  \n",
       "630              2  \n",
       "2240             1  "
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"hierarchy_apex\"] == \"MAPKK\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bioentity</th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>625</th>\n",
       "      <td>MAP2K</td>\n",
       "      <td>BE</td>\n",
       "      <td>MEK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2240</th>\n",
       "      <td>MAPKK</td>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     bioentity type symbol\n",
       "625      MAP2K   BE    MEK\n",
       "2240     MAPKK   BE  MAP2K"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\n",
    "    (joined_df[\"hierarchy_apex\"] == \"MAPKK\") & (joined_df[\"type\"] == \"BE\")\n",
    "][[\"bioentity\", \"type\", \"symbol\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['5604', '5605', '5606', '5607', '5608', '5609', '6416']"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"hierarchy_apex\"] == \"MAPKK\")][\n",
    "    \"ncbigene_id\"\n",
    "].sort_values().dropna().to_list()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentity</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>hierarchy_levels</th>\n",
       "      <th>hierarchy_apex</th>\n",
       "      <th>level_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT1</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6772</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT2</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6773</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>285</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT3</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6774</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>286</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT4</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6775</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>287</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5A</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6776</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>288</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5B</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6777</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>289</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT6</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6778</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>BE</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6776</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     type  symbol bioentity ncbigene_id hierarchy_levels hierarchy_apex  \\\n",
       "283  HGNC   STAT1      STAT        6772           [STAT]           STAT   \n",
       "284  HGNC   STAT2      STAT        6773           [STAT]           STAT   \n",
       "285  HGNC   STAT3      STAT        6774           [STAT]           STAT   \n",
       "286  HGNC   STAT4      STAT        6775           [STAT]           STAT   \n",
       "287  HGNC  STAT5A     STAT5        6776    [STAT, STAT5]           STAT   \n",
       "288  HGNC  STAT5B     STAT5        6777    [STAT, STAT5]           STAT   \n",
       "289  HGNC   STAT6      STAT        6778           [STAT]           STAT   \n",
       "290    BE   STAT5      STAT        6776           [STAT]           STAT   \n",
       "\n",
       "     level_number  \n",
       "283             1  \n",
       "284             1  \n",
       "285             1  \n",
       "286             1  \n",
       "287             2  \n",
       "288             2  \n",
       "289             1  \n",
       "290             1  "
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"hierarchy_apex\"] == \"STAT\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>bioentity</th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>STAT</td>\n",
       "      <td>BE</td>\n",
       "      <td>STAT5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    bioentity type symbol\n",
       "290      STAT   BE  STAT5"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\n",
    "    (joined_df[\"hierarchy_apex\"] == \"STAT\") & (joined_df[\"type\"] == \"BE\")\n",
    "][[\"bioentity\", \"type\", \"symbol\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['6772', '6773', '6774', '6775', '6776', '6776', '6777', '6778']"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"hierarchy_apex\"] == \"STAT\")][\n",
    "    \"ncbigene_id\"\n",
    "].sort_values().dropna().to_list()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## OLD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>hierarchy_path</th>\n",
       "      <th>top_ancestor</th>\n",
       "      <th>hierarchy_levels</th>\n",
       "      <th>hierarchy_apex</th>\n",
       "      <th>level_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT1</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6772</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT2</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6773</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>285</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT3</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6774</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>286</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT4</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6775</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>287</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5A</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6776</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>288</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5B</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6777</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>289</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT6</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6778</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>BE</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6776</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     type  symbol bioentities ncbigene_id hierarchy_path top_ancestor  \\\n",
       "283  HGNC   STAT1        STAT        6772         [STAT]         STAT   \n",
       "284  HGNC   STAT2        STAT        6773         [STAT]         STAT   \n",
       "285  HGNC   STAT3        STAT        6774         [STAT]         STAT   \n",
       "286  HGNC   STAT4        STAT        6775         [STAT]         STAT   \n",
       "287  HGNC  STAT5A       STAT5        6776  [STAT, STAT5]         STAT   \n",
       "288  HGNC  STAT5B       STAT5        6777  [STAT, STAT5]         STAT   \n",
       "289  HGNC   STAT6        STAT        6778         [STAT]         STAT   \n",
       "290    BE   STAT5        STAT        6776         [STAT]         STAT   \n",
       "\n",
       "    hierarchy_levels hierarchy_apex  level_number  \n",
       "283           [STAT]           STAT             1  \n",
       "284           [STAT]           STAT             1  \n",
       "285           [STAT]           STAT             1  \n",
       "286           [STAT]           STAT             1  \n",
       "287    [STAT, STAT5]           STAT             2  \n",
       "288    [STAT, STAT5]           STAT             2  \n",
       "289           [STAT]           STAT             1  \n",
       "290           [STAT]           STAT             1  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"bioentities\"].str.startswith(\"STAT\"))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 331,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
       "      <th>genealogy_chunks</th>\n",
       "      <th>top_ancestor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT1</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6772</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>284</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT2</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6773</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>285</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT3</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6774</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>286</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT4</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6775</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>287</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5A</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6776</td>\n",
       "      <td>STAT,STAT5</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>288</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT5B</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>6777</td>\n",
       "      <td>STAT,STAT5</td>\n",
       "      <td>[STAT, STAT5]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>289</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>STAT6</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6778</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>BE</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6776</td>\n",
       "      <td>STAT</td>\n",
       "      <td>[STAT]</td>\n",
       "      <td>STAT</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     type  symbol bioentities ncbigene_id   genealogy genealogy_chunks  \\\n",
       "283  HGNC   STAT1        STAT        6772        STAT           [STAT]   \n",
       "284  HGNC   STAT2        STAT        6773        STAT           [STAT]   \n",
       "285  HGNC   STAT3        STAT        6774        STAT           [STAT]   \n",
       "286  HGNC   STAT4        STAT        6775        STAT           [STAT]   \n",
       "287  HGNC  STAT5A       STAT5        6776  STAT,STAT5    [STAT, STAT5]   \n",
       "288  HGNC  STAT5B       STAT5        6777  STAT,STAT5    [STAT, STAT5]   \n",
       "289  HGNC   STAT6        STAT        6778        STAT           [STAT]   \n",
       "290    BE   STAT5        STAT        6776        STAT           [STAT]   \n",
       "\n",
       "    top_ancestor  \n",
       "283         STAT  \n",
       "284         STAT  \n",
       "285         STAT  \n",
       "286         STAT  \n",
       "287         STAT  \n",
       "288         STAT  \n",
       "289         STAT  \n",
       "290         STAT  "
      ]
     },
     "execution_count": 331,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"bioentities\"].str.startswith(\"STAT\"))]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "MAP2K == MEK == MAPKK"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 335,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
       "      <th>genealogy_chunks</th>\n",
       "      <th>top_ancestor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>623</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K1</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5604</td>\n",
       "      <td>MAPKK,MAP2K,MEK</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>624</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K2</td>\n",
       "      <td>MEK</td>\n",
       "      <td>5605</td>\n",
       "      <td>MAPKK,MAP2K,MEK</td>\n",
       "      <td>[MAPKK, MAP2K, MEK]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>625</th>\n",
       "      <td>BE</td>\n",
       "      <td>MEK</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>626</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K3</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5606</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>627</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K4</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>6416</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>628</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K5</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5607</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>629</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K6</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5608</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>630</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>MAP2K7</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>5609</td>\n",
       "      <td>MAPKK,MAP2K</td>\n",
       "      <td>[MAPKK, MAP2K]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2240</th>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>NaN</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>[MAPKK]</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type  symbol bioentities ncbigene_id        genealogy  \\\n",
       "623   HGNC  MAP2K1         MEK        5604  MAPKK,MAP2K,MEK   \n",
       "624   HGNC  MAP2K2         MEK        5605  MAPKK,MAP2K,MEK   \n",
       "625     BE     MEK       MAP2K         NaN      MAPKK,MAP2K   \n",
       "626   HGNC  MAP2K3       MAP2K        5606      MAPKK,MAP2K   \n",
       "627   HGNC  MAP2K4       MAP2K        6416      MAPKK,MAP2K   \n",
       "628   HGNC  MAP2K5       MAP2K        5607      MAPKK,MAP2K   \n",
       "629   HGNC  MAP2K6       MAP2K        5608      MAPKK,MAP2K   \n",
       "630   HGNC  MAP2K7       MAP2K        5609      MAPKK,MAP2K   \n",
       "2240    BE   MAP2K       MAPKK         NaN            MAPKK   \n",
       "\n",
       "         genealogy_chunks top_ancestor  \n",
       "623   [MAPKK, MAP2K, MEK]        MAPKK  \n",
       "624   [MAPKK, MAP2K, MEK]        MAPKK  \n",
       "625        [MAPKK, MAP2K]        MAPKK  \n",
       "626        [MAPKK, MAP2K]        MAPKK  \n",
       "627        [MAPKK, MAP2K]        MAPKK  \n",
       "628        [MAPKK, MAP2K]        MAPKK  \n",
       "629        [MAPKK, MAP2K]        MAPKK  \n",
       "630        [MAPKK, MAP2K]        MAPKK  \n",
       "2240              [MAPKK]        MAPKK  "
      ]
     },
     "execution_count": 335,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\n",
    "    (joined_df[\"bioentities\"] == \"MAP2K\")\n",
    "    | (joined_df[\"bioentities\"] == \"MAPKK\")\n",
    "    | (joined_df[\"bioentities\"] == \"MEK\")\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"MAP2K\"))\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"MAPKK\"))\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"MEK\"))\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 330,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
       "      <th>genealogy_chunks</th>\n",
       "      <th>top_ancestor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP1</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1978</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP2</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1979</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>8637</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>[EIF4EBP]</td>\n",
       "      <td>EIF4EBP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA1</td>\n",
       "      <td>Actin</td>\n",
       "      <td>58</td>\n",
       "      <td>Actin</td>\n",
       "      <td>[Actin]</td>\n",
       "      <td>Actin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA2</td>\n",
       "      <td>Actin</td>\n",
       "      <td>59</td>\n",
       "      <td>Actin</td>\n",
       "      <td>[Actin]</td>\n",
       "      <td>Actin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2296</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3691</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2297</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3693</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3694</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3695</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3696</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>[Integrin]</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1947 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentities ncbigene_id genealogy genealogy_chunks  \\\n",
       "0     HGNC  EIF4EBP1     EIF4EBP        1978   EIF4EBP        [EIF4EBP]   \n",
       "1     HGNC  EIF4EBP2     EIF4EBP        1979   EIF4EBP        [EIF4EBP]   \n",
       "2     HGNC  EIF4EBP3     EIF4EBP        8637   EIF4EBP        [EIF4EBP]   \n",
       "3     HGNC     ACTA1       Actin          58     Actin          [Actin]   \n",
       "4     HGNC     ACTA2       Actin          59     Actin          [Actin]   \n",
       "...    ...       ...         ...         ...       ...              ...   \n",
       "2296  HGNC     ITGB4    Integrin        3691  Integrin       [Integrin]   \n",
       "2297  HGNC     ITGB5    Integrin        3693  Integrin       [Integrin]   \n",
       "2298  HGNC     ITGB6    Integrin        3694  Integrin       [Integrin]   \n",
       "2299  HGNC     ITGB7    Integrin        3695  Integrin       [Integrin]   \n",
       "2300  HGNC     ITGB8    Integrin        3696  Integrin       [Integrin]   \n",
       "\n",
       "     top_ancestor  \n",
       "0         EIF4EBP  \n",
       "1         EIF4EBP  \n",
       "2         EIF4EBP  \n",
       "3           Actin  \n",
       "4           Actin  \n",
       "...           ...  \n",
       "2296     Integrin  \n",
       "2297     Integrin  \n",
       "2298     Integrin  \n",
       "2299     Integrin  \n",
       "2300     Integrin  \n",
       "\n",
       "[1947 rows x 7 columns]"
      ]
     },
     "execution_count": 330,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"bioentities\"] == joined_df[\"top_ancestor\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 312,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBA</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>3624</td>\n",
       "      <td>Activin,Activin_A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBA</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>3624</td>\n",
       "      <td>Activin,Activin_AB</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBB</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>3625</td>\n",
       "      <td>Activin,Activin_AB</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBB</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>3625</td>\n",
       "      <td>Activin,Activin_B</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHA</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>3623</td>\n",
       "      <td>Inhibin,Inhibin_A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2158</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN1C</td>\n",
       "      <td>CDKN1</td>\n",
       "      <td>1028</td>\n",
       "      <td>CDKN,CDKN1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2159</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN2A</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>1029</td>\n",
       "      <td>CDKN,CDKN2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2160</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN2B</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>1030</td>\n",
       "      <td>CDKN,CDKN2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2161</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN2C</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>1031</td>\n",
       "      <td>CDKN,CDKN2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2162</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN2D</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>1032</td>\n",
       "      <td>CDKN,CDKN2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>354 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type  symbol bioentities ncbigene_id           genealogy\n",
       "14    HGNC   INHBA   Activin_A        3624   Activin,Activin_A\n",
       "15    HGNC   INHBA  Activin_AB        3624  Activin,Activin_AB\n",
       "16    HGNC   INHBB  Activin_AB        3625  Activin,Activin_AB\n",
       "17    HGNC   INHBB   Activin_B        3625   Activin,Activin_B\n",
       "18    HGNC    INHA   Inhibin_A        3623   Inhibin,Inhibin_A\n",
       "...    ...     ...         ...         ...                 ...\n",
       "2158  HGNC  CDKN1C       CDKN1        1028          CDKN,CDKN1\n",
       "2159  HGNC  CDKN2A       CDKN2        1029          CDKN,CDKN2\n",
       "2160  HGNC  CDKN2B       CDKN2        1030          CDKN,CDKN2\n",
       "2161  HGNC  CDKN2C       CDKN2        1031          CDKN,CDKN2\n",
       "2162  HGNC  CDKN2D       CDKN2        1032          CDKN,CDKN2\n",
       "\n",
       "[354 rows x 5 columns]"
      ]
     },
     "execution_count": 312,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\n",
    "    (joined_df[\"genealogy\"].str.contains(\",\"))\n",
    "    & (joined_df[\"genealogy\"].notnull())\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 265,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AMPK\n",
      "AP1\n",
      "ATP_synthase\n",
      "Actin\n",
      "Activin\n",
      "Apolipoprotein\n",
      "CAMK\n",
      "CDKN\n",
      "COX\n",
      "Caspase\n",
      "Chemokine\n",
      "Cyclin\n",
      "GRK\n",
      "Galpha\n",
      "HDAC\n",
      "HIF\n",
      "HSP90\n",
      "HSP90A\n",
      "['HSP90']\n",
      "HSP90\n",
      "['HSP90']\n",
      "Inhibin\n",
      "['HSP90']\n",
      "Interferon\n",
      "['HSP90']\n",
      "MAP2K\n",
      "['MAPKK']\n",
      "MAPKK\n",
      "['MAPKK', 'HSP90']\n",
      "MAP3K\n",
      "['MAPKK', 'HSP90']\n",
      "MAPK\n",
      "['MAPKK', 'HSP90']\n",
      "MAPKK\n",
      "['MAPKK', 'HSP90']\n",
      "MYL\n",
      "['MAPKK', 'HSP90']\n",
      "NFKB\n",
      "['MAPKK', 'HSP90']\n",
      "NRG\n",
      "['MAPKK', 'HSP90']\n",
      "Na_K_ATPase\n",
      "['MAPKK', 'HSP90']\n",
      "PDE\n",
      "['MAPKK', 'HSP90']\n",
      "PI3K\n",
      "['MAPKK', 'HSP90']\n",
      "PIK3R_I\n",
      "['PI3K']\n",
      "PI3K\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PKA\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PLA2\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PLC\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PPP1\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PPP2\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "PPP3\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "RSK\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "SMAD\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "STAT\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "Troponin\n",
      "['PI3K', 'MAPKK', 'HSP90']\n",
      "Tubulin\n",
      "['PI3K', 'MAPKK', 'HSP90']\n"
     ]
    }
   ],
   "source": [
    "i = 0\n",
    "myd = dict()\n",
    "\n",
    "for bioentities, df in joined_df[joined_df[\"type\"] == \"BE\"].groupby(\n",
    "    \"bioentities\"\n",
    "):\n",
    "    result = get_parents(bioentities)\n",
    "    if len(result) > 0:\n",
    "        print(result)\n",
    "    #    print(bioentities)\n",
    "    #    print(df)\n",
    "    #    mysd = dict()\n",
    "    #    myd[\"bioentities\"] = mysd\n",
    "\n",
    "    #    parent = joined_df[joined_df[\"symbol\"] == bioentities]\n",
    "    #    has_parent = len(parent) > 0\n",
    "    #    print(has_parent)\n",
    "\n",
    "    #    for s in df[\"symbol\"].to_list():\n",
    "    #        children = joined_df[joined_df[\"bioentities\"] == s]\n",
    "    #        mysd[\"children\"] = children\n",
    "    #        has_children = len(children) > 0\n",
    "    #        print(has_children)\n",
    "    #        # print(j)\n",
    "    #        # print(s)\n",
    "    #        # display(joined_df[joined_df[\"bioentities\"] == s])\n",
    "    i += 1\n",
    "    if int(i) > 100:\n",
    "        break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 226,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead tr th {\n",
       "        text-align: left;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr>\n",
       "      <th></th>\n",
       "      <th colspan=\"2\" halign=\"left\">weight</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th></th>\n",
       "      <th>kg</th>\n",
       "      <th>pounds</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>cat</th>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>dog</th>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    weight       \n",
       "        kg pounds\n",
       "cat      1      2\n",
       "dog      2      4"
      ]
     },
     "execution_count": 226,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "multicol1 = pd.MultiIndex.from_tuples([(\"weight\", \"kg\"), (\"weight\", \"pounds\")])\n",
    "df_multi_level_cols1 = pd.DataFrame(\n",
    "    [[1, 2], [2, 4]], index=[\"cat\", \"dog\"], columns=multicol1\n",
    ")\n",
    "df_multi_level_cols1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 227,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>weight</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">cat</th>\n",
       "      <th>kg</th>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pounds</th>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">dog</th>\n",
       "      <th>kg</th>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pounds</th>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            weight\n",
       "cat kg           1\n",
       "    pounds       2\n",
       "dog kg           2\n",
       "    pounds       4"
      ]
     },
     "execution_count": 227,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_multi_level_cols1.stack()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 229,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>bioentities</th>\n",
       "      <th>symbol</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"3\" valign=\"top\">EIF4EBP</th>\n",
       "      <th>EIF4EBP1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>1978</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EIF4EBP2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>1979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EIF4EBP3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>8637</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">Actin</th>\n",
       "      <th>ACTA1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACTA2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">Integrin</th>\n",
       "      <th>ITGB4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>3691</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ITGB5</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>3693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ITGB6</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>3694</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ITGB7</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>3695</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ITGB8</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>3696</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2301 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      type ncbigene_id\n",
       "bioentities symbol                    \n",
       "EIF4EBP     EIF4EBP1  HGNC        1978\n",
       "            EIF4EBP2  HGNC        1979\n",
       "            EIF4EBP3  HGNC        8637\n",
       "Actin       ACTA1     HGNC          58\n",
       "            ACTA2     HGNC          59\n",
       "...                    ...         ...\n",
       "Integrin    ITGB4     HGNC        3691\n",
       "            ITGB5     HGNC        3693\n",
       "            ITGB6     HGNC        3694\n",
       "            ITGB7     HGNC        3695\n",
       "            ITGB8     HGNC        3696\n",
       "\n",
       "[2301 rows x 2 columns]"
      ]
     },
     "execution_count": 229,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "multi_df = joined_df.copy().set_index([\"bioentities\", \"symbol\"])\n",
    "multi_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 237,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>symbol</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>STAT1</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>6772</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STAT2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>6773</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STAT3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>6774</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STAT4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>6775</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STAT6</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>6778</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STAT5</th>\n",
       "      <td>BE</td>\n",
       "      <td>6776</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        type ncbigene_id\n",
       "symbol                  \n",
       "STAT1   HGNC        6772\n",
       "STAT2   HGNC        6773\n",
       "STAT3   HGNC        6774\n",
       "STAT4   HGNC        6775\n",
       "STAT6   HGNC        6778\n",
       "STAT5     BE        6776"
      ]
     },
     "execution_count": 237,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "multi_df.loc[\"STAT\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 230,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['type', 'ncbigene_id'], dtype='object')"
      ]
     },
     "execution_count": 230,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "multi_df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 234,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'EIF4EBP'"
      ]
     },
     "execution_count": 234,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "multi_df.index[0][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 225,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2127</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_I</td>\n",
       "      <td>Troponin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2128</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_T</td>\n",
       "      <td>Troponin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2163</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN1</td>\n",
       "      <td>CDKN</td>\n",
       "      <td>1026</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2164</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>CDKN</td>\n",
       "      <td>1029</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2240</th>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>MAPKK</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>102 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     type      symbol bioentities ncbigene_id\n",
       "9      BE   Activin_A     Activin         NaN\n",
       "10     BE  Activin_AB     Activin         NaN\n",
       "11     BE   Activin_B     Activin         NaN\n",
       "12     BE   Inhibin_A     Inhibin         NaN\n",
       "13     BE   Inhibin_B     Inhibin         NaN\n",
       "...   ...         ...         ...         ...\n",
       "2127   BE  Troponin_I    Troponin         NaN\n",
       "2128   BE  Troponin_T    Troponin         NaN\n",
       "2163   BE       CDKN1        CDKN        1026\n",
       "2164   BE       CDKN2        CDKN        1029\n",
       "2240   BE       MAP2K       MAPKK         NaN\n",
       "\n",
       "[102 rows x 4 columns]"
      ]
     },
     "execution_count": 225,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"type\"] == \"BE\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 222,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>190</th>\n",
       "      <td>BE</td>\n",
       "      <td>ERK</td>\n",
       "      <td>MAPK</td>\n",
       "      <td>2048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>BE</td>\n",
       "      <td>STAT5</td>\n",
       "      <td>STAT</td>\n",
       "      <td>6776</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>374</th>\n",
       "      <td>BE</td>\n",
       "      <td>TUBB</td>\n",
       "      <td>Tubulin</td>\n",
       "      <td>203068</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>375</th>\n",
       "      <td>BE</td>\n",
       "      <td>TUBG</td>\n",
       "      <td>Tubulin</td>\n",
       "      <td>7283</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>498</th>\n",
       "      <td>BE</td>\n",
       "      <td>IFNA</td>\n",
       "      <td>Interferon</td>\n",
       "      <td>3440</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>499</th>\n",
       "      <td>BE</td>\n",
       "      <td>IFNB</td>\n",
       "      <td>Interferon</td>\n",
       "      <td>3456</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>710</th>\n",
       "      <td>BE</td>\n",
       "      <td>p38</td>\n",
       "      <td>MAPK</td>\n",
       "      <td>7965</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>952</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX4</td>\n",
       "      <td>COX</td>\n",
       "      <td>1327</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>953</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX6A</td>\n",
       "      <td>COX</td>\n",
       "      <td>1337</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>954</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX6B</td>\n",
       "      <td>COX</td>\n",
       "      <td>1340</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>955</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX7A</td>\n",
       "      <td>COX</td>\n",
       "      <td>1346</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>956</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX7B</td>\n",
       "      <td>COX</td>\n",
       "      <td>1349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>957</th>\n",
       "      <td>BE</td>\n",
       "      <td>COX8</td>\n",
       "      <td>COX</td>\n",
       "      <td>1351</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1293</th>\n",
       "      <td>BE</td>\n",
       "      <td>JNK</td>\n",
       "      <td>MAPK</td>\n",
       "      <td>5599</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1457</th>\n",
       "      <td>BE</td>\n",
       "      <td>PLA2G4</td>\n",
       "      <td>PLA2</td>\n",
       "      <td>5321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1997</th>\n",
       "      <td>BE</td>\n",
       "      <td>ATP1B</td>\n",
       "      <td>Na_K_ATPase</td>\n",
       "      <td>481</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2052</th>\n",
       "      <td>BE</td>\n",
       "      <td>ATP5G</td>\n",
       "      <td>ATP_synthase</td>\n",
       "      <td>516</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2163</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN1</td>\n",
       "      <td>CDKN</td>\n",
       "      <td>1026</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2164</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>CDKN</td>\n",
       "      <td>1029</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     type  symbol   bioentities ncbigene_id\n",
       "190    BE     ERK          MAPK        2048\n",
       "290    BE   STAT5          STAT        6776\n",
       "374    BE    TUBB       Tubulin      203068\n",
       "375    BE    TUBG       Tubulin        7283\n",
       "498    BE    IFNA    Interferon        3440\n",
       "499    BE    IFNB    Interferon        3456\n",
       "710    BE     p38          MAPK        7965\n",
       "952    BE    COX4           COX        1327\n",
       "953    BE   COX6A           COX        1337\n",
       "954    BE   COX6B           COX        1340\n",
       "955    BE   COX7A           COX        1346\n",
       "956    BE   COX7B           COX        1349\n",
       "957    BE    COX8           COX        1351\n",
       "1293   BE     JNK          MAPK        5599\n",
       "1457   BE  PLA2G4          PLA2        5321\n",
       "1997   BE   ATP1B   Na_K_ATPase         481\n",
       "2052   BE   ATP5G  ATP_synthase         516\n",
       "2163   BE   CDKN1          CDKN        1026\n",
       "2164   BE   CDKN2          CDKN        1029"
      ]
     },
     "execution_count": 222,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[(joined_df[\"ncbigene_id\"].notnull()) & (joined_df[\"type\"] == \"BE\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 315,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHA</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>3623</td>\n",
       "      <td>Inhibin,Inhibin_A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBA</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>3624</td>\n",
       "      <td>Inhibin,Inhibin_A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHA</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>3623</td>\n",
       "      <td>Inhibin,Inhibin_B</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>INHBB</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>3625</td>\n",
       "      <td>Inhibin,Inhibin_B</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    type     symbol bioentities ncbigene_id          genealogy\n",
       "12    BE  Inhibin_A     Inhibin         NaN            Inhibin\n",
       "13    BE  Inhibin_B     Inhibin         NaN            Inhibin\n",
       "18  HGNC       INHA   Inhibin_A        3623  Inhibin,Inhibin_A\n",
       "19  HGNC      INHBA   Inhibin_A        3624  Inhibin,Inhibin_A\n",
       "20  HGNC       INHA   Inhibin_B        3623  Inhibin,Inhibin_B\n",
       "21  HGNC      INHBB   Inhibin_B        3625  Inhibin,Inhibin_B"
      ]
     },
     "execution_count": 315,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"genealogy\"].str.contains(\"Inhibin\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 316,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>ncbigene_id</th>\n",
       "      <th>genealogy</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP1</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>1978</td>\n",
       "      <td>EIF4EBP</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HGNC</td>\n",
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       "      <td>EIF4EBP</td>\n",
       "      <td>1979</td>\n",
       "      <td>EIF4EBP</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
       "      <td>EIF4EBP</td>\n",
       "      <td>8637</td>\n",
       "      <td>EIF4EBP</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA1</td>\n",
       "      <td>Actin</td>\n",
       "      <td>58</td>\n",
       "      <td>Actin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ACTA2</td>\n",
       "      <td>Actin</td>\n",
       "      <td>59</td>\n",
       "      <td>Actin</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2296</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3691</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2297</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3693</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3694</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3695</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3696</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1947 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentities ncbigene_id genealogy\n",
       "0     HGNC  EIF4EBP1     EIF4EBP        1978   EIF4EBP\n",
       "1     HGNC  EIF4EBP2     EIF4EBP        1979   EIF4EBP\n",
       "2     HGNC  EIF4EBP3     EIF4EBP        8637   EIF4EBP\n",
       "3     HGNC     ACTA1       Actin          58     Actin\n",
       "4     HGNC     ACTA2       Actin          59     Actin\n",
       "...    ...       ...         ...         ...       ...\n",
       "2296  HGNC     ITGB4    Integrin        3691  Integrin\n",
       "2297  HGNC     ITGB5    Integrin        3693  Integrin\n",
       "2298  HGNC     ITGB6    Integrin        3694  Integrin\n",
       "2299  HGNC     ITGB7    Integrin        3695  Integrin\n",
       "2300  HGNC     ITGB8    Integrin        3696  Integrin\n",
       "\n",
       "[1947 rows x 5 columns]"
      ]
     },
     "execution_count": 316,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"genealogy\"] == joined_df[\"bioentities\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 323,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <tbody>\n",
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       "      <th>2</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>EIF4EBP3</td>\n",
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       "      <td>Actin</td>\n",
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       "      <th>4</th>\n",
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       "      <td>Actin</td>\n",
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       "      <th>2296</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB4</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3691</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2297</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB5</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3693</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2298</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB6</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3694</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2299</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB7</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3695</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2300</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>ITGB8</td>\n",
       "      <td>Integrin</td>\n",
       "      <td>3696</td>\n",
       "      <td>Integrin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1947 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type    symbol bioentities ncbigene_id genealogy\n",
       "0     HGNC  EIF4EBP1     EIF4EBP        1978   EIF4EBP\n",
       "1     HGNC  EIF4EBP2     EIF4EBP        1979   EIF4EBP\n",
       "2     HGNC  EIF4EBP3     EIF4EBP        8637   EIF4EBP\n",
       "3     HGNC     ACTA1       Actin          58     Actin\n",
       "4     HGNC     ACTA2       Actin          59     Actin\n",
       "...    ...       ...         ...         ...       ...\n",
       "2296  HGNC     ITGB4    Integrin        3691  Integrin\n",
       "2297  HGNC     ITGB5    Integrin        3693  Integrin\n",
       "2298  HGNC     ITGB6    Integrin        3694  Integrin\n",
       "2299  HGNC     ITGB7    Integrin        3695  Integrin\n",
       "2300  HGNC     ITGB8    Integrin        3696  Integrin\n",
       "\n",
       "[1947 rows x 5 columns]"
      ]
     },
     "execution_count": 323,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"genealogy\"] == joined_df[\"bioentities\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 328,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0        EIF4EBP\n",
       "1        EIF4EBP\n",
       "2        EIF4EBP\n",
       "3          Actin\n",
       "4          Actin\n",
       "          ...   \n",
       "2296    Integrin\n",
       "2297    Integrin\n",
       "2298    Integrin\n",
       "2299    Integrin\n",
       "2300    Integrin\n",
       "Name: genealogy_chunks, Length: 2301, dtype: object"
      ]
     },
     "execution_count": 328,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 314,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>Inhibin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   type     symbol bioentities ncbigene_id genealogy\n",
       "12   BE  Inhibin_A     Inhibin         NaN   Inhibin\n",
       "13   BE  Inhibin_B     Inhibin         NaN   Inhibin"
      ]
     },
     "execution_count": 314,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[\n",
    "    (joined_df[\"bioentities\"] == \"Inhibin\")\n",
    "    | (joined_df[\"bioentities\"] == \"inhibin\")\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"Inhibin\"))\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"INHBE\"))\n",
    "    | (joined_df[\"symbol\"].str.startswith(\"inhibin\"))\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 215,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "      <th>ncbigene_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>Activin</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   type      symbol bioentities ncbigene_id\n",
       "9    BE   Activin_A     Activin         NaN\n",
       "10   BE  Activin_AB     Activin         NaN\n",
       "11   BE   Activin_B     Activin         NaN"
      ]
     },
     "execution_count": 215,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "joined_df[joined_df[\"symbol\"].str.startswith(\"Activin\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 187,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 187,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 173,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'BE', 'HGNC', 'UP'}"
      ]
     },
     "execution_count": 173,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "set(bioentities_df[\"type\"].to_list())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_A</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BE</td>\n",
       "      <td>Inhibin_B</td>\n",
       "      <td>Inhibin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2136</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_I</td>\n",
       "      <td>Troponin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2137</th>\n",
       "      <td>BE</td>\n",
       "      <td>Troponin_T</td>\n",
       "      <td>Troponin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2172</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN1</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2173</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2249</th>\n",
       "      <td>BE</td>\n",
       "      <td>MAP2K</td>\n",
       "      <td>MAPKK</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>102 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     type      symbol bioentities\n",
       "9      BE   Activin_A     Activin\n",
       "10     BE  Activin_AB     Activin\n",
       "11     BE   Activin_B     Activin\n",
       "12     BE   Inhibin_A     Inhibin\n",
       "13     BE   Inhibin_B     Inhibin\n",
       "...   ...         ...         ...\n",
       "2136   BE  Troponin_I    Troponin\n",
       "2137   BE  Troponin_T    Troponin\n",
       "2172   BE       CDKN1        CDKN\n",
       "2173   BE       CDKN2        CDKN\n",
       "2249   BE       MAP2K       MAPKK\n",
       "\n",
       "[102 rows x 3 columns]"
      ]
     },
     "execution_count": 194,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"type\"] == \"BE\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 197,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2172</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN1</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2173</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2174</th>\n",
       "      <td>HGNC</td>\n",
       "      <td>CDKN3</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      type symbol bioentities\n",
       "2172    BE  CDKN1        CDKN\n",
       "2173    BE  CDKN2        CDKN\n",
       "2174  HGNC  CDKN3        CDKN"
      ]
     },
     "execution_count": 197,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"bioentities\"] == \"CDKN\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 199,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hgnc</th>\n",
       "      <th>ncbigene</th>\n",
       "      <th>variable</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>176696</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>previous_symbol</td>\n",
       "      <td>CDKN1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             hgnc ncbigene         variable  value\n",
       "176696  HGNC:1784     1026  previous_symbol  CDKN1"
      ]
     },
     "execution_count": 199,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hgnc_df[hgnc_df[\"value\"] == \"CDKN1\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 204,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'A1BG': '1',\n",
       " 'RNA5SP48': '100873287',\n",
       " 'RNA5SP49': '100873288',\n",
       " 'RNA5SP50': '106478992',\n",
       " 'RNA5SP51': '100873289',\n",
       " 'RNA5SP52': '100873290',\n",
       " 'RNA5SP53': '100873291',\n",
       " 'RNA5SP54': '100873292',\n",
       " 'RNA5SP55': '100873293',\n",
       " 'RNA5SP56': '100873294',\n",
       " 'RNA5SP57': '106480754',\n",
       " 'RNA5SP59': '106480357',\n",
       " 'RNA5SP60': '100873295',\n",
       " 'RNA5SP61': '100873296',\n",
       " 'RNA5SP62': '100873297',\n",
       " 'RNA5SP63': '100873298',\n",
       " 'RNA5SP47': '100873286',\n",
       " 'RNA5SP46': '100873285',\n",
       " 'RNA5SP45': '100873284',\n",
       " 'RNA5SP44': '100873283',\n",
       " 'RNA5SP27': '100873359',\n",
       " 'RNA5SP28': '100873360',\n",
       " 'RNA5SP29': '100873361',\n",
       " 'RNA5SP30': '100873362',\n",
       " 'RNA5SP31': '100873363',\n",
       " 'RNA5SP33': '100873365',\n",
       " 'RNA5SP34': '100873366',\n",
       " 'RNA5SP64': '100873299',\n",
       " 'RNA5SP35': '100873367',\n",
       " 'RNA5SP37': '100873369',\n",
       " 'RNA5SP38': '100873370',\n",
       " 'RNA5SP39': '100873371',\n",
       " 'RNA5SP40': '100873279',\n",
       " 'RNA5SP41': '100873280',\n",
       " 'RNA5SP42': '100873281',\n",
       " 'RNA5SP43': '100873282',\n",
       " 'RNA5SP36': '100873368',\n",
       " 'RNA5SP26': '100873358',\n",
       " 'RNA5SP65': '100873300',\n",
       " 'RNA5SP67': '100873302',\n",
       " 'RNA5SP90': '100873323',\n",
       " 'RNA5SP91': '100873324',\n",
       " 'RNA5SP92': '100873325',\n",
       " 'RNA5SP93': '100873326',\n",
       " 'RNA5SP94': '100873327',\n",
       " 'RNA5SP95': '100873328',\n",
       " 'RNA5SP96': '100873329',\n",
       " 'RNA5SP97': '100873330',\n",
       " 'RNA5SP98': '100873331',\n",
       " 'RNA5SP99': '106478993',\n",
       " 'RNA5SP100': '106480755',\n",
       " 'RNA5SP101': '100873372',\n",
       " 'RNA5SP102': '100873373',\n",
       " 'RNA5SP103': '100873374',\n",
       " 'RNA5SP104': '100873375',\n",
       " 'RNA5SP89': '100873322',\n",
       " 'RNA5SP88': '100873321',\n",
       " 'RNA5SP87': '100873320',\n",
       " 'RNA5SP86': '100873319',\n",
       " 'RNA5SP68': '100873303',\n",
       " 'RNA5SP69': '100873304',\n",
       " 'RNA5SP70': '106480436',\n",
       " 'RNA5SP71': '100873305',\n",
       " 'RNA5SP72': '100873306',\n",
       " 'RNA5SP73': '100873307',\n",
       " 'RNA5SP74': '100873308',\n",
       " 'RNA5SP66': '100873301',\n",
       " 'RNA5SP75': '100873309',\n",
       " 'RNA5SP77': '100873311',\n",
       " 'RNA5SP78': '100873312',\n",
       " 'RNA5SP79': '100873313',\n",
       " 'RNA5SP80': '100873314',\n",
       " 'RNA5SP82': '100873316',\n",
       " 'RNA5SP84': '100873317',\n",
       " 'RNA5SP85': '100873318',\n",
       " 'RNA5SP76': '100873310',\n",
       " 'RNA5SP25': '100873357',\n",
       " 'RNA5SP24': '100873356',\n",
       " 'RNA5SP23': '100873278',\n",
       " 'RN7SL850P': '106479532',\n",
       " 'RN7SL851P': '106480537',\n",
       " 'RN7SL853P': '106481153',\n",
       " 'RN7SL854P': '106480383',\n",
       " 'RN7SL856P': '106479533',\n",
       " 'RN7SL860P': '106635537',\n",
       " 'RN7SL861P': '106479534',\n",
       " 'RN7SL862P': '106479535',\n",
       " 'RN7SL863P': '106480538',\n",
       " 'RN7SL864P': '106479536',\n",
       " 'RN7SL865P': '106481154',\n",
       " 'RN7SL868P': '106479537',\n",
       " 'RN7SL869P': '106481864',\n",
       " 'RN7SL870P': '106481155',\n",
       " 'RNA5-8S1': '106632263',\n",
       " 'RN7SL849P': '106479531',\n",
       " 'RN7SL847P': '106481152',\n",
       " 'RN7SL846P': '106479530',\n",
       " 'RN7SL845P': '106481863',\n",
       " 'RN7SL825P': '107080654',\n",
       " 'RN7SL826P': '106479523',\n",
       " 'RN7SL827P': '106481762',\n",
       " 'RN7SL828P': '106481147',\n",
       " 'RN7SL831P': '106481862',\n",
       " 'RN7SL832P': '106479524',\n",
       " 'RN7SL833P': '106479525',\n",
       " 'RNA5-8S2': '106632262',\n",
       " 'RN7SL834P': '106481148',\n",
       " 'RN7SL836P': '106481149',\n",
       " 'RN7SL837P': '106480536',\n",
       " 'RN7SL838P': '106479527',\n",
       " 'RN7SL840P': '106479528',\n",
       " 'RN7SL841P': '106481150',\n",
       " 'RN7SL842P': '106479529',\n",
       " 'RN7SL843P': '106481151',\n",
       " 'RN7SL835P': '106479526',\n",
       " 'RNA5-8S3': '106632261',\n",
       " 'RNA5-8S4': '110255166',\n",
       " 'RNA5-8S5': '110255170',\n",
       " 'RNA5S7': '100169758',\n",
       " 'RNA5S8': '100169759',\n",
       " 'RNA5S9': '100169760',\n",
       " 'RNA5S10': '100169761',\n",
       " 'RNA5S11': '100169762',\n",
       " 'RNA5S12': '100169763',\n",
       " 'RNA5S13': '100169764',\n",
       " 'RNA5S6': '100169757',\n",
       " 'RNA5S14': '100169765',\n",
       " 'RNA5S16': '100169767',\n",
       " 'RNA5S17': '100169768',\n",
       " 'RNA5SP18': '100873273',\n",
       " 'RNA5SP19': '100873274',\n",
       " 'RNA5SP20': '100873275',\n",
       " 'RNA5SP21': '100873276',\n",
       " 'RNA5SP22': '100873277',\n",
       " 'RNA5S15': '100169766',\n",
       " 'RNA5SP105': '100873376',\n",
       " 'RNA5S5': '100169756',\n",
       " 'RNA5S3': '100169754',\n",
       " 'RNA5-8SN1': '106632260',\n",
       " 'RNA5-8SN2': '109864281',\n",
       " 'RNA5-8SN3': '109910381',\n",
       " 'RNA5-8SN4': '109864274',\n",
       " 'RNA5-8SN5': '100008587',\n",
       " 'RNA5-8SP2': '100873571',\n",
       " 'RNA5-8SP3': '100873334',\n",
       " 'RNA5S4': '100169755',\n",
       " 'RNA5-8SP4': '100873572',\n",
       " 'RNA5-8SP6': '100873336',\n",
       " 'RNA5-8SP7': '100873573',\n",
       " 'RNA5-8SP8': '109864278',\n",
       " 'RNA5-8SP9': '109864276',\n",
       " 'RNA5-8SP10': '109910384',\n",
       " 'RNA5S1': '100169751',\n",
       " 'RNA5S2': '100169753',\n",
       " 'RNA5-8SP5': '100873335',\n",
       " 'RNA5SP106': '106478994',\n",
       " 'RNA5SP107': '100873377',\n",
       " 'RNA5SP108': '100873378',\n",
       " 'RNA5SP208': '100873468',\n",
       " 'RNA5SP209': '100873469',\n",
       " 'RNA5SP210': '100873470',\n",
       " 'RNA5SP211': '100873471',\n",
       " 'RNA5SP212': '100873472',\n",
       " 'RNA5SP213': '100873473',\n",
       " 'RNA5SP214': '100873474',\n",
       " 'RNA5SP215': '100873475',\n",
       " 'RNA5SP216': '100873476',\n",
       " 'RNA5SP217': '100873477',\n",
       " 'RNA5SP218': '100873478',\n",
       " 'RNA5SP219': '100873479',\n",
       " 'RNA5SP220': '100873480',\n",
       " 'RNA5SP221': '106480759',\n",
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       " 'RNA5SP207': '100873467',\n",
       " 'RNA5SP206': '106478999',\n",
       " 'RNA5SP205': '100873466',\n",
       " 'RNA5SP204': '100873465',\n",
       " 'RNA5SP188': '100873450',\n",
       " 'RNA5SP189': '100873451',\n",
       " 'RNA5SP190': '100873452',\n",
       " 'RNA5SP191': '100873453',\n",
       " 'RNA5SP192': '100873454',\n",
       " 'RNA5SP193': '100873455',\n",
       " 'RNA5SP194': '100873456',\n",
       " 'RNA5SP223': '100873482',\n",
       " 'RNA5SP195': '100873457',\n",
       " 'RNA5SP197': '100873459',\n",
       " 'RNA5SP198': '100873460',\n",
       " 'RNA5SP199': '106480438',\n",
       " 'RNA5SP200': '100873461',\n",
       " 'RNA5SP201': '100873462',\n",
       " 'RNA5SP202': '100873463',\n",
       " 'RNA5SP203': '100873464',\n",
       " 'RNA5SP196': '100873458',\n",
       " 'RNA5SP224': '100873483',\n",
       " 'RNA5SP225': '100873484',\n",
       " 'RNA5SP226': '106479000',\n",
       " 'RNA5SP247': '100873503',\n",
       " 'RNA5SP248': '100873504',\n",
       " 'RNA5SP249': '100873505',\n",
       " 'RNA5SP250': '100873506',\n",
       " 'RNA5SP251': '100873507',\n",
       " 'RNA5SP252': '100873508',\n",
       " 'RNA5SP253': '106480760',\n",
       " 'RNA5SP246': '100873502',\n",
       " 'RNA5SP254': '106481793',\n",
       " 'RNA5SP256': '100873510',\n",
       " 'RNA5SP257': '100873511',\n",
       " 'RNA5SP258': '100873512',\n",
       " 'RNA5SP259': '100873513',\n",
       " 'RNA5SP260': '100873514',\n",
       " 'RNA5SP261': '100873515',\n",
       " 'RNA5SP262': '100873516',\n",
       " 'RNA5SP255': '100873509',\n",
       " 'RNA5SP187': '100873449',\n",
       " 'RNA5SP245': '100873501',\n",
       " 'RNA5SP243': '106479001',\n",
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       " 'RNA5SP228': '100873486',\n",
       " 'RNA5SP229': '100873487',\n",
       " 'RNA5SP230': '100873488',\n",
       " 'RNA5SP231': '100873489',\n",
       " 'RNA5SP232': '100873490',\n",
       " 'RNA5SP233': '100873491',\n",
       " 'RNA5SP244': '100885864',\n",
       " 'RNA5SP234': '100873492',\n",
       " 'RNA5SP236': '100873494',\n",
       " 'RNA5SP237': '100873495',\n",
       " 'RNA5SP238': '100873496',\n",
       " 'RNA5SP239': '100873497',\n",
       " 'RNA5SP240': '100873498',\n",
       " 'RNA5SP241': '100873499',\n",
       " 'RNA5SP242': '100873500',\n",
       " 'RNA5SP235': '100873493',\n",
       " 'RN7SL824P': '106481146',\n",
       " 'RNA5SP186': '100873448',\n",
       " 'RNA5SP184': '100873446',\n",
       " 'RNA5SP129': '100873399',\n",
       " 'RNA5SP130': '106478995',\n",
       " 'RNA5SP131': '100873400',\n",
       " 'RNA5SP132': '100873401',\n",
       " 'RNA5SP133': '100873402',\n",
       " 'RNA5SP134': '106480756',\n",
       " 'RNA5SP135': '100873403',\n",
       " 'RNA5SP136': '100873404',\n",
       " 'RNA5SP137': '100873405',\n",
       " 'RNA5SP138': '100873406',\n",
       " 'RNA5SP139': '100873407',\n",
       " 'RNA5SP140': '106478996',\n",
       " 'RNA5SP141': '100873408',\n",
       " 'RNA5SP142': '100873409',\n",
       " 'RNA5SP143': '100873410',\n",
       " 'RNA5SP128': '100873398',\n",
       " 'RNA5SP127': '100873397',\n",
       " 'RNA5SP126': '100873396',\n",
       " 'RNA5SP125': '100873395',\n",
       " 'RNA5SP109': '100873379',\n",
       " 'RNA5SP110': '100873380',\n",
       " 'RNA5SP111': '100873381',\n",
       " 'RNA5SP112': '100873382',\n",
       " 'RNA5SP113': '100873383',\n",
       " 'RNA5SP114': '100873384',\n",
       " 'RNA5SP115': '100873385',\n",
       " 'RNA5SP144': '100873411',\n",
       " 'RNA5SP116': '100873386',\n",
       " 'RNA5SP118': '100873388',\n",
       " 'RNA5SP119': '100873389',\n",
       " 'RNA5SP120': '100873390',\n",
       " 'RNA5SP121': '100873391',\n",
       " 'RNA5SP122': '100873392',\n",
       " 'RNA5SP123': '100873393',\n",
       " 'RNA5SP124': '100873394',\n",
       " 'RNA5SP117': '100873387',\n",
       " 'RNA5SP145': '100873412',\n",
       " 'RNA5SP146': '100873413',\n",
       " 'RNA5SP147': '100873414',\n",
       " 'RNA5SP168': '100873433',\n",
       " 'RNA5SP169': '100873434',\n",
       " 'RNA5SP170': '100873435',\n",
       " 'RNA5SP171': '100873436',\n",
       " 'RNA5SP172': '106478997',\n",
       " 'RNA5SP173': '100873437',\n",
       " 'RNA5SP174': '106478998',\n",
       " 'RNA5SP167': '100873432',\n",
       " 'RNA5SP175': '106480758',\n",
       " 'RNA5SP177': '100873439',\n",
       " 'RNA5SP178': '100873440',\n",
       " 'RNA5SP179': '100873441',\n",
       " 'RNA5SP180': '100873442',\n",
       " 'RNA5SP181': '100873443',\n",
       " 'RNA5SP182': '100873444',\n",
       " 'RNA5SP183': '100873445',\n",
       " 'RNA5SP176': '100873438',\n",
       " 'RNA5SP185': '100873447',\n",
       " 'RNA5SP166': '100873431',\n",
       " 'RNA5SP164': '100873429',\n",
       " 'RNA5SP148': '100873415',\n",
       " 'RNA5SP149': '106480437',\n",
       " 'RNA5SP150': '100873416',\n",
       " 'RNA5SP151': '100873417',\n",
       " 'RNA5SP152': '100873418',\n",
       " 'RNA5SP153': '100873419',\n",
       " 'RNA5SP154': '100873420',\n",
       " 'RNA5SP165': '100873430',\n",
       " 'RNA5SP155': '100873421',\n",
       " 'RNA5SP157': '100873423',\n",
       " 'RNA5SP158': '100873424',\n",
       " 'RNA5SP159': '100873425',\n",
       " 'RNA5SP160': '100873426',\n",
       " 'RNA5SP161': '106480757',\n",
       " 'RNA5SP162': '100873427',\n",
       " 'RNA5SP163': '100873428',\n",
       " 'RNA5SP156': '100873422',\n",
       " 'RN7SL823P': '106479522',\n",
       " 'RN7SL822P': '106479521',\n",
       " 'RN7SL820P': '106480535',\n",
       " 'RN7SL554P': '106479423',\n",
       " 'RN7SL555P': '106479424',\n",
       " 'RN7SL556P': '106481073',\n",
       " 'RN7SL557P': '106479425',\n",
       " 'RN7SL558P': '106481074',\n",
       " 'RN7SL559P': '106481849',\n",
       " 'RN7SL560P': '106479426',\n",
       " 'RN7SL561P': '106481075',\n",
       " 'RN7SL563P': '106479427',\n",
       " 'RN7SL564P': '106479428',\n",
       " 'RN7SL565P': '106481076',\n",
       " 'RN7SL566P': '106481850',\n",
       " 'RN7SL567P': '106481976',\n",
       " 'RN7SL568P': '106479429',\n",
       " 'RN7SL569P': '106481077',\n",
       " 'RN7SL553P': '106480518',\n",
       " 'RN7SL552P': '106481072',\n",
       " 'RN7SL551P': '106479422',\n",
       " 'RN7SL549P': '106481071',\n",
       " 'RN7SL524P': '106481066',\n",
       " 'RN7SL525P': '106480516',\n",
       " 'RN7SL526P': '106479415',\n",
       " 'RN7SL530P': '106481067',\n",
       " 'RN7SL531P': '106479416',\n",
       " 'RN7SL535P': '106479417',\n",
       " 'RN7SL536P': '106481068',\n",
       " 'RN7SL570P': '106479430',\n",
       " 'RN7SL538P': '106480517',\n",
       " 'RN7SL541P': '106481069',\n",
       " 'RN7SL542P': '106479419',\n",
       " 'RN7SL543P': '106480378',\n",
       " 'RN7SL544P': '106481070',\n",
       " 'RN7SL545P': '106481848',\n",
       " 'RN7SL546P': '106479420',\n",
       " 'RN7SL547P': '106479421',\n",
       " 'RN7SL539P': '106479418',\n",
       " 'RN7SL571P': '106479431',\n",
       " 'RN7SL573P': '106481078',\n",
       " 'RN7SL574P': '106481079',\n",
       " 'RN7SL602P': '106479441',\n",
       " 'RN7SL604P': '106479442',\n",
       " 'RN7SL605P': '106481087',\n",
       " 'RN7SL606P': '106479443',\n",
       " 'RN7SL607P': '106481088',\n",
       " 'RN7SL608P': '106480521',\n",
       " 'RN7SL610P': '106479444',\n",
       " 'RN7SL601P': '106480520',\n",
       " 'RN7SL612P': '106479445',\n",
       " 'RN7SL615P': '106479446',\n",
       " 'RN7SL616P': '106481090',\n",
       " 'RN7SL617P': '106481852',\n",
       " 'RN7SL618P': '106479447',\n",
       " 'RN7SL619P': '106481091',\n",
       " 'RN7SL620P': '106479448',\n",
       " 'RN7SL621P': '106479449',\n",
       " 'RN7SL614P': '106481089',\n",
       " 'RN7SL523P': '106479414',\n",
       " 'RN7SL600P': '106481086',\n",
       " 'RN7SL597P': '106479440',\n",
       " 'RN7SL575P': '106479432',\n",
       " 'RN7SL577P': '106481080',\n",
       " 'RN7SL578P': '106479433',\n",
       " 'RN7SL580P': '106481081',\n",
       " 'RN7SL581P': '106479434',\n",
       " 'RN7SL582P': '106479435',\n",
       " 'RN7SL583P': '106481082',\n",
       " 'RN7SL598P': '106481759',\n",
       " 'RN7SL584P': '106480519',\n",
       " 'RN7SL586P': '106481083',\n",
       " 'RN7SL587P': '106479437',\n",
       " 'RN7SL589P': '106479438',\n",
       " 'RN7SL591P': '106481084',\n",
       " 'RN7SL592P': '106481851',\n",
       " 'RN7SL594P': '106479439',\n",
       " 'RN7SL596P': '106481085',\n",
       " 'RN7SL585P': '106479436',\n",
       " 'RN7SL622P': '106481092',\n",
       " 'RN7SL521P': '106479413',\n",
       " 'RN7SL519P': '106479412',\n",
       " 'RN7SL452P': '106479387',\n",
       " 'RN7SL453P': '106481046',\n",
       " 'RN7SL454P': '106479388',\n",
       " 'RN7SL455P': '106479389',\n",
       " 'RN7SL456P': '106480511',\n",
       " 'RN7SL457P': '106481047',\n",
       " 'RN7SL459P': '106479390',\n",
       " 'RN7SL460P': '106481048',\n",
       " 'RN7SL461P': '106481844',\n",
       " 'RN7SL462P': '106479391',\n",
       " 'RN7SL464P': '106481049',\n",
       " 'RN7SL465P': '106479392',\n",
       " 'RN7SL466P': '106479393',\n",
       " 'RN7SL468P': '106481050',\n",
       " 'RN7SL469P': '106480512',\n",
       " 'RN7SL451P': '106480377',\n",
       " 'RN7SL449P': '106481045',\n",
       " 'RN7SL448P': '106481843',\n",
       " 'RN7SL447P': '106479386',\n",
       " 'RN7SL426P': '106481842',\n",
       " 'RN7SL428P': '106479379',\n",
       " 'RN7SL429P': '106479380',\n",
       " 'RN7SL430P': '106481040',\n",
       " 'RN7SL431P': '106866913',\n",
       " 'RN7SL432P': '106481041',\n",
       " 'RN7SL434P': '106480509',\n",
       " 'RN7SL470P': '106479394',\n",
       " 'RN7SL435P': '106479381',\n",
       " 'RN7SL440P': '106481042',\n",
       " 'RN7SL441P': '106479383',\n",
       " 'RN7SL442P': '106481043',\n",
       " 'RN7SL443P': '106480510',\n",
       " 'RN7SL444P': '106479384',\n",
       " 'RN7SL445P': '106481044',\n",
       " 'RN7SL446P': '106479385',\n",
       " 'RN7SL438P': '106479382',\n",
       " 'RN7SL471P': '106481051',\n",
       " 'RN7SL472P': '106479395',\n",
       " 'RN7SL473P': '106479396',\n",
       " 'RN7SL498P': '106479405',\n",
       " 'RN7SL499P': '106481059',\n",
       " 'RN7SL500P': '106479406',\n",
       " 'RN7SL502P': '106479407',\n",
       " 'RN7SL503P': '106481060',\n",
       " 'RN7SL504P': '106480515',\n",
       " 'RN7SL505P': '106481758',\n",
       " 'RN7SL497P': '106481846',\n",
       " 'RN7SL507P': '106479408',\n",
       " 'RN7SL509P': '106479409',\n",
       " 'RN7SL510P': '106479410',\n",
       " 'RN7SL513P': '106481062',\n",
       " 'RN7SL515P': '106481063',\n",
       " 'RN7SL516P': '106479411',\n",
       " 'RN7SL517P': '106481064',\n",
       " 'RN7SL518P': '106481847',\n",
       " 'RN7SL508P': '106481061',\n",
       " 'RN7SL520P': '106481065',\n",
       " 'RN7SL496P': '106481058',\n",
       " 'RN7SL494P': '106481057',\n",
       " 'RN7SL474P': '106481052',\n",
       " 'RN7SL475P': '106481845',\n",
       " 'RN7SL477P': '106479397',\n",
       " 'RN7SL478P': '106481053',\n",
       " 'RN7SL479P': '106479398',\n",
       " 'RN7SL480P': '106481757',\n",
       " 'RN7SL481P': '106481054',\n",
       " 'RN7SL495P': '106479404',\n",
       " 'RN7SL482P': '106480513',\n",
       " 'RN7SL484P': '106479400',\n",
       " 'RN7SL487P': '106481055',\n",
       " 'RN7SL488P': '106479401',\n",
       " 'RN7SL489P': '106481056',\n",
       " 'RN7SL491P': '106480514',\n",
       " 'RN7SL492P': '106479402',\n",
       " 'RN7SL493P': '106479403',\n",
       " 'RN7SL483P': '106479399',\n",
       " 'RNA5SP263': '106479002',\n",
       " 'RN7SL623P': '106480522',\n",
       " 'RN7SL625P': '106479450',\n",
       " 'RN7SL752P': '106481127',\n",
       " 'RN7SL753P': '106479496',\n",
       " 'RN7SL754P': '106479497',\n",
       " 'RN7SL756P': '106481128',\n",
       " 'RN7SL757P': '106480530',\n",
       " 'RN7SL759P': '106479498',\n",
       " 'RN7SL760P': '106481129',\n",
       " 'RN7SL761P': '106479499',\n",
       " 'RN7SL762P': '106479500',\n",
       " 'RN7SL763P': '106481130',\n",
       " 'RN7SL764P': '106480531',\n",
       " 'RN7SL766P': '106479501',\n",
       " 'RN7SL767P': '106481131',\n",
       " 'RN7SL769P': '106479502',\n",
       " 'RN7SL771P': '106481132',\n",
       " 'RN7SL751P': '106479495',\n",
       " 'RN7SL750P': '106481126',\n",
       " 'RN7SL749P': '106479494',\n",
       " 'RN7SL748P': '106481125',\n",
       " 'RN7SL726P': '106479488',\n",
       " 'RN7SL727P': '106481121',\n",
       " 'RN7SL728P': '106481857',\n",
       " 'RN7SL731P': '107048981',\n",
       " 'RN7SL732P': '106481122',\n",
       " 'RN7SL733P': '106479489',\n",
       " 'RN7SL734P': '106479490',\n",
       " 'RN7SL774P': '106481761',\n",
       " 'RN7SL735P': '106480529',\n",
       " 'RN7SL737P': '106481123',\n",
       " 'RN7SL738P': '106480695',\n",
       " 'RN7SL740P': '106479491',\n",
       " 'RN7SL741P': '106481124',\n",
       " 'RN7SL743P': '106479492',\n",
       " 'RN7SL744P': '106479493',\n",
       " 'RN7SL745P': '106481858',\n",
       " 'RN7SL736P': '107080652',\n",
       " 'RN7SL775P': '106481859',\n",
       " 'RN7SL776P': '106479503',\n",
       " 'RN7SL778P': '106479504',\n",
       " 'RN7SL802P': '106479513',\n",
       " 'RN7SL803P': '106479514',\n",
       " 'RN7SL804P': '106481140',\n",
       " 'RN7SL806P': '106479515',\n",
       " 'RN7SL807P': '106481141',\n",
       " 'RN7SL808P': '106481861',\n",
       " 'RN7SL809P': '106479516',\n",
       " 'RN7SL801P': '106481139',\n",
       " 'RN7SL810P': '106481142',\n",
       " 'RN7SL812P': '106479518',\n",
       " 'RN7SL813P': '106480534',\n",
       " 'RN7SL814P': '106481143',\n",
       " 'RN7SL815P': '106479519',\n",
       " 'RN7SL817P': '106481144',\n",
       " 'RN7SL818P': '106479520',\n",
       " 'RN7SL819P': '106481145',\n",
       " 'RN7SL811P': '106479517',\n",
       " 'RN7SL725P': '106481120',\n",
       " 'RN7SL800P': '106479512',\n",
       " 'RN7SL798P': '106480533',\n",
       " 'RN7SL782P': '106481133',\n",
       " 'RN7SL783P': '106479505',\n",
       " 'RN7SL784P': '106481134',\n",
       " 'RN7SL785P': '106480532',\n",
       " 'RN7SL786P': '106479506',\n",
       " 'RN7SL787P': '106479507',\n",
       " 'RN7SL788P': '106481135',\n",
       " 'RN7SL799P': '106480382',\n",
       " 'RN7SL789P': '106479508',\n",
       " 'RN7SL791P': '106481860',\n",
       " 'RN7SL792P': '106479509',\n",
       " 'RN7SL793P': '106481137',\n",
       " 'RN7SL794P': '106479510',\n",
       " 'RN7SL795P': '106479511',\n",
       " 'RN7SL796P': '107080653',\n",
       " 'RN7SL797P': '106481138',\n",
       " 'RN7SL790P': '106481136',\n",
       " 'RN7SL624P': '106480379',\n",
       " 'RN7SL724P': '106479487',\n",
       " 'RN7SL720P': '106480528',\n",
       " 'RN7SL653P': '106481101',\n",
       " 'RN7SL654P': '106479461',\n",
       " 'RN7SL655P': '106481102',\n",
       " 'RN7SL656P': '106481760',\n",
       " 'RN7SL657P': '107074708',\n",
       " 'RN7SL658P': '106480524',\n",
       " 'RN7SL659P': '106479462',\n",
       " 'RN7SL660P': '106479463',\n",
       " 'RN7SL663P': '106481103',\n",
       " 'RN7SL664P': '106479464',\n",
       " 'RN7SL665P': '106481104',\n",
       " 'RN7SL666P': '106481854',\n",
       " 'RN7SL667P': '106479465',\n",
       " 'RN7SL668P': '106479466',\n",
       " 'RN7SL670P': '106481105',\n",
       " 'RN7SL652P': '106479460',\n",
       " 'RN7SL650P': '106480523',\n",
       " 'RN7SL649P': '106481100',\n",
       " 'RN7SL648P': '106479459',\n",
       " 'RN7SL627P': '106481093',\n",
       " 'RN7SL628P': '106479451',\n",
       " 'RN7SL629P': '106479452',\n",
       " 'RN7SL630P': '106481094',\n",
       " 'RN7SL632P': '106481095',\n",
       " 'RN7SL633P': '106479453',\n",
       " 'RN7SL634P': '106481096',\n",
       " 'RN7SL671P': '106479467',\n",
       " 'RN7SL635P': '106479454',\n",
       " 'RN7SL638P': '106479455',\n",
       " 'RN7SL640P': '106479456',\n",
       " 'RN7SL643P': '106481098',\n",
       " 'RN7SL644P': '106481853',\n",
       " 'RN7SL645P': '106479457',\n",
       " 'RN7SL646P': '106481099',\n",
       " 'RN7SL647P': '106479458',\n",
       " 'RN7SL636P': '106481097',\n",
       " 'RN7SL672P': '106481106',\n",
       " 'RN7SL673P': '106480525',\n",
       " 'RN7SL674P': '106479468',\n",
       " 'RN7SL702P': '106481114',\n",
       " 'RN7SL703P': '106479479',\n",
       " 'RN7SL704P': '106481115',\n",
       " 'RN7SL705P': '106481856',\n",
       " 'RN7SL706P': '106479480',\n",
       " 'RN7SL708P': '106479481',\n",
       " 'RN7SL709P': '106481116',\n",
       " 'RN7SL700P': '106479478',\n",
       " 'RN7SL711P': '106479482',\n",
       " 'RN7SL713P': '106480381',\n",
       " 'RN7SL714P': '106480527',\n",
       " 'RN7SL715P': '106479483',\n",
       " 'RN7SL716P': '106479484',\n",
       " 'RN7SL717P': '106481118',\n",
       " 'RN7SL718P': '106479485',\n",
       " 'RN7SL719P': '106481119',\n",
       " 'RN7SL712P': '106481117',\n",
       " 'RN7SL722P': '106479486',\n",
       " 'RN7SL698P': '106481113',\n",
       " 'RN7SL693P': '106479477',\n",
       " 'RN7SL675P': '106481107',\n",
       " 'RN7SL676P': '106479469',\n",
       " 'RN7SL677P': '106479470',\n",
       " 'RN7SL678P': '106481108',\n",
       " 'RN7SL679P': '106481855',\n",
       " 'RN7SL680P': '106480380',\n",
       " 'RN7SL681P': '106479471',\n",
       " 'RN7SL697P': '106480526',\n",
       " 'RN7SL683P': '106481109',\n",
       " 'RN7SL685P': '106479473',\n",
       " 'RN7SL687P': '106481110',\n",
       " 'RN7SL688P': '106479474',\n",
       " 'RN7SL689P': '106481111',\n",
       " 'RN7SL690P': '106479475',\n",
       " 'RN7SL691P': '106481112',\n",
       " 'RN7SL692P': '106479476',\n",
       " 'RN7SL684P': '106479472',\n",
       " 'RNA5SP264': '100873517',\n",
       " 'RNA5SP265': '100873518',\n",
       " 'RNA5SP266': '100873519',\n",
       " 'RNF187': '149603',\n",
       " 'RNF207': '388591',\n",
       " 'RNF207-AS1': '102724450',\n",
       " 'RNF208': '727800',\n",
       " 'RNF212': '285498',\n",
       " 'RNF212B': '100507650',\n",
       " 'RNF213': '57674',\n",
       " 'RNF213-AS1': '100294362',\n",
       " 'RNF214': '257160',\n",
       " 'RNF215': '200312',\n",
       " 'RNF216': '54476',\n",
       " 'RNF216P1': '441191',\n",
       " 'RNF217': '154214',\n",
       " 'RNF217-AS1': '7955',\n",
       " 'RNF220': '55182',\n",
       " 'RNF186': '54546',\n",
       " 'RNF185': '91445',\n",
       " 'RNF183': '138065',\n",
       " 'RNF182': '221687',\n",
       " 'RNF149': '284996',\n",
       " 'RNF150': '57484',\n",
       " 'RNF151': '146310',\n",
       " 'RNF152': '220441',\n",
       " 'RNF152P1': '100419687',\n",
       " 'RNF157': '114804',\n",
       " 'RNF157-AS1': '100507218',\n",
       " 'RNF222': '643904',\n",
       " 'RNF165': '494470',\n",
       " 'RNF167': '26001',\n",
       " 'RNF168': '165918',\n",
       " 'RNF169': '254225',\n",
       " 'RNF170': '81790',\n",
       " 'RNF175': '285533',\n",
       " 'RNF180': '285671',\n",
       " 'RNF181': '51255',\n",
       " 'RNF166': '115992',\n",
       " 'RNF223': '401934',\n",
       " 'RNF224': '643596',\n",
       " 'RNF225': '646862',\n",
       " 'RNR5': '6056',\n",
       " 'RNU1-1': '26871',\n",
       " 'RNU1-2': '26870',\n",
       " 'RNU1-3': '26869',\n",
       " 'RNU1-4': '6060',\n",
       " 'RNU1-5P': '107105261',\n",
       " 'RNU1-6P': '106480152',\n",
       " 'RNR4': '6055',\n",
       " 'RNU1-7P': '106481952',\n",
       " 'RNU1-11P': '26861',\n",
       " 'RNU1-14P': '26859',\n",
       " 'RNU1-15P': '26858',\n",
       " 'RNU1-16P': '100873860',\n",
       " 'RNU1-17P': '100873814',\n",
       " 'RNU1-18P': '100873815',\n",
       " 'RNU1-19P': '100873861',\n",
       " 'RNU1-8P': '106481604',\n",
       " 'RNF148': '378925',\n",
       " 'RNR3': '6054',\n",
       " 'RNR1': '6052',\n",
       " 'RNF227': '284023',\n",
       " 'RNFT1': '51136',\n",
       " 'RNFT1-DT': '101927755',\n",
       " 'RNFT1P1': '100420886',\n",
       " 'RNFT1P2': '100132264',\n",
       " 'RNFT2': '84900',\n",
       " 'RNGTT': '8732',\n",
       " 'RNR2': '6053',\n",
       " 'RNGTTP1': '100421428',\n",
       " 'RNLS': '55328',\n",
       " 'RNMT': '8731',\n",
       " 'RNPC3': '55599',\n",
       " 'RNPC3P1': '654340',\n",
       " 'RNPEP': '6051',\n",
       " 'RNPEPL1': '57140',\n",
       " 'RNPS1': '10921',\n",
       " 'RNH1': '6050',\n",
       " 'RNU1-20P': '100873816',\n",
       " 'RNF146': '81847',\n",
       " 'RNF144B': '255488',\n",
       " 'RNF7P1': '100506872',\n",
       " 'RNF8': '9025',\n",
       " 'RNF10': '9921',\n",
       " 'RNF10P1': '100419599',\n",
       " 'RNF11': '26994',\n",
       " 'RNF11P1': '100131695',\n",
       " 'RNF11P2': '170543',\n",
       " 'RNF13': '11342',\n",
       " 'RNF14': '9604',\n",
       " 'RNF14P1': '100129375',\n",
       " 'RNF14P3': '100419643',\n",
       " 'RNF14P4': '100419645',\n",
       " 'RNF17': '56163',\n",
       " 'RNF19A': '25897',\n",
       " 'RNF19B': '127544',\n",
       " 'RNF7': '9616',\n",
       " 'RNF6P1': '100420924',\n",
       " 'RNF6': '6049',\n",
       " 'RNF5P1': '286140',\n",
       " 'RNASEH1P3': '199827',\n",
       " 'RNASEH2A': '10535',\n",
       " 'RNASEH2B': '79621',\n",
       " 'RNASEH2C': '84153',\n",
       " 'RNASEH2CP1': '386608',\n",
       " 'RNASEK': '440400',\n",
       " 'RNASEK-C17orf49': '100529209',\n",
       " 'RNF19BPX': '100419788',\n",
       " 'RNASEL': '6041',\n",
       " 'RND1': '27289',\n",
       " 'RND2': '8153',\n",
       " 'RND3': '390',\n",
       " 'RNF2': '6045',\n",
       " 'RNF2P1': '100132467',\n",
       " 'RNF4': '6047',\n",
       " 'RNF5': '6048',\n",
       " 'RNASET2': '8635',\n",
       " 'RNF19BPY': '100419722',\n",
       " 'RNF20': '56254',\n",
       " 'RNF25': '64320',\n",
       " 'RNF122': '79845',\n",
       " 'RNF123': '63891',\n",
       " 'RNF125': '54941',\n",
       " 'RNF126': '55658',\n",
       " 'RNF126P1': '376412',\n",
       " 'RNF128': '79589',\n",
       " 'RNF130': '55819',\n",
       " 'RNF121': '55298',\n",
       " 'RNF133': '168433',\n",
       " 'RNF138': '51444',\n",
       " 'RNF138P1': '379013',\n",
       " 'RNF138P2': '100419777',\n",
       " 'RNF139': '11236',\n",
       " 'RNF139-AS1': '101927612',\n",
       " 'RNF141': '50862',\n",
       " 'RNF144A': '9781',\n",
       " 'RNF135': '84282',\n",
       " 'RNF145': '153830',\n",
       " 'RNF115': '27246',\n",
       " 'RNF113B': '140432',\n",
       " 'RNF26': '79102',\n",
       " 'RNF31': '55072',\n",
       " 'RNF32': '140545',\n",
       " 'RNF32-AS1': '101927858',\n",
       " 'RNF34': '80196',\n",
       " 'RNF38': '152006',\n",
       " 'RNF39': '80352',\n",
       " 'RNF114': '55905',\n",
       " 'RNF40': '9810',\n",
       " 'RNF43': '54894',\n",
       " 'RNF44': '22838',\n",
       " 'RNF103': '7844',\n",
       " 'RNF103-CHMP3': '100526767',\n",
       " 'RNF111': '54778',\n",
       " 'RNF112': '7732',\n",
       " 'RNF113A': '7737',\n",
       " 'RNF41': '10193',\n",
       " 'RNASEH1P2': '390766',\n",
       " 'RNU1-21P': '100873862',\n",
       " 'RNU1-23P': '106478980',\n",
       " 'RNU2-2P': '26855',\n",
       " 'RNU2-3P': '26854',\n",
       " 'RNU2-4P': '26853',\n",
       " 'RNU2-5P': '26852',\n",
       " 'RNU2-6P': '100873825',\n",
       " 'RNU2-7P': '100873824',\n",
       " 'RNU2-8P': '106480200',\n",
       " 'RNU2-9P': '106481636',\n",
       " 'RNU2-10P': '106480201',\n",
       " 'RNU2-11P': '106481637',\n",
       " 'RNU2-12P': '106480202',\n",
       " 'RNU2-13P': '106480203',\n",
       " 'RNU2-14P': '106481638',\n",
       " 'RNU2-15P': '106866980',\n",
       " 'RNU2-16P': '106481639',\n",
       " 'RNU2-1': '6066',\n",
       " 'RNU1-155P': '115409986',\n",
       " 'RNU1-154P': '115409990',\n",
       " 'RNU1-153P': '115409985',\n",
       " 'RNU1-132P': '106481958',\n",
       " 'RNU1-133P': '106481631',\n",
       " 'RNU1-134P': '106480194',\n",
       " 'RNU1-136P': '106481632',\n",
       " 'RNU1-138P': '106480195',\n",
       " 'RNU1-139P': '106480196',\n",
       " 'RNU1-140P': '106480669',\n",
       " 'RNU2-17P': '106480204',\n",
       " 'RNU1-141P': '106481633',\n",
       " 'RNU1-143P': '106481634',\n",
       " 'RNU1-146P': '106480198',\n",
       " 'RNU1-148P': '106481635',\n",
       " 'RNU1-149P': '107048983',\n",
       " 'RNU1-150P': '106480413',\n",
       " 'RNU1-151P': '110806291',\n",
       " 'RNU1-152P': '107521952',\n",
       " 'RNU1-142P': '106480197',\n",
       " 'RNU2-18P': '106480205',\n",
       " 'RNU2-19P': '106481959',\n",
       " 'RNU2-20P': '106481640',\n",
       " 'RNU2-41P': '106480215',\n",
       " 'RNU2-42P': '106481647',\n",
       " 'RNU2-43P': '106480216',\n",
       " 'RNU2-44P': '106481648',\n",
       " 'RNU2-45P': '106480217',\n",
       " 'RNU2-46P': '106480218',\n",
       " 'RNU2-47P': '106480672',\n",
       " 'RNU2-40P': '106480671',\n",
       " 'RNU2-48P': '106481649',\n",
       " 'RNU2-50P': '106481650',\n",
       " 'RNU2-51P': '106480415',\n",
       " 'RNU2-52P': '107080629',\n",
       " 'RNU2-53P': '106480220',\n",
       " 'RNU2-54P': '106481651',\n",
       " 'RNU2-55P': '106481961',\n",
       " 'RNU2-56P': '106480221',\n",
       " 'RNU2-49P': '106480219',\n",
       " 'RNU1-131P': '106480193',\n",
       " 'RNU2-39P': '106480214',\n",
       " 'RNU2-37P': '106480213',\n",
       " 'RNU2-21P': '106480206',\n",
       " 'RNU2-22P': '106660611',\n",
       " 'RNU2-23P': '106481641',\n",
       " 'RNU2-24P': '106480207',\n",
       " 'RNU2-25P': '106480208',\n",
       " 'RNU2-26P': '106480414',\n",
       " 'RNU2-27P': '106481642',\n",
       " 'RNU2-38P': '106481646',\n",
       " 'RNU2-28P': '106480670',\n",
       " 'RNU2-30P': '106481643',\n",
       " 'RNU2-31P': '106480210',\n",
       " 'RNU2-32P': '106481644',\n",
       " 'RNU2-33P': '106480211',\n",
       " 'RNU2-34P': '106481960',\n",
       " 'RNU2-35P': '106480212',\n",
       " 'RNU2-36P': '106481645',\n",
       " 'RNU2-29P': '106480209',\n",
       " 'RNU1-22P': '100873863',\n",
       " 'RNU1-130P': '106480192',\n",
       " 'RNU1-128P': '106480191',\n",
       " 'RNU1-48P': '107080628',\n",
       " 'RNU1-51P': '106480163',\n",
       " 'RNU1-52P': '106480164',\n",
       " 'RNU1-54P': '106481611',\n",
       " 'RNU1-55P': '106481954',\n",
       " 'RNU1-56P': '106480165',\n",
       " 'RNU1-57P': '106480166',\n",
       " 'RNU1-58P': '106481612',\n",
       " 'RNU1-61P': '106481980',\n",
       " 'RNU1-62P': '106481613',\n",
       " 'RNU1-63P': '106480664',\n",
       " 'RNU1-64P': '106480168',\n",
       " 'RNU1-65P': '106481614',\n",
       " 'RNU1-67P': '106480169',\n",
       " 'RNU1-68P': '106481615',\n",
       " 'RNU1-47P': '106480161',\n",
       " 'RNU1-46P': '106480663',\n",
       " 'RNU1-45P': '106481610',\n",
       " 'RNU1-44P': '106480160',\n",
       " 'RNU1-24P': '100873865',\n",
       " 'RNU1-27P': '26865',\n",
       " 'RNU1-28P': '26866',\n",
       " 'RNU1-29P': '106480154',\n",
       " 'RNU1-30P': '106480662',\n",
       " 'RNU1-31P': '106481606',\n",
       " 'RNU1-32P': '106480155',\n",
       " 'RNU1-70P': '107105264',\n",
       " 'RNU1-33P': '106480156',\n",
       " 'RNU1-35P': '106480157',\n",
       " 'RNU1-36P': '106481783',\n",
       " 'RNU1-38P': '106481608',\n",
       " 'RNU1-39P': '106481953',\n",
       " 'RNU1-40P': '106480158',\n",
       " 'RNU1-42P': '106481609',\n",
       " 'RNU1-43P': '106480159',\n",
       " 'RNU1-34P': '106481607',\n",
       " 'RNU1-72P': '106481955',\n",
       " 'RNU1-73P': '106481616',\n",
       " 'RNU1-74P': '106480171',\n",
       " 'RNU1-101P': '106480667',\n",
       " 'RNU1-103P': '106481623',\n",
       " 'RNU1-104P': '106480184',\n",
       " 'RNU1-105P': '106480185',\n",
       " 'RNU1-107P': '106480186',\n",
       " 'RNU1-108P': '106481957',\n",
       " 'RNU1-109P': '106481625',\n",
       " 'RNU1-100P': '106480183',\n",
       " 'RNU1-112P': '106480187',\n",
       " 'RNU1-115P': '106480188',\n",
       " 'RNU1-116P': '107521946',\n",
       " 'RNU1-117P': '106480189',\n",
       " 'RNU1-119P': '106480668',\n",
       " 'RNU1-123P': '106481628',\n",
       " 'RNU1-124P': '106481629',\n",
       " 'RNU1-125P': '106866915',\n",
       " 'RNU1-114P': '106481626',\n",
       " 'RNU1-129P': '106481630',\n",
       " 'RNU1-98P': '106481622',\n",
       " 'RNU1-96P': '106480181',\n",
       " 'RNU1-75P': '106480172',\n",
       " 'RNU1-76P': '106481617',\n",
       " 'RNU1-77P': '106480173',\n",
       " 'RNU1-78P': '106480665',\n",
       " 'RNU1-79P': '107521942',\n",
       " 'RNU1-80P': '106480174',\n",
       " 'RNU1-82P': '106480175',\n",
       " 'RNU1-97P': '106480182',\n",
       " 'RNU1-83P': '106480176',\n",
       " 'RNU1-86P': '106480666',\n",
       " 'RNU1-88P': '106481619',\n",
       " 'RNU1-89P': '106480412',\n",
       " 'RNU1-91P': '106480179',\n",
       " 'RNU1-93P': '106480180',\n",
       " 'RNU1-94P': '106481956',\n",
       " 'RNU1-95P': '106481621',\n",
       " 'RNU1-84P': '106481618',\n",
       " 'RN7SL425P': '106481039',\n",
       " 'RNASEH1P1': '284203',\n",
       " 'RNASEH1': '246243',\n",
       " 'RNA5SP369': '100873628',\n",
       " 'RNA5SP370': '106480765',\n",
       " 'RNA5SP371': '100873629',\n",
       " 'RNA5SP372': '100873630',\n",
       " 'RNA5SP373': '100873631',\n",
       " 'RNA5SP374': '100873632',\n",
       " 'RNA5SP375': '100873633',\n",
       " 'RNA5SP376': '106479010',\n",
       " 'RNA5SP377': '106479011',\n",
       " 'RNA5SP378': '100873634',\n",
       " 'RNA5SP379': '100873635',\n",
       " 'RNA5SP380': '100873636',\n",
       " 'RNA5SP382': '100873637',\n",
       " 'RNA5SP383': '100873638',\n",
       " 'RNA5SP384': '100873639',\n",
       " 'RNA5SP368': '100873627',\n",
       " 'RNA5SP367': '100873626',\n",
       " 'RNA5SP366': '100873625',\n",
       " 'RNA5SP365': '100873624',\n",
       " 'RNA5SP349': '100873611',\n",
       " 'RNA5SP350': '106481794',\n",
       " 'RNA5SP351': '106480764',\n",
       " 'RNA5SP352': '100873612',\n",
       " 'RNA5SP353': '100873613',\n",
       " 'RNA5SP354': '100873614',\n",
       " 'RNA5SP355': '106479009',\n",
       " 'RNA5SP385': '100873640',\n",
       " 'RNA5SP356': '100873615',\n",
       " 'RNA5SP358': '100873617',\n",
       " 'RNA5SP359': '100873618',\n",
       " 'RNA5SP360': '100873619',\n",
       " 'RNA5SP361': '100873620',\n",
       " 'RNA5SP362': '100873621',\n",
       " 'RNA5SP363': '100873622',\n",
       " 'RNA5SP364': '100873623',\n",
       " 'RNA5SP357': '100873616',\n",
       " 'RNA5SP386': '100873641',\n",
       " 'RNA5SP387': '107133508',\n",
       " 'RNA5SP388': '100873642',\n",
       " 'RNA5SP410': '100873662',\n",
       " 'RNA5SP411': '100887740',\n",
       " 'RNA5SP412': '100873663',\n",
       " 'RNA5SP413': '100873664',\n",
       " 'RNA5SP414': '100873665',\n",
       " 'RNA5SP415': '100873666',\n",
       " 'RNA5SP416': '100873667',\n",
       " 'RNA5SP409': '100873661',\n",
       " 'RNA5SP417': '100873668',\n",
       " 'RNA5SP419': '100873670',\n",
       " 'RNA5SP420': '100873671',\n",
       " 'RNA5SP421': '100873672',\n",
       " 'RNA5SP422': '100873673',\n",
       " ...}"
      ]
     },
     "execution_count": 204,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ncbigene_ids_by_symbol = (\n",
    "    hgnc_df[[\"ncbigene_id\", \"value\"]]\n",
    "    .set_index(\"value\")\n",
    "    .to_dict()[\"ncbigene_id\"]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 200,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hgnc</th>\n",
       "      <th>ncbigene</th>\n",
       "      <th>variable</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9942</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>approved_symbol</td>\n",
       "      <td>CDKN1A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>176696</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>previous_symbol</td>\n",
       "      <td>CDKN1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93319</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>P21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93325</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>p21Cip1/Waf1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93324</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>p21CIP1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93323</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>CAP20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93322</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>SDI1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93321</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>WAF1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93320</th>\n",
       "      <td>HGNC:1784</td>\n",
       "      <td>1026</td>\n",
       "      <td>alias_symbol</td>\n",
       "      <td>CIP1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             hgnc ncbigene         variable         value\n",
       "9942    HGNC:1784     1026  approved_symbol        CDKN1A\n",
       "176696  HGNC:1784     1026  previous_symbol         CDKN1\n",
       "93319   HGNC:1784     1026     alias_symbol           P21\n",
       "93325   HGNC:1784     1026     alias_symbol  p21Cip1/Waf1\n",
       "93324   HGNC:1784     1026     alias_symbol       p21CIP1\n",
       "93323   HGNC:1784     1026     alias_symbol         CAP20\n",
       "93322   HGNC:1784     1026     alias_symbol          SDI1\n",
       "93321   HGNC:1784     1026     alias_symbol          WAF1\n",
       "93320   HGNC:1784     1026     alias_symbol          CIP1"
      ]
     },
     "execution_count": 200,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hgnc_df[hgnc_df[\"hgnc\"] == \"HGNC:1784\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 198,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2173</th>\n",
       "      <td>BE</td>\n",
       "      <td>CDKN2</td>\n",
       "      <td>CDKN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     type symbol bioentities\n",
       "2173   BE  CDKN2        CDKN"
      ]
     },
     "execution_count": 198,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"symbol\"] == \"CDKN2\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 195,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_AB</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_B</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   type      symbol bioentities\n",
       "9    BE   Activin_A     Activin\n",
       "10   BE  Activin_AB     Activin\n",
       "11   BE   Activin_B     Activin"
      ]
     },
     "execution_count": 195,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"bioentities\"] == \"Activin\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 196,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BE</td>\n",
       "      <td>Activin_A</td>\n",
       "      <td>Activin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  type     symbol bioentities\n",
       "9   BE  Activin_A     Activin"
      ]
     },
     "execution_count": 196,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"symbol\"] == \"Activin_A\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 174,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>isa</th>\n",
       "      <th>type2</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>247</th>\n",
       "      <td>UP</td>\n",
       "      <td>P0C0S8</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>249</th>\n",
       "      <td>UP</td>\n",
       "      <td>P0C5Y9</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>264</th>\n",
       "      <td>UP</td>\n",
       "      <td>P04908</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>265</th>\n",
       "      <td>UP</td>\n",
       "      <td>Q6FI13</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H2A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>266</th>\n",
       "      <td>UP</td>\n",
       "      <td>P62807</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H2B</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>285</th>\n",
       "      <td>UP</td>\n",
       "      <td>P68431</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>286</th>\n",
       "      <td>UP</td>\n",
       "      <td>Q71DI3</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>288</th>\n",
       "      <td>UP</td>\n",
       "      <td>P84243</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>290</th>\n",
       "      <td>UP</td>\n",
       "      <td>P62805</td>\n",
       "      <td>isa</td>\n",
       "      <td>BE</td>\n",
       "      <td>Histone_H4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    type  symbol  isa type2  bioentities\n",
       "247   UP  P0C0S8  isa    BE  Histone_H2A\n",
       "249   UP  P0C5Y9  isa    BE  Histone_H2A\n",
       "264   UP  P04908  isa    BE  Histone_H2A\n",
       "265   UP  Q6FI13  isa    BE  Histone_H2A\n",
       "266   UP  P62807  isa    BE  Histone_H2B\n",
       "285   UP  P68431  isa    BE   Histone_H3\n",
       "286   UP  Q71DI3  isa    BE   Histone_H3\n",
       "288   UP  P84243  isa    BE   Histone_H3\n",
       "290   UP  P62805  isa    BE   Histone_H4"
      ]
     },
     "execution_count": 174,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"type\"] == \"UP\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 175,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>symbol</th>\n",
       "      <th>isa</th>\n",
       "      <th>type2</th>\n",
       "      <th>bioentities</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [type, symbol, isa, type2, bioentities]\n",
       "Index: []"
      ]
     },
     "execution_count": 175,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioentities_df[bioentities_df[\"type2\"] == \"UP\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 176,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'BE'}"
      ]
     },
     "execution_count": 176,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "set(bioentities_df[\"type2\"].to_list())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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