MEDLINE.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "#this method of P value is calculated based on all diseases from disease ontology.\n",
    "#can not filter to alz disease first and do calculation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Compute symptom-disease cooccurrence for Hetionet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.core.interactiveshell import InteractiveShell\n",
    "InteractiveShell.ast_node_interactivity = \"all\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "download_dir = '../data/MEDLINE'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "import io\n",
    "import gzip\n",
    "\n",
    "import pandas\n",
    "import requests\n",
    "import networkx\n",
    "\n",
    "#import eutility\n",
    "#import cooccurrence"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## defined functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"\\nimport time\\n\\nimport xml.etree.ElementTree as ET\\n\\nimport requests\\n\\ndef esearch_query(payload, retmax = 100, sleep=2):\\n    #Query the esearch E-utility.\\n    #This function can not get results more than 10000\\n    url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'\\n    payload['retmax'] = retmax\\n    payload['retstart'] = 0\\n    ids = list()\\n    count = 1\\n    while payload['retstart'] < count:\\n        response = requests.get(url, params=payload)\\n        xml = ET.fromstring(response.content)\\n        if xml.findtext('Count') is not None:\\n            count = int(xml.findtext('Count'))\\n        ids += [xml_id.text for xml_id in xml.findall('IdList/Id')]\\n        payload['retstart'] += retmax\\n        time.sleep(sleep)\\n    return ids\\n\""
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#https://www.ncbi.nlm.nih.gov/books/NBK25500/\n",
    "\"\"\"\n",
    "import time\n",
    "\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "import requests\n",
    "\n",
    "def esearch_query(payload, retmax = 100, sleep=2):\n",
    "    #Query the esearch E-utility.\n",
    "    #This function can not get results more than 10000\n",
    "    url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'\n",
    "    payload['retmax'] = retmax\n",
    "    payload['retstart'] = 0\n",
    "    ids = list()\n",
    "    count = 1\n",
    "    while payload['retstart'] < count:\n",
    "        response = requests.get(url, params=payload)\n",
    "        xml = ET.fromstring(response.content)\n",
    "        if xml.findtext('Count') is not None:\n",
    "            count = int(xml.findtext('Count'))\n",
    "        ids += [xml_id.text for xml_id in xml.findall('IdList/Id')]\n",
    "        payload['retstart'] += retmax\n",
    "        time.sleep(sleep)\n",
    "    return ids\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import subprocess\n",
    "import re\n",
    "\n",
    "# Function to format disease name into a valid file name\n",
    "def format_filename(name):\n",
    "    # Replace spaces with underscores and remove special characters\n",
    "    filename = re.sub(r'\\W+', '_', name.strip())\n",
    "    # Add suffix\n",
    "    #return os.path.join(download_dir, filename + \"result.txt\")\n",
    "    return filename + \"result.txt\"\n",
    "\n",
    "# fetching data for {query_term}. Results saved in {output_file}\n",
    "def efetch_query(query_term):\n",
    "    # Run the command with the current disease name and output file name\n",
    "    output_file = format_filename(query_term)\n",
    "    command = f'esearch -db pubmed -query \"{query_term}\" | efetch -format xml | xtract -pattern PubmedArticle -element MedlineCitation/PMID > {output_file}'\n",
    "    subprocess.run(command, shell=True)\n",
    "\n",
    "    print(f\"Completed fetching data for {query_term}. Results saved in {output_file}\")\n",
    "    return output_file\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "import itertools\n",
    "from typing import Any, Dict, List, Set\n",
    "\n",
    "import scipy.stats\n",
    "import pandas\n",
    "\n",
    "\n",
    "def read_pmids_tsv(path, key, min_articles = 1):\n",
    "    term_to_pmids = dict()\n",
    "    pmids_df = pandas.read_table(path, compression='gzip')\n",
    "    pmids_df = pmids_df[pmids_df.n_articles >= min_articles]\n",
    "    for i, row in pmids_df.iterrows():\n",
    "        term = row[key]\n",
    "        pmids = row.pubmed_ids.split('|')\n",
    "        term_to_pmids[term] = set(pmids)\n",
    "    pmids_df.drop('pubmed_ids', axis=1, inplace=True)\n",
    "    return pmids_df, term_to_pmids\n",
    "\n",
    "def score_pmid_cooccurrence(term0_to_pmids, term1_to_pmids, term0_name='term_0', term1_name='term_1', verbose=True):\n",
    "    \"\"\"\n",
    "    Find pubmed cooccurrence between topics of two classes.\n",
    "\n",
    "    term0_to_pmids -- a dictionary that returns the pubmed_ids for each term of class 0\n",
    "    term0_to_pmids -- a dictionary that returns the pubmed_ids for each term of class 1\n",
    "    \"\"\"\n",
    "    all_pmids0 = set.union(*term0_to_pmids.values())\n",
    "    all_pmids1 = set.union(*term1_to_pmids.values())\n",
    "    pmids_in_both = all_pmids0 & all_pmids1\n",
    "    total_pmids = len(pmids_in_both)\n",
    "    if verbose:\n",
    "        print('Total articles containing a {}: {}'.format(term0_name, len(all_pmids0)))\n",
    "        print('Total articles containing a {}: {}'.format(term1_name, len(all_pmids1)))\n",
    "        print('Total articles containing both a {} and {}: {}'.format(term0_name, term1_name, total_pmids))\n",
    "\n",
    "    term0_to_pmids = term0_to_pmids.copy()\n",
    "    term1_to_pmids = term1_to_pmids.copy()\n",
    "    for d in term0_to_pmids, term1_to_pmids:\n",
    "        for key, value in list(d.items()):\n",
    "            d[key] = value & pmids_in_both\n",
    "            if not d[key]:\n",
    "                del d[key]\n",
    "\n",
    "    if verbose:\n",
    "        print('\\nAfter removing terms without any cooccurences:')\n",
    "        print('+ {} {}s remain'.format(len(term0_to_pmids), term0_name))\n",
    "        print('+ {} {}s remain'.format(len(term1_to_pmids), term1_name))\n",
    "\n",
    "    rows = list()\n",
    "    for term0, term1 in itertools.product(term0_to_pmids, term1_to_pmids):\n",
    "        pmids0 = term0_to_pmids[term0]\n",
    "        pmids1 = term1_to_pmids[term1]\n",
    "        row = {\n",
    "            term0_name: term0,\n",
    "            term1_name: term1,\n",
    "            **cooccurrence_metrics(pmids0, pmids1, total_pmids=total_pmids)\n",
    "        }\n",
    "        rows.append(row)\n",
    "    df = pandas.DataFrame(rows)\n",
    "\n",
    "    if verbose:\n",
    "        print('\\nCooccurrence scores calculated for {} {} -- {} pairs'.format(len(df), term0_name, term1_name))\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def cooccurrence_metrics(source_pmids: Set[str], target_pmids: Set[str], total_pmids: int) -> Dict[str, Any]:\n",
    "    \"\"\"\n",
    "    Compute metrics of cooccurrence between two sets of pubmed ids.\n",
    "    Requires providing the total number of pubmed ids in the corpus.\n",
    "    \"\"\"\n",
    "    a = len(source_pmids & target_pmids)\n",
    "    b = len(source_pmids) - a\n",
    "    c = len(target_pmids) - a\n",
    "    d = total_pmids - (a + b + c)\n",
    "    contingency_table = [[a, b], [c, d]]\n",
    "    # discussion on this formula in https://github.com/hetio/medline/issues/1\n",
    "    expected = len(source_pmids) * len(target_pmids) / total_pmids\n",
    "    enrichment = a / expected\n",
    "    odds_ratio, p_fisher = scipy.stats.fisher_exact(contingency_table, alternative='greater')\n",
    "    return {\n",
    "        \"cooccurrence\": a,\n",
    "        \"expected\": expected,\n",
    "        \"enrichment\": enrichment,\n",
    "        \"odds_ratio\": odds_ratio,\n",
    "        \"p_fisher\": p_fisher,\n",
    "        \"n_source\": len(source_pmids),\n",
    "        \"n_target\": len(target_pmids),\n",
    "    }"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Diseases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#install e-direct by following https://www.ncbi.nlm.nih.gov/books/NBK179288/\n",
    "#run with vpn"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    },
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(127, 3)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/plain": [
       "(127, 4)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/plain": [
       "(125, 4)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "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",
       "        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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>hematologic cancer</td>\n",
       "      <td>D019337</td>\n",
       "      <td>Hematologic Neoplasms</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DOID:1319</td>\n",
       "      <td>brain cancer</td>\n",
       "      <td>D001932</td>\n",
       "      <td>Brain Neoplasms</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DOID:263</td>\n",
       "      <td>kidney cancer</td>\n",
       "      <td>D007680</td>\n",
       "      <td>Kidney Neoplasms</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DOID:1793</td>\n",
       "      <td>pancreatic cancer</td>\n",
       "      <td>D010190</td>\n",
       "      <td>Pancreatic Neoplasms</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DOID:4159</td>\n",
       "      <td>skin cancer</td>\n",
       "      <td>D012878</td>\n",
       "      <td>Skin Neoplasms</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   doid_code           doid_name  mesh_id              mesh_name\n",
       "0  DOID:2531  hematologic cancer  D019337  Hematologic Neoplasms\n",
       "1  DOID:1319        brain cancer  D001932        Brain Neoplasms\n",
       "2   DOID:263       kidney cancer  D007680       Kidney Neoplasms\n",
       "3  DOID:1793   pancreatic cancer  D010190   Pancreatic Neoplasms\n",
       "4  DOID:4159         skin cancer  D012878         Skin Neoplasms"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read mappings for DO Slim terms\n",
    "url = '../data/DiseaseOntology/xrefs-slim.tsv'\n",
    "disease_df = pandas.read_table(url)\n",
    "disease_df = disease_df.query('resource == \"MESH\"').drop(columns=['resource']) #change MSH to MESH\n",
    "disease_df = disease_df.rename(columns={'resource_id': 'mesh_id'})\n",
    "disease_df.shape\n",
    "\n",
    "# Read MeSH terms to MeSH names\n",
    "url = '../data/MESH/terms.tsv'\n",
    "mesh_df = pandas.read_table(url)\n",
    "disease_df = disease_df.merge(mesh_df)\n",
    "disease_df.shape\n",
    "\n",
    "# Manually remove problematic xrefs\n",
    "# https://github.com/obophenotype/human-disease-ontology/issues/45\n",
    "disease_df = disease_df.query(\"mesh_id != 'D003327' and mesh_id != 'D017202'\")\n",
    "disease_df.shape\n",
    "disease_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    },
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import pandas\n",
    "\n",
    "rows_out = list()\n",
    "\n",
    "for i, row in disease_df.iterrows():\n",
    "    term_query = '{disease}[MeSH Major Topic]'.format(disease = row.mesh_name.lower())\n",
    "    print(term_query)\n",
    "    #payload = {'db': 'pubmed', 'term': term_query}\n",
    "    #pmids = esearch_query(payload, retmax = 10000)\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "\n",
    "disease_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "validate with the url (open with chrome) https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=alzheimer%20disease[MeSH%20Major%20Topic]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# rerun case with error\n",
    "error_terms = ['Stomach Neoplasms', 'Urinary Bladder Neoplasms', 'Neoplasms, Germ Cell and Embryonal'\n",
    "              ]\n",
    "error_out = list()\n",
    "for i in error_terms:\n",
    "    term_query = '{disease}[MeSH Major Topic]'.format(disease = i.lower())\n",
    "    print(term_query)\n",
    "    row = disease_pmids_df.loc[disease_pmids_df['mesh_name'] == i].squeeze()\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    error_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), i))\n",
    "\n",
    "disease_error_df = pandas.DataFrame(error_out)\n",
    "disease_error_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>DOID:10534</td>\n",
       "      <td>stomach cancer</td>\n",
       "      <td>D013274</td>\n",
       "      <td>Stomach Neoplasms</td>\n",
       "      <td>stomach neoplasms[MeSH Major Topic]</td>\n",
       "      <td>98656</td>\n",
       "      <td>2794|3839|7075|7818|7958|11530|14374|14377|175...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>DOID:11054</td>\n",
       "      <td>urinary bladder cancer</td>\n",
       "      <td>D001749</td>\n",
       "      <td>Urinary Bladder Neoplasms</td>\n",
       "      <td>urinary bladder neoplasms[MeSH Major Topic]</td>\n",
       "      <td>55298</td>\n",
       "      <td>6146|12890|13929|26492|33571|36123|36278|36279...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>DOID:2994</td>\n",
       "      <td>germ cell cancer</td>\n",
       "      <td>D009373</td>\n",
       "      <td>Neoplasms, Germ Cell and Embryonal</td>\n",
       "      <td>neoplasms, germ cell and embryonal[MeSH Major ...</td>\n",
       "      <td>335022</td>\n",
       "      <td>471|1140|1456|1745|1891|2828|3117|3627|3662|36...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code               doid_name  mesh_id  \\\n",
       "14  DOID:10534          stomach cancer  D013274   \n",
       "15  DOID:11054  urinary bladder cancer  D001749   \n",
       "27   DOID:2994        germ cell cancer  D009373   \n",
       "\n",
       "                             mesh_name  \\\n",
       "14                   Stomach Neoplasms   \n",
       "15           Urinary Bladder Neoplasms   \n",
       "27  Neoplasms, Germ Cell and Embryonal   \n",
       "\n",
       "                                           term_query  n_articles  \\\n",
       "14                stomach neoplasms[MeSH Major Topic]       98656   \n",
       "15        urinary bladder neoplasms[MeSH Major Topic]       55298   \n",
       "27  neoplasms, germ cell and embryonal[MeSH Major ...      335022   \n",
       "\n",
       "                                           pubmed_ids  \n",
       "14  2794|3839|7075|7818|7958|11530|14374|14377|175...  \n",
       "15  6146|12890|13929|26492|33571|36123|36278|36279...  \n",
       "27  471|1140|1456|1745|1891|2828|3117|3627|3662|36...  "
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#validate with first run\n",
    "disease_pmids_df.loc[disease_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>DOID:10534</td>\n",
       "      <td>stomach cancer</td>\n",
       "      <td>D013274</td>\n",
       "      <td>Stomach Neoplasms</td>\n",
       "      <td>stomach neoplasms[MeSH Major Topic]</td>\n",
       "      <td>99119</td>\n",
       "      <td>2794|3839|7075|7818|7958|11530|14374|14377|175...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>DOID:11054</td>\n",
       "      <td>urinary bladder cancer</td>\n",
       "      <td>D001749</td>\n",
       "      <td>Urinary Bladder Neoplasms</td>\n",
       "      <td>urinary bladder neoplasms[MeSH Major Topic]</td>\n",
       "      <td>55940</td>\n",
       "      <td>6146|12890|13929|26492|33571|36123|36278|36279...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>DOID:2994</td>\n",
       "      <td>germ cell cancer</td>\n",
       "      <td>D009373</td>\n",
       "      <td>Neoplasms, Germ Cell and Embryonal</td>\n",
       "      <td>neoplasms, germ cell and embryonal[MeSH Major ...</td>\n",
       "      <td>335043</td>\n",
       "      <td>471|1140|1456|1745|1891|2828|3117|3627|3662|36...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code               doid_name  mesh_id  \\\n",
       "14  DOID:10534          stomach cancer  D013274   \n",
       "15  DOID:11054  urinary bladder cancer  D001749   \n",
       "27   DOID:2994        germ cell cancer  D009373   \n",
       "\n",
       "                             mesh_name  \\\n",
       "14                   Stomach Neoplasms   \n",
       "15           Urinary Bladder Neoplasms   \n",
       "27  Neoplasms, Germ Cell and Embryonal   \n",
       "\n",
       "                                           term_query  n_articles  \\\n",
       "14                stomach neoplasms[MeSH Major Topic]       99119   \n",
       "15        urinary bladder neoplasms[MeSH Major Topic]       55940   \n",
       "27  neoplasms, germ cell and embryonal[MeSH Major ...      335043   \n",
       "\n",
       "                                           pubmed_ids  \n",
       "14  2794|3839|7075|7818|7958|11530|14374|14377|175...  \n",
       "15  6146|12890|13929|26492|33571|36123|36278|36279...  \n",
       "27  471|1140|1456|1745|1891|2828|3117|3627|3662|36...  "
      ]
     },
     "execution_count": 67,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#update results and check values\n",
    "disease_pmids_df.loc[disease_pmids_df.mesh_name.isin(disease_error_df.mesh_name), ['n_articles', 'pubmed_ids']] = disease_error_df[['n_articles', 'pubmed_ids']]\n",
    "disease_pmids_df.loc[disease_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "with gzip.open(os.path.join(download_dir,'disease-pmids.tsv.gz'), 'w') as write_file:\n",
    "    write_file = io.TextIOWrapper(write_file)\n",
    "    disease_pmids_df.to_csv(write_file, sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(125, 7)"
      ]
     },
     "execution_count": 89,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_pmids_df.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# disease-disease-cooccurrence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "download_dir = '../data/MEDLINE'\n",
    "disease_df, disease_to_pmids = read_pmids_tsv(os.path.join(download_dir,'disease-pmids.tsv.gz'), key='doid_code')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total articles containing a doid_code_0: 4906736\n",
      "Total articles containing a doid_code_1: 4906736\n",
      "Total articles containing both a doid_code_0 and doid_code_1: 4906736\n",
      "\n",
      "After removing terms without any cooccurences:\n",
      "+ 121 doid_code_0s remain\n",
      "+ 121 doid_code_1s remain\n",
      "\n",
      "Cooccurrence scores calculated for 14641 doid_code_0 -- doid_code_1 pairs\n"
     ]
    }
   ],
   "source": [
    "cooc_df = score_pmid_cooccurrence(disease_to_pmids, disease_to_pmids, 'doid_code_0', 'doid_code_1')"
   ]
  },
  {
   "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>hematologic cancer</td>\n",
       "      <td>D019337</td>\n",
       "      <td>Hematologic Neoplasms</td>\n",
       "      <td>hematologic neoplasms[MeSH Major Topic]</td>\n",
       "      <td>20412</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DOID:1319</td>\n",
       "      <td>brain cancer</td>\n",
       "      <td>D001932</td>\n",
       "      <td>Brain Neoplasms</td>\n",
       "      <td>brain neoplasms[MeSH Major Topic]</td>\n",
       "      <td>148009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DOID:263</td>\n",
       "      <td>kidney cancer</td>\n",
       "      <td>D007680</td>\n",
       "      <td>Kidney Neoplasms</td>\n",
       "      <td>kidney neoplasms[MeSH Major Topic]</td>\n",
       "      <td>74244</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DOID:1793</td>\n",
       "      <td>pancreatic cancer</td>\n",
       "      <td>D010190</td>\n",
       "      <td>Pancreatic Neoplasms</td>\n",
       "      <td>pancreatic neoplasms[MeSH Major Topic]</td>\n",
       "      <td>80499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DOID:4159</td>\n",
       "      <td>skin cancer</td>\n",
       "      <td>D012878</td>\n",
       "      <td>Skin Neoplasms</td>\n",
       "      <td>skin neoplasms[MeSH Major Topic]</td>\n",
       "      <td>175588</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   doid_code           doid_name  mesh_id              mesh_name  \\\n",
       "0  DOID:2531  hematologic cancer  D019337  Hematologic Neoplasms   \n",
       "1  DOID:1319        brain cancer  D001932        Brain Neoplasms   \n",
       "2   DOID:263       kidney cancer  D007680       Kidney Neoplasms   \n",
       "3  DOID:1793   pancreatic cancer  D010190   Pancreatic Neoplasms   \n",
       "4  DOID:4159         skin cancer  D012878         Skin Neoplasms   \n",
       "\n",
       "                                term_query  n_articles  \n",
       "0  hematologic neoplasms[MeSH Major Topic]       20412  \n",
       "1        brain neoplasms[MeSH Major Topic]      148009  \n",
       "2       kidney neoplasms[MeSH Major Topic]       74244  \n",
       "3   pancreatic neoplasms[MeSH Major Topic]       80499  \n",
       "4         skin neoplasms[MeSH Major Topic]      175588  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "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>doid_code_0</th>\n",
       "      <th>doid_code_1</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>20412</td>\n",
       "      <td>84.913829</td>\n",
       "      <td>240.384872</td>\n",
       "      <td>inf</td>\n",
       "      <td>0.0</td>\n",
       "      <td>20412</td>\n",
       "      <td>20412</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>DOID:1319</td>\n",
       "      <td>104</td>\n",
       "      <td>615.716784</td>\n",
       "      <td>0.168909</td>\n",
       "      <td>0.164065</td>\n",
       "      <td>1.0</td>\n",
       "      <td>20412</td>\n",
       "      <td>148009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>DOID:263</td>\n",
       "      <td>68</td>\n",
       "      <td>308.854711</td>\n",
       "      <td>0.220168</td>\n",
       "      <td>0.216844</td>\n",
       "      <td>1.0</td>\n",
       "      <td>20412</td>\n",
       "      <td>74244</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>DOID:1793</td>\n",
       "      <td>22</td>\n",
       "      <td>334.875483</td>\n",
       "      <td>0.065696</td>\n",
       "      <td>0.064432</td>\n",
       "      <td>1.0</td>\n",
       "      <td>20412</td>\n",
       "      <td>80499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>DOID:4159</td>\n",
       "      <td>318</td>\n",
       "      <td>730.445301</td>\n",
       "      <td>0.435351</td>\n",
       "      <td>0.425374</td>\n",
       "      <td>1.0</td>\n",
       "      <td>20412</td>\n",
       "      <td>175588</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  doid_code_0 doid_code_1  cooccurrence    expected  enrichment  odds_ratio  \\\n",
       "0   DOID:2531   DOID:2531         20412   84.913829  240.384872         inf   \n",
       "1   DOID:2531   DOID:1319           104  615.716784    0.168909    0.164065   \n",
       "2   DOID:2531    DOID:263            68  308.854711    0.220168    0.216844   \n",
       "3   DOID:2531   DOID:1793            22  334.875483    0.065696    0.064432   \n",
       "4   DOID:2531   DOID:4159           318  730.445301    0.435351    0.425374   \n",
       "\n",
       "   p_fisher  n_source  n_target  \n",
       "0       0.0     20412     20412  \n",
       "1       1.0     20412    148009  \n",
       "2       1.0     20412     74244  \n",
       "3       1.0     20412     80499  \n",
       "4       1.0     20412    175588  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cooc_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooc_df = cooc_df[cooc_df['doid_code_0'] != cooc_df['doid_code_1']]\n",
    "doid_name_df = disease_df[['doid_code', 'doid_name']].drop_duplicates()\n",
    "cooc_df = doid_name_df.rename(columns={'doid_code': 'doid_code_1', 'doid_name': 'doid_name_1'}).merge(cooc_df)\n",
    "cooc_df = doid_name_df.rename(columns={'doid_code': 'doid_code_0', 'doid_name': 'doid_name_0'}).merge(cooc_df)\n",
    "cooc_df = cooc_df.sort_values(by=['doid_name_0', 'p_fisher'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "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>doid_code_0</th>\n",
       "      <th>doid_name_0</th>\n",
       "      <th>doid_code_1</th>\n",
       "      <th>doid_name_1</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>7866</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>DOID:14330</td>\n",
       "      <td>Parkinson's disease</td>\n",
       "      <td>2521</td>\n",
       "      <td>1562.065225</td>\n",
       "      <td>1.613889</td>\n",
       "      <td>1.651428</td>\n",
       "      <td>8.873145e-115</td>\n",
       "      <td>104084</td>\n",
       "      <td>73639</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7886</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>157</td>\n",
       "      <td>116.223134</td>\n",
       "      <td>1.350850</td>\n",
       "      <td>1.361746</td>\n",
       "      <td>1.558560e-04</td>\n",
       "      <td>104084</td>\n",
       "      <td>5479</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7878</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>DOID:332</td>\n",
       "      <td>amyotrophic lateral sclerosis</td>\n",
       "      <td>330</td>\n",
       "      <td>451.698379</td>\n",
       "      <td>0.730576</td>\n",
       "      <td>0.725465</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>104084</td>\n",
       "      <td>21294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7800</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>hematologic cancer</td>\n",
       "      <td>2</td>\n",
       "      <td>432.988978</td>\n",
       "      <td>0.004619</td>\n",
       "      <td>0.004502</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>104084</td>\n",
       "      <td>20412</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7801</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>DOID:1319</td>\n",
       "      <td>brain cancer</td>\n",
       "      <td>51</td>\n",
       "      <td>3139.636768</td>\n",
       "      <td>0.016244</td>\n",
       "      <td>0.015422</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>104084</td>\n",
       "      <td>148009</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code_0          doid_name_0 doid_code_1  \\\n",
       "7866  DOID:10652  Alzheimer's disease  DOID:14330   \n",
       "7886  DOID:10652  Alzheimer's disease  DOID:11949   \n",
       "7878  DOID:10652  Alzheimer's disease    DOID:332   \n",
       "7800  DOID:10652  Alzheimer's disease   DOID:2531   \n",
       "7801  DOID:10652  Alzheimer's disease   DOID:1319   \n",
       "\n",
       "                        doid_name_1  cooccurrence     expected  enrichment  \\\n",
       "7866            Parkinson's disease          2521  1562.065225    1.613889   \n",
       "7886      Creutzfeldt-Jakob disease           157   116.223134    1.350850   \n",
       "7878  amyotrophic lateral sclerosis           330   451.698379    0.730576   \n",
       "7800             hematologic cancer             2   432.988978    0.004619   \n",
       "7801                   brain cancer            51  3139.636768    0.016244   \n",
       "\n",
       "      odds_ratio       p_fisher  n_source  n_target  \n",
       "7866    1.651428  8.873145e-115    104084     73639  \n",
       "7886    1.361746   1.558560e-04    104084      5479  \n",
       "7878    0.725465   1.000000e+00    104084     21294  \n",
       "7800    0.004502   1.000000e+00    104084     20412  \n",
       "7801    0.015422   1.000000e+00    104084    148009  "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cooc_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "14520"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(cooc_df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "500"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(cooc_df[cooc_df.p_fisher <= 0.005])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooc_df.to_csv(os.path.join(download_dir,'disease-disease-cooccurrence.tsv'), index=False, sep='\\t')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Symptoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(505, 3)"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read MeSH Symptoms\n",
    "url = '../data/MESH/symptoms.tsv'\n",
    "symptom_df = pandas.read_table(url)\n",
    "symptom_df.shape #505"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "438"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "url = 'https://raw.githubusercontent.com/dhimmel/mesh/e561301360e6de2140dedeaa7c7e17ce4714eb7f/data/symptoms.tsv'\n",
    "hetionet_symptom_df = pandas.read_table(url)\n",
    "hetionet_symptom_ls = hetionet_symptom_df['mesh_name'].tolist()\n",
    "len(hetionet_symptom_ls)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "rows_out = list()\n",
    "\n",
    "for i, row in symptom_df.iterrows(): \n",
    "    term_query = '{symptom}[MeSH Terms:noexp]'.format(symptom = row.mesh_name.lower())\n",
    "    print(row.mesh_name)\n",
    "    if row.mesh_name in hetionet_symptom_ls: # ran thoes terms previously when validating code\n",
    "        path = os.path.join('..s/data/MEDLINE/dhimmel_medline/esearch', format_filename(term_query))\n",
    "        pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    else:\n",
    "        path = efetch_query(term_query)\n",
    "        path = os.path.join(os.getcwd(), path)\n",
    "        pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "    \n",
    "symptom_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[mesh_id                                                 D000006\n",
       " mesh_name                                        Abdomen, Acute\n",
       " in_hsdn                                                       1\n",
       " term_query                     abdomen, acute[MeSH Terms:noexp]\n",
       " n_articles                                                 9939\n",
       " pubmed_ids    11344|28849|29373|38875|42826|45697|46444|4762...\n",
       " Name: 0, dtype: object,\n",
       " mesh_id                                              D000067329\n",
       " mesh_name                         Obesity, Metabolically Benign\n",
       " in_hsdn                                                       0\n",
       " term_query      obesity, metabolically benign[MeSH Terms:noexp]\n",
       " n_articles                                                  498\n",
       " pubmed_ids    23928805|24670711|25443068|25449143|25515498|2...\n",
       " Name: 1, dtype: object,\n",
       " mesh_id                                              D000067404\n",
       " mesh_name                         Social Communication Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query      social communication disorder[MeSH Terms:noexp]\n",
       " n_articles                                                  122\n",
       " pubmed_ids    22928858|24659736|24756919|25039503|25240938|2...\n",
       " Name: 2, dtype: object,\n",
       " mesh_id                                              D000067454\n",
       " mesh_name                      Childhood-Onset Fluency Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query    childhood-onset fluency disorder[MeSH Terms:no...\n",
       " n_articles                                                    4\n",
       " pubmed_ids                  26296615|30142643|32013722|32267336\n",
       " Name: 3, dtype: object,\n",
       " mesh_id                                              D000067559\n",
       " mesh_name                            Specific Learning Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query         specific learning disorder[MeSH Terms:noexp]\n",
       " n_articles                                                   88\n",
       " pubmed_ids    25124507|25243500|25349093|25609675|25807176|2...\n",
       " Name: 4, dtype: object,\n",
       " mesh_id                                              D000068376\n",
       " mesh_name                                    Compassion Fatigue\n",
       " in_hsdn                                                       0\n",
       " term_query                 compassion fatigue[MeSH Terms:noexp]\n",
       " n_articles                                                 1098\n",
       " pubmed_ids    24175955|24306284|24444742|24658288|24698172|2...\n",
       " Name: 5, dtype: object,\n",
       " mesh_id                                              D000068959\n",
       " mesh_name                               Body Weight Maintenance\n",
       " in_hsdn                                                       0\n",
       " term_query            body weight maintenance[MeSH Terms:noexp]\n",
       " n_articles                                                  439\n",
       " pubmed_ids    23482708|24383502|24521459|24670075|24676275|2...\n",
       " Name: 6, dtype: object,\n",
       " mesh_id                                              D000070607\n",
       " mesh_name                                        Morton Neuroma\n",
       " in_hsdn                                                       0\n",
       " term_query                     morton neuroma[MeSH Terms:noexp]\n",
       " n_articles                                                  108\n",
       " pubmed_ids    25920337|25945935|26253529|26344448|26808745|2...\n",
       " Name: 7, dtype: object,\n",
       " mesh_id                                              D000071057\n",
       " mesh_name                                    Tardive Dyskinesia\n",
       " in_hsdn                                                       0\n",
       " term_query                 tardive dyskinesia[MeSH Terms:noexp]\n",
       " n_articles                                                  372\n",
       " pubmed_ids    24595968|26293144|26391425|26398367|26679687|2...\n",
       " Name: 8, dtype: object,\n",
       " mesh_id                                              D000071064\n",
       " mesh_name                       Alert Fatigue, Health Personnel\n",
       " in_hsdn                                                       0\n",
       " term_query    alert fatigue, health personnel[MeSH Terms:noexp]\n",
       " n_articles                                                   71\n",
       " pubmed_ids    25591100|25840128|25849772|26107794|27045060|2...\n",
       " Name: 9, dtype: object,\n",
       " mesh_id                                              D000071257\n",
       " mesh_name                                    Emergence Delirium\n",
       " in_hsdn                                                       0\n",
       " term_query                 emergence delirium[MeSH Terms:noexp]\n",
       " n_articles                                                  841\n",
       " pubmed_ids    24861721|25493435|25976839|26129873|26186683|2...\n",
       " Name: 10, dtype: object,\n",
       " mesh_id                                              D000071697\n",
       " mesh_name                                             Cellulite\n",
       " in_hsdn                                                       0\n",
       " term_query                          cellulite[MeSH Terms:noexp]\n",
       " n_articles                                                  126\n",
       " pubmed_ids    26581783|26687236|27128238|27128239|27264715|2...\n",
       " Name: 11, dtype: object,\n",
       " mesh_id                                              D000071699\n",
       " mesh_name                              Bilateral Vestibulopathy\n",
       " in_hsdn                                                       0\n",
       " term_query           bilateral vestibulopathy[MeSH Terms:noexp]\n",
       " n_articles                                                  197\n",
       " pubmed_ids    26918638|26972747|26980338|27164706|27341473|2...\n",
       " Name: 12, dtype: object,\n",
       " mesh_id                                              D000071896\n",
       " mesh_name                        Medically Unexplained Symptoms\n",
       " in_hsdn                                                       0\n",
       " term_query     medically unexplained symptoms[MeSH Terms:noexp]\n",
       " n_articles                                                 1087\n",
       " pubmed_ids    24953100|25684117|25800718|25979224|26200244|2...\n",
       " Name: 13, dtype: object,\n",
       " mesh_id                                              D000072716\n",
       " mesh_name                                           Cancer Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                        cancer pain[MeSH Terms:noexp]\n",
       " n_articles                                                 2524\n",
       " pubmed_ids    25163678|25324418|25376224|25384692|25434499|2...\n",
       " Name: 14, dtype: object,\n",
       " mesh_id                                              D000073818\n",
       " mesh_name                                      Pain, Procedural\n",
       " in_hsdn                                                       0\n",
       " term_query                   pain, procedural[MeSH Terms:noexp]\n",
       " n_articles                                                  818\n",
       " pubmed_ids    26625989|26685099|26735141|26889618|26914846|2...\n",
       " Name: 15, dtype: object,\n",
       " mesh_id                                              D000073839\n",
       " mesh_name                                   Trisomy 13 Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                trisomy 13 syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  585\n",
       " pubmed_ids    13874423|13922200|14047475|14104609|14117602|1...\n",
       " Name: 16, dtype: object,\n",
       " mesh_id                                              D000073923\n",
       " mesh_name                                      Food Intolerance\n",
       " in_hsdn                                                       0\n",
       " term_query                   food intolerance[MeSH Terms:noexp]\n",
       " n_articles                                                  158\n",
       " pubmed_ids    26082336|26968464|27085755|27355647|27356007|2...\n",
       " Name: 17, dtype: object,\n",
       " mesh_id                                              D000075122\n",
       " mesh_name                           Smoldering Multiple Myeloma\n",
       " in_hsdn                                                       0\n",
       " term_query        smoldering multiple myeloma[MeSH Terms:noexp]\n",
       " n_articles                                                  181\n",
       " pubmed_ids    27402144|27605200|27768092|27804161|27908223|2...\n",
       " Name: 18, dtype: object,\n",
       " mesh_id                                              D000075562\n",
       " mesh_name                               Charles Bonnet Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query            charles bonnet syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   81\n",
       " pubmed_ids    27296495|27425775|27984353|28038923|28081973|2...\n",
       " Name: 19, dtype: object,\n",
       " mesh_id                                              D000076042\n",
       " mesh_name                          Alcoholic Korsakoff Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query       alcoholic korsakoff syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   16\n",
       " pubmed_ids    27567191|28340112|28988573|29079031|29273599|2...\n",
       " Name: 20, dtype: object,\n",
       " mesh_id                                              D000076082\n",
       " mesh_name                                Travel-Related Illness\n",
       " in_hsdn                                                       0\n",
       " term_query             travel-related illness[MeSH Terms:noexp]\n",
       " n_articles                                                 1097\n",
       " pubmed_ids    21170723|22231864|22892092|23042064|23202153|2...\n",
       " Name: 21, dtype: object,\n",
       " mesh_id                                              D000077260\n",
       " mesh_name                                            Sleepiness\n",
       " in_hsdn                                                       0\n",
       " term_query                         sleepiness[MeSH Terms:noexp]\n",
       " n_articles                                                 1003\n",
       " pubmed_ids    27662510|27754703|27880055|28057497|28153870|2...\n",
       " Name: 22, dtype: object,\n",
       " mesh_id                                              D000077295\n",
       " mesh_name                          Urinary Bladder, Underactive\n",
       " in_hsdn                                                       0\n",
       " term_query       urinary bladder, underactive[MeSH Terms:noexp]\n",
       " n_articles                                                  204\n",
       " pubmed_ids    27436428|27891667|27979541|28054476|28122392|2...\n",
       " Name: 23, dtype: object,\n",
       " mesh_id                                              D000077962\n",
       " mesh_name                                Body-Weight Trajectory\n",
       " in_hsdn                                                       0\n",
       " term_query             body-weight trajectory[MeSH Terms:noexp]\n",
       " n_articles                                                  269\n",
       " pubmed_ids    28276623|28668555|28877776|29089100|29117506|2...\n",
       " Name: 24, dtype: object,\n",
       " mesh_id                                              D000078064\n",
       " mesh_name                               Gestational Weight Gain\n",
       " in_hsdn                                                       0\n",
       " term_query            gestational weight gain[MeSH Terms:noexp]\n",
       " n_articles                                                 1493\n",
       " pubmed_ids    27653336|28110579|28220604|28279085|28398550|2...\n",
       " Name: 25, dtype: object,\n",
       " mesh_id                                              D000079262\n",
       " mesh_name                                     Obesity, Maternal\n",
       " in_hsdn                                                       0\n",
       " term_query                  obesity, maternal[MeSH Terms:noexp]\n",
       " n_articles                                                  716\n",
       " pubmed_ids    29764530|29797415|29976116|30010829|30102071|3...\n",
       " Name: 26, dtype: object,\n",
       " mesh_id                                              D000079689\n",
       " mesh_name                           Opioid-Induced Constipation\n",
       " in_hsdn                                                       0\n",
       " term_query        opioid-induced constipation[MeSH Terms:noexp]\n",
       " n_articles                                                  122\n",
       " pubmed_ids    29207909|29730600|30125008|30181003|30821019|3...\n",
       " Name: 27, dtype: object,\n",
       " mesh_id                                              D000080311\n",
       " mesh_name                                           Synesthesia\n",
       " in_hsdn                                                       0\n",
       " term_query                        synesthesia[MeSH Terms:noexp]\n",
       " n_articles                                                  326\n",
       " pubmed_ids    13429016|14368215|20273043|21745663|22060011|2...\n",
       " Name: 28, dtype: object,\n",
       " mesh_id                                              D000080422\n",
       " mesh_name                                    Locked-In Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                 locked-in syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   54\n",
       " pubmed_ids    28750192|29024696|30609233|30663899|30700310|3...\n",
       " Name: 29, dtype: object,\n",
       " mesh_id                                              D000080888\n",
       " mesh_name                            Specific Language Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query         specific language disorder[MeSH Terms:noexp]\n",
       " n_articles                                                   76\n",
       " pubmed_ids    29790413|29800056|29800148|30102084|30183450|3...\n",
       " Name: 30, dtype: object,\n",
       " mesh_id                                              D000082643\n",
       " mesh_name                            Cerebral Cortical Thinning\n",
       " in_hsdn                                                       0\n",
       " term_query         cerebral cortical thinning[MeSH Terms:noexp]\n",
       " n_articles                                                  120\n",
       " pubmed_ids    31615588|31696728|31901790|32067281|32088317|3...\n",
       " Name: 31, dtype: object,\n",
       " mesh_id                                              D000084462\n",
       " mesh_name                                          Hyperthermia\n",
       " in_hsdn                                                       0\n",
       " term_query                       hyperthermia[MeSH Terms:noexp]\n",
       " n_articles                                                  392\n",
       " pubmed_ids    30764960|30961698|31051045|31449000|31548181|3...\n",
       " Name: 32, dtype: object,\n",
       " mesh_id                                              D000086582\n",
       " mesh_name                                               Anosmia\n",
       " in_hsdn                                                       0\n",
       " term_query                            anosmia[MeSH Terms:noexp]\n",
       " n_articles                                                  653\n",
       " pubmed_ids    31377305|31606429|31650878|31863844|31864071|3...\n",
       " Name: 33, dtype: object,\n",
       " mesh_id                                              D000086722\n",
       " mesh_name                                            Rhinorrhea\n",
       " in_hsdn                                                       0\n",
       " term_query                         rhinorrhea[MeSH Terms:noexp]\n",
       " n_articles                                                  120\n",
       " pubmed_ids    31021428|31581835|31838209|31982378|32001132|3...\n",
       " Name: 34, dtype: object,\n",
       " mesh_id                                              D000087122\n",
       " mesh_name                                                 Mania\n",
       " in_hsdn                                                       0\n",
       " term_query                              mania[MeSH Terms:noexp]\n",
       " n_articles                                                  599\n",
       " pubmed_ids    30022042|30418230|30761816|30873919|30887861|3...\n",
       " Name: 35, dtype: object,\n",
       " mesh_id                                              D000089083\n",
       " mesh_name                                             Body Odor\n",
       " in_hsdn                                                       0\n",
       " term_query                          body odor[MeSH Terms:noexp]\n",
       " n_articles                                                   43\n",
       " pubmed_ids    33482257|33622150|34133735|34312746|34343779|3...\n",
       " Name: 36, dtype: object,\n",
       " mesh_id                                              D000089965\n",
       " mesh_name                                      Erythema Ab Igne\n",
       " in_hsdn                                                       0\n",
       " term_query                   erythema ab igne[MeSH Terms:noexp]\n",
       " n_articles                                                   15\n",
       " pubmed_ids    34086363|34750732|34793750|35753063|35830702|3...\n",
       " Name: 37, dtype: object,\n",
       " mesh_id                                              D000091323\n",
       " mesh_name                     Psychogenic Nonepileptic Seizures\n",
       " in_hsdn                                                       0\n",
       " term_query    psychogenic nonepileptic seizures[MeSH Terms:n...\n",
       " n_articles                                                   70\n",
       " pubmed_ids    34126844|34288577|34339046|34396517|34408004|3...\n",
       " Name: 38, dtype: object,\n",
       " mesh_id                                              D000091622\n",
       " mesh_name                                        Weight Cycling\n",
       " in_hsdn                                                       0\n",
       " term_query                     weight cycling[MeSH Terms:noexp]\n",
       " n_articles                                                   24\n",
       " pubmed_ids    32745374|33002323|33285599|33938536|34470676|3...\n",
       " Name: 39, dtype: object,\n",
       " mesh_id                                              D000092129\n",
       " mesh_name                        Platypnea Orthodeoxia Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query     platypnea orthodeoxia syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   16\n",
       " pubmed_ids    34118260|36104196|36681524|36869700|37092323|3...\n",
       " Name: 40, dtype: object,\n",
       " mesh_id                                              D000092162\n",
       " mesh_name                                          Crystalluria\n",
       " in_hsdn                                                       0\n",
       " term_query                       crystalluria[MeSH Terms:noexp]\n",
       " n_articles                                                    6\n",
       " pubmed_ids    36179111|36896674|37120787|37552266|38480876|3...\n",
       " Name: 41, dtype: object,\n",
       " mesh_id                                              D000092164\n",
       " mesh_name                                         Lagophthalmos\n",
       " in_hsdn                                                       0\n",
       " term_query                      lagophthalmos[MeSH Terms:noexp]\n",
       " n_articles                                                   31\n",
       " pubmed_ids    35788264|35801669|35880799|35969387|36008056|3...\n",
       " Name: 42, dtype: object,\n",
       " mesh_id                         D000092582\n",
       " mesh_name                       Drug Fever\n",
       " in_hsdn                                  0\n",
       " term_query    drug fever[MeSH Terms:noexp]\n",
       " n_articles                               2\n",
       " pubmed_ids               35421323|37690845\n",
       " Name: 43, dtype: object,\n",
       " mesh_id                                              D000094222\n",
       " mesh_name                                 Dropped Head Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query              dropped head syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   11\n",
       " pubmed_ids    36781488|36984527|37106329|37462538|37594757|3...\n",
       " Name: 44, dtype: object,\n",
       " mesh_id                                    D000095027\n",
       " mesh_name                       Overtraining Syndrome\n",
       " in_hsdn                                             0\n",
       " term_query    overtraining syndrome[MeSH Terms:noexp]\n",
       " n_articles                                          3\n",
       " pubmed_ids                 36195264|38068774|38256312\n",
       " Name: 45, dtype: object,\n",
       " mesh_id                                              D000096822\n",
       " mesh_name                                         Chronic Cough\n",
       " in_hsdn                                                       0\n",
       " term_query                      chronic cough[MeSH Terms:noexp]\n",
       " n_articles                                                   56\n",
       " pubmed_ids    34969556|35012819|37078851|37210335|37289310|3...\n",
       " Name: 46, dtype: object,\n",
       " mesh_id                                            D000097742\n",
       " mesh_name                       Patient-Ventilator Asynchrony\n",
       " in_hsdn                                                     0\n",
       " term_query    patient-ventilator asynchrony[MeSH Terms:noexp]\n",
       " n_articles                                                  3\n",
       " pubmed_ids                         38267230|38267232|38384216\n",
       " Name: 47, dtype: object,\n",
       " mesh_id                                              D000097815\n",
       " mesh_name                                  Emotional Exhaustion\n",
       " in_hsdn                                                       0\n",
       " term_query               emotional exhaustion[MeSH Terms:noexp]\n",
       " n_articles                                                   49\n",
       " pubmed_ids    35707875|37000679|37011228|37235818|37237140|3...\n",
       " Name: 48, dtype: object,\n",
       " mesh_id                                         D000097942\n",
       " mesh_name                             Hearing Loss, Hidden\n",
       " in_hsdn                                                  0\n",
       " term_query          hearing loss, hidden[MeSH Terms:noexp]\n",
       " n_articles                                               5\n",
       " pubmed_ids    38096707|38335624|38345574|38570765|38677986\n",
       " Name: 49, dtype: object,\n",
       " mesh_id                                                 D000270\n",
       " mesh_name                                         Adie Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                      adie syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  347\n",
       " pubmed_ids    130187|165138|304687|333920|427422|431019|4347...\n",
       " Name: 50, dtype: object,\n",
       " mesh_id                                                 D000326\n",
       " mesh_name                                  Adrenoleukodystrophy\n",
       " in_hsdn                                                       0\n",
       " term_query               adrenoleukodystrophy[MeSH Terms:noexp]\n",
       " n_articles                                                 1934\n",
       " pubmed_ids    803065|1279999|1282286|1303197|1308395|1313076...\n",
       " Name: 51, dtype: object,\n",
       " mesh_id                                                 D000334\n",
       " mesh_name                                             Aerophagy\n",
       " in_hsdn                                                       1\n",
       " term_query                          aerophagy[MeSH Terms:noexp]\n",
       " n_articles                                                  292\n",
       " pubmed_ids    7223|110642|119877|259191|550616|560312|617555...\n",
       " Name: 52, dtype: object,\n",
       " mesh_id                                                 D000370\n",
       " mesh_name                                               Ageusia\n",
       " in_hsdn                                                       1\n",
       " term_query                            ageusia[MeSH Terms:noexp]\n",
       " n_articles                                                  522\n",
       " pubmed_ids    47475|47586|48964|90241|134235|136568|219460|3...\n",
       " Name: 53, dtype: object,\n",
       " mesh_id                                                 D000377\n",
       " mesh_name                                               Agnosia\n",
       " in_hsdn                                                       1\n",
       " term_query                            agnosia[MeSH Terms:noexp]\n",
       " n_articles                                                 2542\n",
       " pubmed_ids    21131|64315|80763|90746|92327|93071|96302|1048...\n",
       " Name: 54, dtype: object,\n",
       " mesh_id                                                 D000381\n",
       " mesh_name                                              Agraphia\n",
       " in_hsdn                                                       1\n",
       " term_query                           agraphia[MeSH Terms:noexp]\n",
       " n_articles                                                 1043\n",
       " pubmed_ids    82254|186900|268518|326279|355914|438836|44055...\n",
       " Name: 55, dtype: object,\n",
       " mesh_id                                                 D000419\n",
       " mesh_name                                           Albuminuria\n",
       " in_hsdn                                                       1\n",
       " term_query                        albuminuria[MeSH Terms:noexp]\n",
       " n_articles                                                16785\n",
       " pubmed_ids    2994|31993|46019|50606|50607|50608|50609|51408...\n",
       " Name: 56, dtype: object,\n",
       " mesh_id                                                 D000472\n",
       " mesh_name                                Alkalosis, Respiratory\n",
       " in_hsdn                                                       0\n",
       " term_query             alkalosis, respiratory[MeSH Terms:noexp]\n",
       " n_articles                                                  951\n",
       " pubmed_ids    132|210|911|940|1867|2014|4414|4415|5742|7012|...\n",
       " Name: 57, dtype: object,\n",
       " mesh_id                                                 D000550\n",
       " mesh_name                                             Amblyopia\n",
       " in_hsdn                                                       1\n",
       " term_query                          amblyopia[MeSH Terms:noexp]\n",
       " n_articles                                                 7405\n",
       " pubmed_ids    76084|76250|78334|97607|97608|98048|104083|114...\n",
       " Name: 58, dtype: object,\n",
       " mesh_id                                                 D000647\n",
       " mesh_name                                               Amnesia\n",
       " in_hsdn                                                       1\n",
       " term_query                            amnesia[MeSH Terms:noexp]\n",
       " n_articles                                                 7726\n",
       " pubmed_ids    3429|4082|7093|7285|11493|11960|13599|13600|14...\n",
       " Name: 59, dtype: object,\n",
       " mesh_id                                                 D000648\n",
       " mesh_name                                   Amnesia, Retrograde\n",
       " in_hsdn                                                       1\n",
       " term_query                amnesia, retrograde[MeSH Terms:noexp]\n",
       " n_articles                                                  961\n",
       " pubmed_ids    9838|16586|20664|34806|74520|101643|172961|183...\n",
       " Name: 60, dtype: object,\n",
       " mesh_id                                                 D000787\n",
       " mesh_name                                       Angina Pectoris\n",
       " in_hsdn                                                       1\n",
       " term_query                    angina pectoris[MeSH Terms:noexp]\n",
       " n_articles                                                33231\n",
       " pubmed_ids    458|523|837|1567|2092|2455|2973|3701|3894|4080...\n",
       " Name: 61, dtype: object,\n",
       " mesh_id                                                 D000788\n",
       " mesh_name                              Angina Pectoris, Variant\n",
       " in_hsdn                                                       1\n",
       " term_query           angina pectoris, variant[MeSH Terms:noexp]\n",
       " n_articles                                                 2002\n",
       " pubmed_ids    16737|25720|28835|28836|31165|39319|43362|7548...\n",
       " Name: 62, dtype: object,\n",
       " mesh_id                                                 D000789\n",
       " mesh_name                                      Angina, Unstable\n",
       " in_hsdn                                                       1\n",
       " term_query                   angina, unstable[MeSH Terms:noexp]\n",
       " n_articles                                                 9440\n",
       " pubmed_ids    1284005|1284135|1285959|1286473|1287305|128883...\n",
       " Name: 63, dtype: object,\n",
       " mesh_id                                                 D000849\n",
       " mesh_name                                                Anomia\n",
       " in_hsdn                                                       1\n",
       " term_query                             anomia[MeSH Terms:noexp]\n",
       " n_articles                                                 1114\n",
       " pubmed_ids    90437|95004|261360|476474|477337|487066|487071...\n",
       " Name: 64, dtype: object,\n",
       " mesh_id                                                 D000855\n",
       " mesh_name                                              Anorexia\n",
       " in_hsdn                                                       1\n",
       " term_query                           anorexia[MeSH Terms:noexp]\n",
       " n_articles                                                 5534\n",
       " pubmed_ids    2658|2670|12272|18079|19680|37457|43548|52853|...\n",
       " Name: 65, dtype: object,\n",
       " mesh_id                                                 D000857\n",
       " mesh_name                                   Olfaction Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                olfaction disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 5883\n",
       " pubmed_ids    15231|39377|40902|47475|48964|63653|66751|8127...\n",
       " Name: 66, dtype: object,\n",
       " mesh_id                                                 D000860\n",
       " mesh_name                                               Hypoxia\n",
       " in_hsdn                                                       1\n",
       " term_query                            hypoxia[MeSH Terms:noexp]\n",
       " n_articles                                                75836\n",
       " pubmed_ids    23|103|111|132|171|210|535|756|821|930|935|119...\n",
       " Name: 67, dtype: object,\n",
       " mesh_id                                                 D001037\n",
       " mesh_name                                               Aphasia\n",
       " in_hsdn                                                       1\n",
       " term_query                            aphasia[MeSH Terms:noexp]\n",
       " n_articles                                                11021\n",
       " pubmed_ids    12560|17757|21131|29248|32831|47157|49227|4973...\n",
       " Name: 68, dtype: object,\n",
       " mesh_id                                                 D001039\n",
       " mesh_name                                        Aphasia, Broca\n",
       " in_hsdn                                                       1\n",
       " term_query                     aphasia, broca[MeSH Terms:noexp]\n",
       " n_articles                                                 1683\n",
       " pubmed_ids    90437|93771|94417|95004|261360|388738|396957|4...\n",
       " Name: 69, dtype: object,\n",
       " mesh_id                                                 D001041\n",
       " mesh_name                                     Aphasia, Wernicke\n",
       " in_hsdn                                                       1\n",
       " term_query                  aphasia, wernicke[MeSH Terms:noexp]\n",
       " n_articles                                                  905\n",
       " pubmed_ids    90437|92323|94417|95004|225810|261360|388738|4...\n",
       " Name: 70, dtype: object,\n",
       " mesh_id                                                 D001044\n",
       " mesh_name                                               Aphonia\n",
       " in_hsdn                                                       1\n",
       " term_query                            aphonia[MeSH Terms:noexp]\n",
       " n_articles                                                  365\n",
       " pubmed_ids    52730|68230|69128|127286|135162|155261|186892|...\n",
       " Name: 71, dtype: object,\n",
       " mesh_id                                                 D001049\n",
       " mesh_name                                                 Apnea\n",
       " in_hsdn                                                       1\n",
       " term_query                              apnea[MeSH Terms:noexp]\n",
       " n_articles                                                 7782\n",
       " pubmed_ids    2432|4588|5894|6374|11459|12578|14066|14241|16...\n",
       " Name: 72, dtype: object,\n",
       " mesh_id                                                 D001072\n",
       " mesh_name                                              Apraxias\n",
       " in_hsdn                                                       1\n",
       " term_query                           apraxias[MeSH Terms:noexp]\n",
       " n_articles                                                 3209\n",
       " pubmed_ids    56586|90746|172774|174346|186900|242381|246410...\n",
       " Name: 73, dtype: object,\n",
       " mesh_id                                                 D001184\n",
       " mesh_name                                Articulation Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query             articulation disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 1823\n",
       " pubmed_ids    83329|282235|291350|293303|295003|358035|36589...\n",
       " Name: 74, dtype: object,\n",
       " mesh_id                                                 D001247\n",
       " mesh_name                                              Asthenia\n",
       " in_hsdn                                                       1\n",
       " term_query                           asthenia[MeSH Terms:noexp]\n",
       " n_articles                                                 1796\n",
       " pubmed_ids    5703|24883|113285|115079|120237|151377|153486|...\n",
       " Name: 75, dtype: object,\n",
       " mesh_id                                                 D001259\n",
       " mesh_name                                                Ataxia\n",
       " in_hsdn                                                       1\n",
       " term_query                             ataxia[MeSH Terms:noexp]\n",
       " n_articles                                                 9259\n",
       " pubmed_ids    1978|4581|6289|8592|10587|19262|19327|32746|35...\n",
       " Name: 76, dtype: object,\n",
       " mesh_id                                                 D001260\n",
       " mesh_name                                 Ataxia Telangiectasia\n",
       " in_hsdn                                                       0\n",
       " term_query              ataxia telangiectasia[MeSH Terms:noexp]\n",
       " n_articles                                                 3530\n",
       " pubmed_ids    20760|21141|42947|46982|49401|52431|52619|5354...\n",
       " Name: 77, dtype: object,\n",
       " mesh_id                                                 D001264\n",
       " mesh_name                                             Athetosis\n",
       " in_hsdn                                                       1\n",
       " term_query                          athetosis[MeSH Terms:noexp]\n",
       " n_articles                                                 1367\n",
       " pubmed_ids    42528|51076|72935|75957|124239|132674|145391|1...\n",
       " Name: 78, dtype: object,\n",
       " mesh_id                                                 D001308\n",
       " mesh_name                         Auditory Perceptual Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query      auditory perceptual disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 1496\n",
       " pubmed_ids    489864|491550|509854|523867|555248|573491|1353...\n",
       " Name: 79, dtype: object,\n",
       " mesh_id                                                 D001416\n",
       " mesh_name                                             Back Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                          back pain[MeSH Terms:noexp]\n",
       " n_articles                                                19262\n",
       " pubmed_ids    14381|16992|17090|21068|29540|34814|43329|4704...\n",
       " Name: 80, dtype: object,\n",
       " mesh_id                                                 D001724\n",
       " mesh_name                                          Birth Weight\n",
       " in_hsdn                                                       1\n",
       " term_query                       birth weight[MeSH Terms:noexp]\n",
       " n_articles                                                45224\n",
       " pubmed_ids    545|2130|2137|4009|4863|7767|12636|13347|14248...\n",
       " Name: 81, dtype: object,\n",
       " mesh_id                                                 D001750\n",
       " mesh_name                           Urinary Bladder, Neurogenic\n",
       " in_hsdn                                                       1\n",
       " term_query        urinary bladder, neurogenic[MeSH Terms:noexp]\n",
       " n_articles                                                 8037\n",
       " pubmed_ids    4915|13031|16422|17757|18862|20562|21482|24019...\n",
       " Name: 82, dtype: object,\n",
       " mesh_id                                                 D001766\n",
       " mesh_name                                             Blindness\n",
       " in_hsdn                                                       1\n",
       " term_query                          blindness[MeSH Terms:noexp]\n",
       " n_articles                                                21757\n",
       " pubmed_ids    7131|8644|11193|11692|17757|17900|22827|35865|...\n",
       " Name: 83, dtype: object,\n",
       " mesh_id                                          D001832\n",
       " mesh_name                       Body Temperature Changes\n",
       " in_hsdn                                                0\n",
       " term_query    body temperature changes[MeSH Terms:noexp]\n",
       " n_articles                                             0\n",
       " pubmed_ids                                              \n",
       " Name: 84, dtype: object,\n",
       " mesh_id                                                 D001835\n",
       " mesh_name                                           Body Weight\n",
       " in_hsdn                                                       1\n",
       " term_query                        body weight[MeSH Terms:noexp]\n",
       " n_articles                                               200969\n",
       " pubmed_ids    7|150|185|550|648|691|734|744|1179|1184|1195|1...\n",
       " Name: 85, dtype: object,\n",
       " mesh_id                                                 D001836\n",
       " mesh_name                                   Body Weight Changes\n",
       " in_hsdn                                                       1\n",
       " term_query                body weight changes[MeSH Terms:noexp]\n",
       " n_articles                                                   10\n",
       " pubmed_ids    10591335|10643834|10960507|11023988|20274321|3...\n",
       " Name: 86, dtype: object,\n",
       " mesh_id                                                 D001926\n",
       " mesh_name                                           Brain Death\n",
       " in_hsdn                                                       0\n",
       " term_query                        brain death[MeSH Terms:noexp]\n",
       " n_articles                                                 9627\n",
       " pubmed_ids    4365|7155|27735|28015|34345|34346|34347|36321|...\n",
       " Name: 87, dtype: object,\n",
       " mesh_id                                                 D002032\n",
       " mesh_name                                               Bulimia\n",
       " in_hsdn                                                       1\n",
       " term_query                            bulimia[MeSH Terms:noexp]\n",
       " n_articles                                                 6004\n",
       " pubmed_ids    1285793|1289956|1291541|1291542|1293995|129427...\n",
       " Name: 88, dtype: object,\n",
       " mesh_id                                                 D002100\n",
       " mesh_name                                              Cachexia\n",
       " in_hsdn                                                       1\n",
       " term_query                           cachexia[MeSH Terms:noexp]\n",
       " n_articles                                                 6496\n",
       " pubmed_ids    3045|7132|9747|36657|52395|67497|72639|82238|9...\n",
       " Name: 89, dtype: object,\n",
       " mesh_id                                                 D002303\n",
       " mesh_name                                   Cardiac Output, Low\n",
       " in_hsdn                                                       1\n",
       " term_query                cardiac output, low[MeSH Terms:noexp]\n",
       " n_articles                                                 5621\n",
       " pubmed_ids    316312|383392|396384|399949|401438|477284|4807...\n",
       " Name: 90, dtype: object,\n",
       " mesh_id                                                 D002375\n",
       " mesh_name                                             Catalepsy\n",
       " in_hsdn                                                       1\n",
       " term_query                          catalepsy[MeSH Terms:noexp]\n",
       " n_articles                                                 2565\n",
       " pubmed_ids    9643|10058|11519|12393|12477|14836|15078|18881...\n",
       " Name: 91, dtype: object,\n",
       " mesh_id                                                 D002385\n",
       " mesh_name                                             Cataplexy\n",
       " in_hsdn                                                       0\n",
       " term_query                          cataplexy[MeSH Terms:noexp]\n",
       " n_articles                                                 1100\n",
       " pubmed_ids    51783|57711|67478|72649|78798|86618|91504|9183...\n",
       " Name: 92, dtype: object,\n",
       " mesh_id                                                 D002389\n",
       " mesh_name                                             Catatonia\n",
       " in_hsdn                                                       1\n",
       " term_query                          catatonia[MeSH Terms:noexp]\n",
       " n_articles                                                 2940\n",
       " pubmed_ids    7779|7796|10748|33302|41885|58326|73023|73343|...\n",
       " Name: 93, dtype: object,\n",
       " mesh_id                                                 D002422\n",
       " mesh_name                                             Causalgia\n",
       " in_hsdn                                                       0\n",
       " term_query                          causalgia[MeSH Terms:noexp]\n",
       " n_articles                                                  694\n",
       " pubmed_ids    49238|54286|79303|79817|111063|123575|162892|1...\n",
       " Name: 94, dtype: object,\n",
       " mesh_id                                                 D002524\n",
       " mesh_name                                     Cerebellar Ataxia\n",
       " in_hsdn                                                       1\n",
       " term_query                  cerebellar ataxia[MeSH Terms:noexp]\n",
       " n_articles                                                 5436\n",
       " pubmed_ids    52438|60474|62313|66751|68352|70516|80123|8128...\n",
       " Name: 95, dtype: object,\n",
       " mesh_id                                                 D002534\n",
       " mesh_name                                        Hypoxia, Brain\n",
       " in_hsdn                                                       0\n",
       " term_query                     hypoxia, brain[MeSH Terms:noexp]\n",
       " n_articles                                                 7425\n",
       " pubmed_ids    750|930|1045|1047|1292|6630|7284|11871|12499|1...\n",
       " Name: 96, dtype: object,\n",
       " mesh_id                                                 D002558\n",
       " mesh_name                          Cerebrospinal Fluid Otorrhea\n",
       " in_hsdn                                                       1\n",
       " term_query       cerebrospinal fluid otorrhea[MeSH Terms:noexp]\n",
       " n_articles                                                 1102\n",
       " pubmed_ids    17778|127303|127304|129530|149836|158632|28734...\n",
       " Name: 97, dtype: object,\n",
       " mesh_id                                                 D002559\n",
       " mesh_name                        Cerebrospinal Fluid Rhinorrhea\n",
       " in_hsdn                                                       1\n",
       " term_query     cerebrospinal fluid rhinorrhea[MeSH Terms:noexp]\n",
       " n_articles                                                 3090\n",
       " pubmed_ids    3036|17778|55493|72972|84866|98024|127303|1296...\n",
       " Name: 98, dtype: object,\n",
       " mesh_id                                                 D002637\n",
       " mesh_name                                            Chest Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                         chest pain[MeSH Terms:noexp]\n",
       " n_articles                                                15383\n",
       " pubmed_ids    263848|1279627|1286187|1287109|1287528|1287529...\n",
       " Name: 99, dtype: object,\n",
       " mesh_id                                                 D002639\n",
       " mesh_name                             Cheyne-Stokes Respiration\n",
       " in_hsdn                                                       1\n",
       " term_query          cheyne-stokes respiration[MeSH Terms:noexp]\n",
       " n_articles                                                  814\n",
       " pubmed_ids    103|54248|92669|121191|209541|216294|236120|23...\n",
       " Name: 100, dtype: object,\n",
       " mesh_id                                                 D002819\n",
       " mesh_name                                                Chorea\n",
       " in_hsdn                                                       1\n",
       " term_query                             chorea[MeSH Terms:noexp]\n",
       " n_articles                                                 4595\n",
       " pubmed_ids    607|5704|30103|33450|36255|38189|38580|39203|4...\n",
       " Name: 101, dtype: object,\n",
       " mesh_id                                                 D002832\n",
       " mesh_name                                    Choroid Hemorrhage\n",
       " in_hsdn                                                       0\n",
       " term_query                 choroid hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                  483\n",
       " pubmed_ids    233868|1300298|1300305|1403754|1454320|1454322...\n",
       " Name: 102, dtype: object,\n",
       " mesh_id                                                 D003117\n",
       " mesh_name                                  Color Vision Defects\n",
       " in_hsdn                                                       1\n",
       " term_query               color vision defects[MeSH Terms:noexp]\n",
       " n_articles                                                 4271\n",
       " pubmed_ids    17031|68108|74522|89953|93200|100181|102918|11...\n",
       " Name: 103, dtype: object,\n",
       " mesh_id                                                 D003128\n",
       " mesh_name                                                  Coma\n",
       " in_hsdn                                                       1\n",
       " term_query                               coma[MeSH Terms:noexp]\n",
       " n_articles                                                13383\n",
       " pubmed_ids    608|3270|4950|5022|8960|10876|12405|15481|1548...\n",
       " Name: 104, dtype: object,\n",
       " mesh_id                                                 D003147\n",
       " mesh_name                               Communication Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query            communication disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 2977\n",
       " pubmed_ids    803154|1284525|1284672|1301897|1301898|1301899...\n",
       " Name: 105, dtype: object,\n",
       " mesh_id                                                 D003221\n",
       " mesh_name                                             Confusion\n",
       " in_hsdn                                                       1\n",
       " term_query                          confusion[MeSH Terms:noexp]\n",
       " n_articles                                                 5168\n",
       " pubmed_ids    14487|17757|20459|21577|21943|23037|24615|2894...\n",
       " Name: 106, dtype: object,\n",
       " mesh_id                                                 D003244\n",
       " mesh_name                               Consciousness Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query            consciousness disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 3465\n",
       " pubmed_ids    24394|26808|32517|35450|37487|68103|69688|7964...\n",
       " Name: 107, dtype: object,\n",
       " mesh_id                                                 D003248\n",
       " mesh_name                                          Constipation\n",
       " in_hsdn                                                       1\n",
       " term_query                       constipation[MeSH Terms:noexp]\n",
       " n_articles                                                16545\n",
       " pubmed_ids    772|9893|18033|21388|33647|37142|39581|43813|4...\n",
       " Name: 108, dtype: object,\n",
       " mesh_id                                                 D003294\n",
       " mesh_name                                     Seizures, Febrile\n",
       " in_hsdn                                                       0\n",
       " term_query                  seizures, febrile[MeSH Terms:noexp]\n",
       " n_articles                                                 3317\n",
       " pubmed_ids    11767|23077|23078|32517|65496|69799|75103|8947...\n",
       " Name: 109, dtype: object,\n",
       " mesh_id                                                 D003371\n",
       " mesh_name                                                 Cough\n",
       " in_hsdn                                                       1\n",
       " term_query                              cough[MeSH Terms:noexp]\n",
       " n_articles                                                19141\n",
       " pubmed_ids    2883|3958|6392|8057|11229|14304|22340|24251|25...\n",
       " Name: 110, dtype: object,\n",
       " mesh_id                                                 D003410\n",
       " mesh_name                                  Cri-du-Chat Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query               cri-du-chat syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  702\n",
       " pubmed_ids    48327|83210|123406|123495|123707|124938|126409...\n",
       " Name: 111, dtype: object,\n",
       " mesh_id                                                 D003490\n",
       " mesh_name                                              Cyanosis\n",
       " in_hsdn                                                       1\n",
       " term_query                           cyanosis[MeSH Terms:noexp]\n",
       " n_articles                                                 4915\n",
       " pubmed_ids    2365|5699|10821|11519|16544|24334|47717|48193|...\n",
       " Name: 112, dtype: object,\n",
       " mesh_id                                                 D003635\n",
       " mesh_name                                     De Lange Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                  de lange syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  921\n",
       " pubmed_ids    70333|136323|149292|230869|249473|258458|40913...\n",
       " Name: 113, dtype: object,\n",
       " mesh_id                                                 D003638\n",
       " mesh_name                                              Deafness\n",
       " in_hsdn                                                       1\n",
       " term_query                           deafness[MeSH Terms:noexp]\n",
       " n_articles                                                29556\n",
       " pubmed_ids    2799|3912|8671|9371|11457|13157|16178|16241|16...\n",
       " Name: 114, dtype: object,\n",
       " mesh_id                                                 D003639\n",
       " mesh_name                                  Hearing Loss, Sudden\n",
       " in_hsdn                                                       1\n",
       " term_query               hearing loss, sudden[MeSH Terms:noexp]\n",
       " n_articles                                                 3011\n",
       " pubmed_ids    31054|151724|214643|228139|231159|310011|31209...\n",
       " Name: 115, dtype: object,\n",
       " mesh_id                                                 D003655\n",
       " mesh_name                                     Decerebrate State\n",
       " in_hsdn                                                       1\n",
       " term_query                  decerebrate state[MeSH Terms:noexp]\n",
       " n_articles                                                 4823\n",
       " pubmed_ids    12984|15088|15267|16841|19217|19302|19789|1983...\n",
       " Name: 116, dtype: object,\n",
       " mesh_id                                                 D003693\n",
       " mesh_name                                              Delirium\n",
       " in_hsdn                                                       1\n",
       " term_query                           delirium[MeSH Terms:noexp]\n",
       " n_articles                                                12702\n",
       " pubmed_ids    23492|27120|27121|27202|33971|39037|49905|5453...\n",
       " Name: 117, dtype: object,\n",
       " mesh_id                                                 D003967\n",
       " mesh_name                                              Diarrhea\n",
       " in_hsdn                                                       1\n",
       " term_query                           diarrhea[MeSH Terms:noexp]\n",
       " n_articles                                                53665\n",
       " pubmed_ids    525|612|1346|3456|3677|4734|4770|6360|6368|669...\n",
       " Name: 118, dtype: object,\n",
       " mesh_id                                                 D003968\n",
       " mesh_name                                   Diarrhea, Infantile\n",
       " in_hsdn                                                       1\n",
       " term_query                diarrhea, infantile[MeSH Terms:noexp]\n",
       " n_articles                                                 7016\n",
       " pubmed_ids    274|1346|11438|21469|24379|36051|48924|49677|5...\n",
       " Name: 119, dtype: object,\n",
       " mesh_id                                                 D004172\n",
       " mesh_name                                              Diplopia\n",
       " in_hsdn                                                       1\n",
       " term_query                           diplopia[MeSH Terms:noexp]\n",
       " n_articles                                                 5924\n",
       " pubmed_ids    39182|51064|63653|125831|133026|157137|165771|...\n",
       " Name: 120, dtype: object,\n",
       " mesh_id                                                 D004244\n",
       " mesh_name                                             Dizziness\n",
       " in_hsdn                                                       1\n",
       " term_query                          dizziness[MeSH Terms:noexp]\n",
       " n_articles                                                16496\n",
       " pubmed_ids    3634|4752|8363|9552|13936|32758|35998|37601|38...\n",
       " Name: 121, dtype: object,\n",
       " mesh_id                                                 D004314\n",
       " mesh_name                                         Down Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                      down syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                26825\n",
       " pubmed_ids    2011|5841|29945|32513|37011|46475|47133|47522|...\n",
       " Name: 122, dtype: object,\n",
       " mesh_id                                                 D004401\n",
       " mesh_name                                            Dysarthria\n",
       " in_hsdn                                                       1\n",
       " term_query                         dysarthria[MeSH Terms:noexp]\n",
       " n_articles                                                 2825\n",
       " pubmed_ids    36486|84289|86492|100657|224628|253604|258639|...\n",
       " Name: 123, dtype: object,\n",
       " mesh_id                                                 D004408\n",
       " mesh_name                                             Dysgeusia\n",
       " in_hsdn                                                       1\n",
       " term_query                          dysgeusia[MeSH Terms:noexp]\n",
       " n_articles                                                  693\n",
       " pubmed_ids    134235|136568|279277|443004|715345|797259|1069...\n",
       " Name: 124, dtype: object,\n",
       " mesh_id                                                 D004409\n",
       " mesh_name                              Dyskinesia, Drug-Induced\n",
       " in_hsdn                                                       0\n",
       " term_query           dyskinesia, drug-induced[MeSH Terms:noexp]\n",
       " n_articles                                                 7130\n",
       " pubmed_ids    9966|10587|10603|10748|11277|11317|12469|12666...\n",
       " Name: 125, dtype: object,\n",
       " mesh_id                                                 D004410\n",
       " mesh_name                                              Dyslexia\n",
       " in_hsdn                                                       1\n",
       " term_query                           dyslexia[MeSH Terms:noexp]\n",
       " n_articles                                                 8555\n",
       " pubmed_ids    12627|29248|40354|65465|69262|74845|75959|7646...\n",
       " Name: 126, dtype: object,\n",
       " mesh_id                                                 D004411\n",
       " mesh_name                                    Dyslexia, Acquired\n",
       " in_hsdn                                                       1\n",
       " term_query                 dyslexia, acquired[MeSH Terms:noexp]\n",
       " n_articles                                                  868\n",
       " pubmed_ids    85874|92323|92325|92327|195235|228417|268518|2...\n",
       " Name: 127, dtype: object,\n",
       " mesh_id                                                 D004412\n",
       " mesh_name                                          Dysmenorrhea\n",
       " in_hsdn                                                       1\n",
       " term_query                       dysmenorrhea[MeSH Terms:noexp]\n",
       " n_articles                                                 4758\n",
       " pubmed_ids    23753|25021|25462|33086|37691|40034|50970|5584...\n",
       " Name: 128, dtype: object,\n",
       " mesh_id                                                 D004415\n",
       " mesh_name                                             Dyspepsia\n",
       " in_hsdn                                                       1\n",
       " term_query                          dyspepsia[MeSH Terms:noexp]\n",
       " n_articles                                                 9392\n",
       " pubmed_ids    6187|8837|31675|34810|38446|43588|44432|47488|...\n",
       " Name: 129, dtype: object,\n",
       " mesh_id                                                 D004417\n",
       " mesh_name                                               Dyspnea\n",
       " in_hsdn                                                       1\n",
       " term_query                            dyspnea[MeSH Terms:noexp]\n",
       " n_articles                                                25604\n",
       " pubmed_ids    4751|4753|8819|9881|10809|10813|10814|10820|24...\n",
       " Name: 130, dtype: object,\n",
       " mesh_id                                                 D004418\n",
       " mesh_name                                   Dyspnea, Paroxysmal\n",
       " in_hsdn                                                       1\n",
       " term_query                dyspnea, paroxysmal[MeSH Terms:noexp]\n",
       " n_articles                                                  356\n",
       " pubmed_ids    142958|236066|417308|487840|540696|573963|6046...\n",
       " Name: 131, dtype: object,\n",
       " mesh_id                                                 D004421\n",
       " mesh_name                                              Dystonia\n",
       " in_hsdn                                                       1\n",
       " term_query                           dystonia[MeSH Terms:noexp]\n",
       " n_articles                                                10162\n",
       " pubmed_ids    29498|29687|31503|34142|36644|36755|39286|4026...\n",
       " Name: 132, dtype: object,\n",
       " mesh_id                                                 D004433\n",
       " mesh_name                                               Earache\n",
       " in_hsdn                                                       1\n",
       " term_query                            earache[MeSH Terms:noexp]\n",
       " n_articles                                                  863\n",
       " pubmed_ids    1291101|1291108|1298426|1344536|1405984|144338...\n",
       " Name: 133, dtype: object,\n",
       " mesh_id                                                 D004438\n",
       " mesh_name                                            Ecchymosis\n",
       " in_hsdn                                                       1\n",
       " term_query                         ecchymosis[MeSH Terms:noexp]\n",
       " n_articles                                                 1529\n",
       " pubmed_ids    28343|32849|53128|82839|123655|154860|166764|2...\n",
       " Name: 134, dtype: object,\n",
       " mesh_id                                                 D004454\n",
       " mesh_name                                             Echolalia\n",
       " in_hsdn                                                       1\n",
       " term_query                          echolalia[MeSH Terms:noexp]\n",
       " n_articles                                                  234\n",
       " pubmed_ids    78926|88396|90989|155684|330580|390245|426008|...\n",
       " Name: 135, dtype: object,\n",
       " mesh_id                                                 D004487\n",
       " mesh_name                                                 Edema\n",
       " in_hsdn                                                       1\n",
       " term_query                              edema[MeSH Terms:noexp]\n",
       " n_articles                                                43264\n",
       " pubmed_ids    515|657|973|1042|1049|2693|4901|5887|7668|8042...\n",
       " Name: 136, dtype: object,\n",
       " mesh_id                                                 D004489\n",
       " mesh_name                                        Edema, Cardiac\n",
       " in_hsdn                                                       1\n",
       " term_query                     edema, cardiac[MeSH Terms:noexp]\n",
       " n_articles                                                  818\n",
       " pubmed_ids    3150|17928|87570|87571|87622|98310|105197|1226...\n",
       " Name: 137, dtype: object,\n",
       " mesh_id                                                 D004614\n",
       " mesh_name                                            Emaciation\n",
       " in_hsdn                                                       1\n",
       " term_query                         emaciation[MeSH Terms:noexp]\n",
       " n_articles                                                  694\n",
       " pubmed_ids    52825|103080|124043|129217|185706|190484|32461...\n",
       " Name: 138, dtype: object,\n",
       " mesh_id                                                 D004688\n",
       " mesh_name                                            Encopresis\n",
       " in_hsdn                                                       1\n",
       " term_query                         encopresis[MeSH Terms:noexp]\n",
       " n_articles                                                  672\n",
       " pubmed_ids    43852|243105|253720|258291|263861|354322|35587...\n",
       " Name: 139, dtype: object,\n",
       " mesh_id                                                 D004844\n",
       " mesh_name                                             Epistaxis\n",
       " in_hsdn                                                       0\n",
       " term_query                          epistaxis[MeSH Terms:noexp]\n",
       " n_articles                                                 5309\n",
       " pubmed_ids    5358|10820|34070|47631|58437|64427|72032|12357...\n",
       " Name: 140, dtype: object,\n",
       " mesh_id                                                 D004884\n",
       " mesh_name                                            Eructation\n",
       " in_hsdn                                                       1\n",
       " term_query                         eructation[MeSH Terms:noexp]\n",
       " n_articles                                                  412\n",
       " pubmed_ids    4935|10704|154566|356314|370502|532243|533130|...\n",
       " Name: 141, dtype: object,\n",
       " mesh_id                                                 D004890\n",
       " mesh_name                                              Erythema\n",
       " in_hsdn                                                       0\n",
       " term_query                           erythema[MeSH Terms:noexp]\n",
       " n_articles                                                12988\n",
       " pubmed_ids    972|3150|6706|7668|7789|10772|18997|25854|2739...\n",
       " Name: 142, dtype: object,\n",
       " mesh_id                                                 D004891\n",
       " mesh_name                                    Erythema Induratum\n",
       " in_hsdn                                                       0\n",
       " term_query                 erythema induratum[MeSH Terms:noexp]\n",
       " n_articles                                                  265\n",
       " pubmed_ids    25988|71810|434865|485029|695919|808656|111983...\n",
       " Name: 143, dtype: object,\n",
       " mesh_id                                                 D004892\n",
       " mesh_name                                   Erythema Multiforme\n",
       " in_hsdn                                                       0\n",
       " term_query                erythema multiforme[MeSH Terms:noexp]\n",
       " n_articles                                                 2950\n",
       " pubmed_ids    19978|25404|43214|52244|56860|63220|91086|1107...\n",
       " Name: 144, dtype: object,\n",
       " mesh_id                                                 D004893\n",
       " mesh_name                                      Erythema Nodosum\n",
       " in_hsdn                                                       0\n",
       " term_query                   erythema nodosum[MeSH Terms:noexp]\n",
       " n_articles                                                 3353\n",
       " pubmed_ids    7830|25404|49888|50675|51405|51411|52071|54672...\n",
       " Name: 145, dtype: object,\n",
       " mesh_id                                                 D005130\n",
       " mesh_name                                        Eye Hemorrhage\n",
       " in_hsdn                                                       1\n",
       " term_query                     eye hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                 1020\n",
       " pubmed_ids    1300399|1340907|1390514|1399348|1399352|140376...\n",
       " Name: 146, dtype: object,\n",
       " mesh_id                                                 D005132\n",
       " mesh_name                                    Eye Manifestations\n",
       " in_hsdn                                                       1\n",
       " term_query                 eye manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                 3146\n",
       " pubmed_ids    2110|10587|11363|16373|18637|27311|30059|32148...\n",
       " Name: 147, dtype: object,\n",
       " mesh_id                                                 D005157\n",
       " mesh_name                                           Facial Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                        facial pain[MeSH Terms:noexp]\n",
       " n_articles                                                 7331\n",
       " pubmed_ids    401266|1283628|1290490|1291072|1295046|1296458...\n",
       " Name: 148, dtype: object,\n",
       " mesh_id                                                 D005158\n",
       " mesh_name                                      Facial Paralysis\n",
       " in_hsdn                                                       1\n",
       " term_query                   facial paralysis[MeSH Terms:noexp]\n",
       " n_articles                                                13517\n",
       " pubmed_ids    10248|17066|25361|40540|50416|51046|51052|5269...\n",
       " Name: 149, dtype: object,\n",
       " mesh_id                                                 D005183\n",
       " mesh_name                                     Failure to Thrive\n",
       " in_hsdn                                                       0\n",
       " term_query                  failure to thrive[MeSH Terms:noexp]\n",
       " n_articles                                                 2463\n",
       " pubmed_ids    263867|1281931|1293573|1294495|1303533|1351478...\n",
       " Name: 150, dtype: object,\n",
       " mesh_id                                                 D005207\n",
       " mesh_name                                         Fasciculation\n",
       " in_hsdn                                                       1\n",
       " term_query                      fasciculation[MeSH Terms:noexp]\n",
       " n_articles                                                  800\n",
       " pubmed_ids    218540|218541|262000|375768|434514|434522|4353...\n",
       " Name: 151, dtype: object,\n",
       " mesh_id                                                 D005221\n",
       " mesh_name                                               Fatigue\n",
       " in_hsdn                                                       1\n",
       " term_query                            fatigue[MeSH Terms:noexp]\n",
       " n_articles                                                35781\n",
       " pubmed_ids    1333|3032|4054|5019|7710|7923|10321|10513|1714...\n",
       " Name: 152, dtype: object,\n",
       " mesh_id                                                 D005222\n",
       " mesh_name                                        Mental Fatigue\n",
       " in_hsdn                                                       1\n",
       " term_query                     mental fatigue[MeSH Terms:noexp]\n",
       " n_articles                                                 1919\n",
       " pubmed_ids    524|731|1333|1627|4054|4664|4959|5766|6158|701...\n",
       " Name: 153, dtype: object,\n",
       " mesh_id                                                 D005262\n",
       " mesh_name                                          Feminization\n",
       " in_hsdn                                                       1\n",
       " term_query                       feminization[MeSH Terms:noexp]\n",
       " n_articles                                                  910\n",
       " pubmed_ids    50551|73862|122397|127562|137914|139568|206048...\n",
       " Name: 154, dtype: object,\n",
       " mesh_id                                                 D005311\n",
       " mesh_name                                         Fetal Hypoxia\n",
       " in_hsdn                                                       1\n",
       " term_query                      fetal hypoxia[MeSH Terms:noexp]\n",
       " n_articles                                                 3234\n",
       " pubmed_ids    4762|5104|6341|9427|9499|11642|15789|15790|157...\n",
       " Name: 155, dtype: object,\n",
       " mesh_id                                                 D005316\n",
       " mesh_name                                        Fetal Distress\n",
       " in_hsdn                                                       1\n",
       " term_query                     fetal distress[MeSH Terms:noexp]\n",
       " n_articles                                                 3421\n",
       " pubmed_ids    480|2544|3546|3899|5585|5894|5895|6366|6505|86...\n",
       " Name: 156, dtype: object,\n",
       " mesh_id                                                 D005320\n",
       " mesh_name                                      Fetal Macrosomia\n",
       " in_hsdn                                                       1\n",
       " term_query                   fetal macrosomia[MeSH Terms:noexp]\n",
       " n_articles                                                 3357\n",
       " pubmed_ids    803080|1290237|1290427|1327220|1338707|1347496...\n",
       " Name: 157, dtype: object,\n",
       " mesh_id                                                 D005334\n",
       " mesh_name                                                 Fever\n",
       " in_hsdn                                                       1\n",
       " term_query                              fever[MeSH Terms:noexp]\n",
       " n_articles                                                43933\n",
       " pubmed_ids    862|977|1705|2478|2883|2886|2913|3418|5064|557...\n",
       " Name: 158, dtype: object,\n",
       " mesh_id                                                 D005335\n",
       " mesh_name                               Fever of Unknown Origin\n",
       " in_hsdn                                                       1\n",
       " term_query            fever of unknown origin[MeSH Terms:noexp]\n",
       " n_articles                                                 4540\n",
       " pubmed_ids    10522|15960|28668|39703|42604|120852|128408|16...\n",
       " Name: 159, dtype: object,\n",
       " mesh_id                                                 D005414\n",
       " mesh_name                                            Flatulence\n",
       " in_hsdn                                                       1\n",
       " term_query                         flatulence[MeSH Terms:noexp]\n",
       " n_articles                                                 1658\n",
       " pubmed_ids    37142|47488|48139|48774|48778|50523|51965|5816...\n",
       " Name: 160, dtype: object,\n",
       " mesh_id                                                 D005483\n",
       " mesh_name                                              Flushing\n",
       " in_hsdn                                                       1\n",
       " term_query                           flushing[MeSH Terms:noexp]\n",
       " n_articles                                                 1389\n",
       " pubmed_ids    1309830|1343853|1346472|1346677|1381038|138754...\n",
       " Name: 161, dtype: object,\n",
       " mesh_id                                                 D005600\n",
       " mesh_name                                    Fragile X Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                 fragile x syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 5770\n",
       " pubmed_ids    1292164|1297905|1298036|1301146|1301165|130120...\n",
       " Name: 162, dtype: object,\n",
       " mesh_id                                                 D005683\n",
       " mesh_name                                               Gagging\n",
       " in_hsdn                                                       1\n",
       " term_query                            gagging[MeSH Terms:noexp]\n",
       " n_articles                                                  521\n",
       " pubmed_ids    92719|293337|294416|313151|323306|360492|37931...\n",
       " Name: 163, dtype: object,\n",
       " mesh_id                                                 D005862\n",
       " mesh_name                                    Gerstmann Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query                 gerstmann syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  217\n",
       " pubmed_ids    93071|318903|427951|472615|482532|612874|61856...\n",
       " Name: 164, dtype: object,\n",
       " mesh_id                                                 D005884\n",
       " mesh_name                                   Gingival Hemorrhage\n",
       " in_hsdn                                                       0\n",
       " term_query                gingival hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                 2855\n",
       " pubmed_ids    49034|110916|233272|266390|267620|267764|26906...\n",
       " Name: 165, dtype: object,\n",
       " mesh_id                                                 D005926\n",
       " mesh_name                                            Glossalgia\n",
       " in_hsdn                                                       1\n",
       " term_query                         glossalgia[MeSH Terms:noexp]\n",
       " n_articles                                                  299\n",
       " pubmed_ids    41014|102969|191778|269851|276158|279110|28102...\n",
       " Name: 166, dtype: object,\n",
       " mesh_id                                                 D006209\n",
       " mesh_name                                             Halitosis\n",
       " in_hsdn                                                       1\n",
       " term_query                          halitosis[MeSH Terms:noexp]\n",
       " n_articles                                                 1582\n",
       " pubmed_ids    123537|154272|264535|273847|275323|275399|2775...\n",
       " Name: 167, dtype: object,\n",
       " mesh_id                                                 D006212\n",
       " mesh_name                                        Hallucinations\n",
       " in_hsdn                                                       1\n",
       " term_query                     hallucinations[MeSH Terms:noexp]\n",
       " n_articles                                                12120\n",
       " pubmed_ids    658|4667|4741|11193|14525|19230|19232|19807|19...\n",
       " Name: 168, dtype: object,\n",
       " mesh_id                                                 D006261\n",
       " mesh_name                                              Headache\n",
       " in_hsdn                                                       1\n",
       " term_query                           headache[MeSH Terms:noexp]\n",
       " n_articles                                                32464\n",
       " pubmed_ids    664|665|845|2886|4752|5383|7710|8947|9552|1168...\n",
       " Name: 169, dtype: object,\n",
       " mesh_id                                                 D006311\n",
       " mesh_name                                     Hearing Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                  hearing disorders[MeSH Terms:noexp]\n",
       " n_articles                                                14690\n",
       " pubmed_ids    1924|2689|16209|29932|32590|40169|41025|43805|...\n",
       " Name: 170, dtype: object,\n",
       " mesh_id                                                 D006312\n",
       " mesh_name                               Hearing Loss, Bilateral\n",
       " in_hsdn                                                       1\n",
       " term_query            hearing loss, bilateral[MeSH Terms:noexp]\n",
       " n_articles                                                 2317\n",
       " pubmed_ids    88255|100850|105303|112551|116369|152580|15393...\n",
       " Name: 171, dtype: object,\n",
       " mesh_id                                                 D006313\n",
       " mesh_name                                 Hearing Loss, Central\n",
       " in_hsdn                                                       1\n",
       " term_query              hearing loss, central[MeSH Terms:noexp]\n",
       " n_articles                                                  768\n",
       " pubmed_ids    102064|156776|161775|428727|463515|530706|7032...\n",
       " Name: 172, dtype: object,\n",
       " mesh_id                                                 D006314\n",
       " mesh_name                              Hearing Loss, Conductive\n",
       " in_hsdn                                                       1\n",
       " term_query           hearing loss, conductive[MeSH Terms:noexp]\n",
       " n_articles                                                 4069\n",
       " pubmed_ids    42044|89952|102064|108901|113745|115361|115362...\n",
       " Name: 173, dtype: object,\n",
       " mesh_id                                                 D006315\n",
       " mesh_name                              Hearing Loss, Functional\n",
       " in_hsdn                                                       1\n",
       " term_query           hearing loss, functional[MeSH Terms:noexp]\n",
       " n_articles                                                  222\n",
       " pubmed_ids    114087|216771|383667|400077|478999|536857|5715...\n",
       " Name: 174, dtype: object,\n",
       " mesh_id                                                 D006316\n",
       " mesh_name                          Hearing Loss, High-Frequency\n",
       " in_hsdn                                                       1\n",
       " term_query       hearing loss, high-frequency[MeSH Terms:noexp]\n",
       " n_articles                                                 1036\n",
       " pubmed_ids    84739|100042|113706|299106|299120|299593|37566...\n",
       " Name: 175, dtype: object,\n",
       " mesh_id                                                 D006317\n",
       " mesh_name                           Hearing Loss, Noise-Induced\n",
       " in_hsdn                                                       1\n",
       " term_query        hearing loss, noise-induced[MeSH Terms:noexp]\n",
       " n_articles                                                 7986\n",
       " pubmed_ids    31340|34278|57694|61920|67025|69369|69427|9341...\n",
       " Name: 176, dtype: object,\n",
       " mesh_id                                                 D006319\n",
       " mesh_name                           Hearing Loss, Sensorineural\n",
       " in_hsdn                                                       1\n",
       " term_query        hearing loss, sensorineural[MeSH Terms:noexp]\n",
       " n_articles                                                19546\n",
       " pubmed_ids    41318|81297|85885|100086|100850|102064|104108|...\n",
       " Name: 177, dtype: object,\n",
       " mesh_id                                                 D006337\n",
       " mesh_name                                         Heart Murmurs\n",
       " in_hsdn                                                       1\n",
       " term_query                      heart murmurs[MeSH Terms:noexp]\n",
       " n_articles                                                 3703\n",
       " pubmed_ids    217|7077|8678|25348|38400|39522|45222|46193|48...\n",
       " Name: 178, dtype: object,\n",
       " mesh_id                                                 D006356\n",
       " mesh_name                                             Heartburn\n",
       " in_hsdn                                                       1\n",
       " term_query                          heartburn[MeSH Terms:noexp]\n",
       " n_articles                                                 2319\n",
       " pubmed_ids    123|13649|13747|14050|18788|24352|26899|27414|...\n",
       " Name: 179, dtype: object,\n",
       " mesh_id                                                 D006396\n",
       " mesh_name                                           Hematemesis\n",
       " in_hsdn                                                       1\n",
       " term_query                        hematemesis[MeSH Terms:noexp]\n",
       " n_articles                                                 2543\n",
       " pubmed_ids    65580|92719|106530|112471|117324|125724|174504...\n",
       " Name: 180, dtype: object,\n",
       " mesh_id                                                 D006423\n",
       " mesh_name                                           Hemianopsia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hemianopsia[MeSH Terms:noexp]\n",
       " n_articles                                                 2964\n",
       " pubmed_ids    77500|100469|121064|121712|130870|151702|16987...\n",
       " Name: 181, dtype: object,\n",
       " mesh_id                                                 D006429\n",
       " mesh_name                                            Hemiplegia\n",
       " in_hsdn                                                       1\n",
       " term_query                         hemiplegia[MeSH Terms:noexp]\n",
       " n_articles                                                12103\n",
       " pubmed_ids    5703|11753|20803|33557|35688|40217|43615|48241...\n",
       " Name: 182, dtype: object,\n",
       " mesh_id                                                 D006456\n",
       " mesh_name                                        Hemoglobinuria\n",
       " in_hsdn                                                       1\n",
       " term_query                     hemoglobinuria[MeSH Terms:noexp]\n",
       " n_articles                                                 1687\n",
       " pubmed_ids    9368|11437|37477|43648|54499|65700|67129|86649...\n",
       " Name: 183, dtype: object,\n",
       " mesh_id                                                 D006469\n",
       " mesh_name                                            Hemoptysis\n",
       " in_hsdn                                                       1\n",
       " term_query                         hemoptysis[MeSH Terms:noexp]\n",
       " n_articles                                                 6788\n",
       " pubmed_ids    12696|44656|60602|69598|88310|89391|90469|1098...\n",
       " Name: 184, dtype: object,\n",
       " mesh_id                                                 D006472\n",
       " mesh_name                                       Oral Hemorrhage\n",
       " in_hsdn                                                       1\n",
       " term_query                    oral hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                 2018\n",
       " pubmed_ids    40210|76404|112788|120334|154134|157017|160155...\n",
       " Name: 185, dtype: object,\n",
       " mesh_id                                                 D006606\n",
       " mesh_name                                                Hiccup\n",
       " in_hsdn                                                       1\n",
       " term_query                             hiccup[MeSH Terms:noexp]\n",
       " n_articles                                                 1239\n",
       " pubmed_ids    36761|57220|69960|70711|71568|95764|138173|221...\n",
       " Name: 186, dtype: object,\n",
       " mesh_id                                                 D006628\n",
       " mesh_name                                             Hirsutism\n",
       " in_hsdn                                                       1\n",
       " term_query                          hirsutism[MeSH Terms:noexp]\n",
       " n_articles                                                 4254\n",
       " pubmed_ids    11554|21888|51506|61663|62406|65117|66176|6792...\n",
       " Name: 187, dtype: object,\n",
       " mesh_id                                                 D006685\n",
       " mesh_name                                            Hoarseness\n",
       " in_hsdn                                                       1\n",
       " term_query                         hoarseness[MeSH Terms:noexp]\n",
       " n_articles                                                 2517\n",
       " pubmed_ids    135153|163435|169770|195168|231249|423666|4596...\n",
       " Name: 188, dtype: object,\n",
       " mesh_id                                                 D006732\n",
       " mesh_name                                       Horner Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query                    horner syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 2100\n",
       " pubmed_ids    29419|52144|75260|118668|139514|163071|169444|...\n",
       " Name: 189, dtype: object,\n",
       " mesh_id                                                 D006816\n",
       " mesh_name                                    Huntington Disease\n",
       " in_hsdn                                                       0\n",
       " term_query                 huntington disease[MeSH Terms:noexp]\n",
       " n_articles                                                14016\n",
       " pubmed_ids    3629|4733|7932|8731|10053|11317|12546|12547|12...\n",
       " Name: 190, dtype: object,\n",
       " mesh_id                                                 D006930\n",
       " mesh_name                                          Hyperalgesia\n",
       " in_hsdn                                                       1\n",
       " term_query                       hyperalgesia[MeSH Terms:noexp]\n",
       " n_articles                                                14416\n",
       " pubmed_ids    82800|83479|230542|230543|283654|325973|360302...\n",
       " Name: 191, dtype: object,\n",
       " mesh_id                                                 D006935\n",
       " mesh_name                                           Hypercapnia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hypercapnia[MeSH Terms:noexp]\n",
       " n_articles                                                 9349\n",
       " pubmed_ids    103|652|756|821|1694|1912|2639|3828|4974|4979|...\n",
       " Name: 192, dtype: object,\n",
       " mesh_id                                                 D006939\n",
       " mesh_name                                Hyperemesis Gravidarum\n",
       " in_hsdn                                                       1\n",
       " term_query             hyperemesis gravidarum[MeSH Terms:noexp]\n",
       " n_articles                                                 1815\n",
       " pubmed_ids    78652|168764|208915|224374|231374|236169|25795...\n",
       " Name: 193, dtype: object,\n",
       " mesh_id                                                 D006941\n",
       " mesh_name                                         Hyperesthesia\n",
       " in_hsdn                                                       1\n",
       " term_query                      hyperesthesia[MeSH Terms:noexp]\n",
       " n_articles                                                  930\n",
       " pubmed_ids    30155|44056|48003|68334|68483|71532|103060|127...\n",
       " Name: 194, dtype: object,\n",
       " mesh_id                                                 D006942\n",
       " mesh_name                                Hypergammaglobulinemia\n",
       " in_hsdn                                                       1\n",
       " term_query             hypergammaglobulinemia[MeSH Terms:noexp]\n",
       " n_articles                                                 3622\n",
       " pubmed_ids    1705|3763|19570|43438|44762|46396|46427|47711|...\n",
       " Name: 195, dtype: object,\n",
       " mesh_id                                                 D006948\n",
       " mesh_name                                          Hyperkinesis\n",
       " in_hsdn                                                       1\n",
       " term_query                       hyperkinesis[MeSH Terms:noexp]\n",
       " n_articles                                                 4413\n",
       " pubmed_ids    729|3817|3929|4253|4790|4940|4973|5361|6240|10...\n",
       " Name: 196, dtype: object,\n",
       " mesh_id                                                 D006963\n",
       " mesh_name                                           Hyperphagia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hyperphagia[MeSH Terms:noexp]\n",
       " n_articles                                                 3610\n",
       " pubmed_ids    298349|298731|1317832|1330958|1334320|1349437|...\n",
       " Name: 197, dtype: object,\n",
       " mesh_id                                                 D006970\n",
       " mesh_name                     Disorders of Excessive Somnolence\n",
       " in_hsdn                                                       0\n",
       " term_query    disorders of excessive somnolence[MeSH Terms:n...\n",
       " n_articles                                                 4568\n",
       " pubmed_ids    12530|31685|32228|44863|51746|51783|52503|5771...\n",
       " Name: 198, dtype: object,\n",
       " mesh_id                                                 D006985\n",
       " mesh_name                                      Hyperventilation\n",
       " in_hsdn                                                       1\n",
       " term_query                   hyperventilation[MeSH Terms:noexp]\n",
       " n_articles                                                 5989\n",
       " pubmed_ids    155|1473|2653|3265|3746|4252|4958|4989|5785|64...\n",
       " Name: 199, dtype: object,\n",
       " mesh_id                                                 D006987\n",
       " mesh_name                                           Hypesthesia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hypesthesia[MeSH Terms:noexp]\n",
       " n_articles                                                 3344\n",
       " pubmed_ids    50537|51970|53849|60472|63042|68334|75420|7897...\n",
       " Name: 200, dtype: object,\n",
       " mesh_id                                                 D006988\n",
       " mesh_name                                               Hyphema\n",
       " in_hsdn                                                       0\n",
       " term_query                            hyphema[MeSH Terms:noexp]\n",
       " n_articles                                                 1535\n",
       " pubmed_ids    37471|61728|63437|64958|111202|111203|124815|1...\n",
       " Name: 201, dtype: object,\n",
       " mesh_id                                                 D007024\n",
       " mesh_name                              Hypotension, Orthostatic\n",
       " in_hsdn                                                       0\n",
       " term_query           hypotension, orthostatic[MeSH Terms:noexp]\n",
       " n_articles                                                 6222\n",
       " pubmed_ids    5774|9267|10083|10954|12563|13541|21120|21345|...\n",
       " Name: 202, dtype: object,\n",
       " mesh_id                                                 D007035\n",
       " mesh_name                                           Hypothermia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hypothermia[MeSH Terms:noexp]\n",
       " n_articles                                                15242\n",
       " pubmed_ids    443|644|652|949|1709|3336|5005|5023|5902|8189|...\n",
       " Name: 203, dtype: object,\n",
       " mesh_id                                                 D007040\n",
       " mesh_name                                       Hypoventilation\n",
       " in_hsdn                                                       1\n",
       " term_query                    hypoventilation[MeSH Terms:noexp]\n",
       " n_articles                                                 2311\n",
       " pubmed_ids    1694|3824|4415|13683|14066|17663|19971|24394|2...\n",
       " Name: 204, dtype: object,\n",
       " mesh_id                                                 D007088\n",
       " mesh_name                                             Illusions\n",
       " in_hsdn                                                       1\n",
       " term_query                          illusions[MeSH Terms:noexp]\n",
       " n_articles                                                 6563\n",
       " pubmed_ids    21374|51014|104005|109771|119631|180622|190586...\n",
       " Name: 205, dtype: object,\n",
       " mesh_id                                                 D007319\n",
       " mesh_name            Sleep Initiation and Maintenance Disorders\n",
       " in_hsdn                                                       0\n",
       " term_query    sleep initiation and maintenance disorders[MeS...\n",
       " n_articles                                                18672\n",
       " pubmed_ids    496|2563|3259|3819|4255|6129|6180|7002|8813|88...\n",
       " Name: 206, dtype: object,\n",
       " mesh_id                                                 D007331\n",
       " mesh_name                                          Insulin Coma\n",
       " in_hsdn                                                       0\n",
       " term_query                       insulin coma[MeSH Terms:noexp]\n",
       " n_articles                                                  716\n",
       " pubmed_ids    106474|184599|204622|219511|250609|257693|2595...\n",
       " Name: 207, dtype: object,\n",
       " mesh_id                                                 D007383\n",
       " mesh_name                             Intermittent Claudication\n",
       " in_hsdn                                                       1\n",
       " term_query          intermittent claudication[MeSH Terms:noexp]\n",
       " n_articles                                                 8539\n",
       " pubmed_ids    5171|14471|25060|36056|36115|41389|45258|47099...\n",
       " Name: 208, dtype: object,\n",
       " mesh_id                                                 D007565\n",
       " mesh_name                                              Jaundice\n",
       " in_hsdn                                                       1\n",
       " term_query                           jaundice[MeSH Terms:noexp]\n",
       " n_articles                                                13781\n",
       " pubmed_ids    311|7808|7899|8649|10219|10780|11455|11604|145...\n",
       " Name: 209, dtype: object,\n",
       " mesh_id                                                 D007625\n",
       " mesh_name                                 Kearns-Sayre Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query              kearns-sayre syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  732\n",
       " pubmed_ids    803072|1284549|1289103|1300476|1305030|1312676...\n",
       " Name: 210, dtype: object,\n",
       " mesh_id                                                 D007706\n",
       " mesh_name                            Menkes Kinky Hair Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query         menkes kinky hair syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 1028\n",
       " pubmed_ids    36559|41816|65241|73055|76144|80619|97372|1077...\n",
       " Name: 211, dtype: object,\n",
       " mesh_id                                                 D007805\n",
       " mesh_name                        Language Development Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query     language development disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 7465\n",
       " pubmed_ids    90749|91155|95236|115357|115358|115360|115361|...\n",
       " Name: 212, dtype: object,\n",
       " mesh_id                                                 D007806\n",
       " mesh_name                                    Language Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                 language disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 6764\n",
       " pubmed_ids    51018|63117|74300|77519|78749|78750|85503|8912...\n",
       " Name: 213, dtype: object,\n",
       " mesh_id                                                 D007859\n",
       " mesh_name                                 Learning Disabilities\n",
       " in_hsdn                                                       1\n",
       " term_query              learning disabilities[MeSH Terms:noexp]\n",
       " n_articles                                                14738\n",
       " pubmed_ids    4973|7015|8757|16854|20458|22885|24339|46432|4...\n",
       " Name: 214, dtype: object,\n",
       " mesh_id                                                 D007926\n",
       " mesh_name                                  Lesch-Nyhan Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query               lesch-nyhan syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 1244\n",
       " pubmed_ids    16258|24531|35970|53661|56683|95907|97614|1029...\n",
       " Name: 215, dtype: object,\n",
       " mesh_id                                                 D008065\n",
       " mesh_name               Lipoid Proteinosis of Urbach and Wiethe\n",
       " in_hsdn                                                       0\n",
       " term_query    lipoid proteinosis of urbach and wiethe[MeSH T...\n",
       " n_articles                                                  441\n",
       " pubmed_ids    47394|62069|77850|79901|83775|130880|147583|34...\n",
       " Name: 216, dtype: object,\n",
       " mesh_id                                                 D008305\n",
       " mesh_name                                Malignant Hyperthermia\n",
       " in_hsdn                                                       0\n",
       " term_query             malignant hyperthermia[MeSH Terms:noexp]\n",
       " n_articles                                                 3864\n",
       " pubmed_ids    795|3127|5004|6381|9123|16042|17582|20913|2381...\n",
       " Name: 217, dtype: object,\n",
       " mesh_id                                                 D008569\n",
       " mesh_name                                      Memory Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                   memory disorders[MeSH Terms:noexp]\n",
       " n_articles                                                24528\n",
       " pubmed_ids    4054|15361|15363|27947|32831|51770|54722|63101...\n",
       " Name: 218, dtype: object,\n",
       " mesh_id                                                 D008580\n",
       " mesh_name                                             Meningism\n",
       " in_hsdn                                                       1\n",
       " term_query                          meningism[MeSH Terms:noexp]\n",
       " n_articles                                                  285\n",
       " pubmed_ids    62217|62264|86821|112788|217082|225911|228400|...\n",
       " Name: 219, dtype: object,\n",
       " mesh_id                                                 D008607\n",
       " mesh_name                               Intellectual Disability\n",
       " in_hsdn                                                       1\n",
       " term_query            intellectual disability[MeSH Terms:noexp]\n",
       " n_articles                                                60882\n",
       " pubmed_ids    602|1455|1996|4250|4879|4912|5892|7527|11544|1...\n",
       " Name: 220, dtype: object,\n",
       " mesh_id                                                 D008998\n",
       " mesh_name     Monoclonal Gammopathy of Undetermined Signific...\n",
       " in_hsdn                                                       0\n",
       " term_query    monoclonal gammopathy of undetermined signific...\n",
       " n_articles                                                 1652\n",
       " pubmed_ids    1279127|1283033|1284721|1314413|1315474|132924...\n",
       " Name: 221, dtype: object,\n",
       " mesh_id                                                 D009041\n",
       " mesh_name                                       Motion Sickness\n",
       " in_hsdn                                                       1\n",
       " term_query                    motion sickness[MeSH Terms:noexp]\n",
       " n_articles                                                 2778\n",
       " pubmed_ids    8363|11685|11869|19980|22775|27910|32758|36067...\n",
       " Name: 222, dtype: object,\n",
       " mesh_id                                                 D009058\n",
       " mesh_name                                       Mouth Breathing\n",
       " in_hsdn                                                       1\n",
       " term_query                    mouth breathing[MeSH Terms:noexp]\n",
       " n_articles                                                 1359\n",
       " pubmed_ids    19512|70403|76538|148269|254922|267646|268664|...\n",
       " Name: 223, dtype: object,\n",
       " mesh_id                                                 D009120\n",
       " mesh_name                                          Muscle Cramp\n",
       " in_hsdn                                                       1\n",
       " term_query                       muscle cramp[MeSH Terms:noexp]\n",
       " n_articles                                                 2354\n",
       " pubmed_ids    8774|10205|17766|29377|38507|52730|53338|58242...\n",
       " Name: 224, dtype: object,\n",
       " mesh_id                                                 D009122\n",
       " mesh_name                                     Muscle Hypertonia\n",
       " in_hsdn                                                       1\n",
       " term_query                  muscle hypertonia[MeSH Terms:noexp]\n",
       " n_articles                                                 1073\n",
       " pubmed_ids    33098|120058|216517|284185|398955|401239|41917...\n",
       " Name: 225, dtype: object,\n",
       " mesh_id                                                 D009123\n",
       " mesh_name                                      Muscle Hypotonia\n",
       " in_hsdn                                                       1\n",
       " term_query                   muscle hypotonia[MeSH Terms:noexp]\n",
       " n_articles                                                 3949\n",
       " pubmed_ids    69847|70516|71410|71430|71437|71531|72227|7231...\n",
       " Name: 226, dtype: object,\n",
       " mesh_id                                                 D009127\n",
       " mesh_name                                       Muscle Rigidity\n",
       " in_hsdn                                                       1\n",
       " term_query                    muscle rigidity[MeSH Terms:noexp]\n",
       " n_articles                                                 2274\n",
       " pubmed_ids    1556|38498|39230|45900|48972|52851|55599|68899...\n",
       " Name: 227, dtype: object,\n",
       " mesh_id                                                 D009128\n",
       " mesh_name                                     Muscle Spasticity\n",
       " in_hsdn                                                       1\n",
       " term_query                  muscle spasticity[MeSH Terms:noexp]\n",
       " n_articles                                                10609\n",
       " pubmed_ids    7723|12648|18853|22787|25494|30921|38273|52833...\n",
       " Name: 228, dtype: object,\n",
       " mesh_id                                                 D009133\n",
       " mesh_name                                      Muscular Atrophy\n",
       " in_hsdn                                                       1\n",
       " term_query                   muscular atrophy[MeSH Terms:noexp]\n",
       " n_articles                                                12934\n",
       " pubmed_ids    3799|13802|29081|44056|50299|50411|50425|51074...\n",
       " Name: 229, dtype: object,\n",
       " mesh_id                                                 D009155\n",
       " mesh_name                                                Mutism\n",
       " in_hsdn                                                       1\n",
       " term_query                             mutism[MeSH Terms:noexp]\n",
       " n_articles                                                 1168\n",
       " pubmed_ids    11229|17479|17518|18335|19486|29775|40165|5901...\n",
       " Name: 230, dtype: object,\n",
       " mesh_id                                                 D009207\n",
       " mesh_name                                             Myoclonus\n",
       " in_hsdn                                                       1\n",
       " term_query                          myoclonus[MeSH Terms:noexp]\n",
       " n_articles                                                 5590\n",
       " pubmed_ids    2712|11459|26293|34357|37558|40657|41197|46540...\n",
       " Name: 231, dtype: object,\n",
       " mesh_id                                                 D009222\n",
       " mesh_name                                              Myotonia\n",
       " in_hsdn                                                       1\n",
       " term_query                           myotonia[MeSH Terms:noexp]\n",
       " n_articles                                                 1248\n",
       " pubmed_ids    17357|50411|50708|51068|51920|52555|55468|6203...\n",
       " Name: 232, dtype: object,\n",
       " mesh_id                                                 D009290\n",
       " mesh_name                                            Narcolepsy\n",
       " in_hsdn                                                       0\n",
       " term_query                         narcolepsy[MeSH Terms:noexp]\n",
       " n_articles                                                 4201\n",
       " pubmed_ids    32228|46820|48065|51783|52494|52497|57711|5876...\n",
       " Name: 233, dtype: object,\n",
       " mesh_id                                                 D009325\n",
       " mesh_name                                                Nausea\n",
       " in_hsdn                                                       1\n",
       " term_query                             nausea[MeSH Terms:noexp]\n",
       " n_articles                                                17882\n",
       " pubmed_ids    2377|2995|3453|4672|7347|8837|9780|11869|12665...\n",
       " Name: 234, dtype: object,\n",
       " mesh_id                                                 D009437\n",
       " mesh_name                                             Neuralgia\n",
       " in_hsdn                                                       1\n",
       " term_query                          neuralgia[MeSH Terms:noexp]\n",
       " n_articles                                                18388\n",
       " pubmed_ids    29537|34814|40799|43329|47280|52527|64986|6524...\n",
       " Name: 235, dtype: object,\n",
       " mesh_id                                                 D009461\n",
       " mesh_name                             Neurologic Manifestations\n",
       " in_hsdn                                                       1\n",
       " term_query          neurologic manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                 7323\n",
       " pubmed_ids    3159|6408|6802|7702|7978|11363|11458|12249|144...\n",
       " Name: 236, dtype: object,\n",
       " mesh_id                                                 D009755\n",
       " mesh_name                                       Night Blindness\n",
       " in_hsdn                                                       0\n",
       " term_query                    night blindness[MeSH Terms:noexp]\n",
       " n_articles                                                 1552\n",
       " pubmed_ids    7131|71982|84746|85266|113519|222197|300550|30...\n",
       " Name: 237, dtype: object,\n",
       " mesh_id                                                 D009765\n",
       " mesh_name                                               Obesity\n",
       " in_hsdn                                                       1\n",
       " term_query                            obesity[MeSH Terms:noexp]\n",
       " n_articles                                               224396\n",
       " pubmed_ids    664|744|1895|2834|3242|3833|4873|7132|7234|752...\n",
       " Name: 238, dtype: object,\n",
       " mesh_id                                                 D009767\n",
       " mesh_name                                       Obesity, Morbid\n",
       " in_hsdn                                                       1\n",
       " term_query                    obesity, morbid[MeSH Terms:noexp]\n",
       " n_articles                                                27677\n",
       " pubmed_ids    400923|1287336|1292144|1302256|1302966|1326487...\n",
       " Name: 239, dtype: object,\n",
       " mesh_id                                                 D009846\n",
       " mesh_name                                              Oliguria\n",
       " in_hsdn                                                       1\n",
       " term_query                           oliguria[MeSH Terms:noexp]\n",
       " n_articles                                                 1375\n",
       " pubmed_ids    6803|11438|14318|44394|47473|54147|65691|69840...\n",
       " Name: 240, dtype: object,\n",
       " mesh_id                                                 D009886\n",
       " mesh_name                                       Ophthalmoplegia\n",
       " in_hsdn                                                       1\n",
       " term_query                    ophthalmoplegia[MeSH Terms:noexp]\n",
       " n_articles                                                 8437\n",
       " pubmed_ids    308|11363|23645|40217|48777|54453|58974|61714|...\n",
       " Name: 241, dtype: object,\n",
       " mesh_id                                                 D009903\n",
       " mesh_name                                     Optical Illusions\n",
       " in_hsdn                                                       0\n",
       " term_query                  optical illusions[MeSH Terms:noexp]\n",
       " n_articles                                                 4559\n",
       " pubmed_ids    91151|109771|110612|110914|180622|190586|23514...\n",
       " Name: 242, dtype: object,\n",
       " mesh_id                                                 D009912\n",
       " mesh_name                                   Oral Manifestations\n",
       " in_hsdn                                                       1\n",
       " term_query                oral manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                 1487\n",
       " pubmed_ids    26221|37959|40210|42528|122818|123960|124276|1...\n",
       " Name: 243, dtype: object,\n",
       " mesh_id                                                 D010146\n",
       " mesh_name                                                  Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                               pain[MeSH Terms:noexp]\n",
       " n_articles                                               159557\n",
       " pubmed_ids    425|657|708|981|2091|2981|3098|3158|3815|4289|...\n",
       " Name: 244, dtype: object,\n",
       " mesh_id                                                 D010148\n",
       " mesh_name                                     Pain, Intractable\n",
       " in_hsdn                                                       1\n",
       " term_query                  pain, intractable[MeSH Terms:noexp]\n",
       " n_articles                                                 6418\n",
       " pubmed_ids    473|662|6841|9836|17843|18128|23200|26223|2953...\n",
       " Name: 245, dtype: object,\n",
       " mesh_id                                                 D010149\n",
       " mesh_name                                   Pain, Postoperative\n",
       " in_hsdn                                                       1\n",
       " term_query                pain, postoperative[MeSH Terms:noexp]\n",
       " n_articles                                                50093\n",
       " pubmed_ids    2981|6214|7026|7181|7347|10043|12685|14772|171...\n",
       " Name: 246, dtype: object,\n",
       " mesh_id                                                 D010167\n",
       " mesh_name                                                Pallor\n",
       " in_hsdn                                                       1\n",
       " term_query                             pallor[MeSH Terms:noexp]\n",
       " n_articles                                                  372\n",
       " pubmed_ids    319219|348123|405870|630781|703714|856911|9053...\n",
       " Name: 247, dtype: object,\n",
       " mesh_id                                                 D010243\n",
       " mesh_name                                             Paralysis\n",
       " in_hsdn                                                       1\n",
       " term_query                          paralysis[MeSH Terms:noexp]\n",
       " n_articles                                                22062\n",
       " pubmed_ids    5715|6227|10604|12852|16536|20275|20293|24665|...\n",
       " Name: 248, dtype: object,\n",
       " mesh_id                                                 D010264\n",
       " mesh_name                                            Paraplegia\n",
       " in_hsdn                                                       1\n",
       " term_query                         paraplegia[MeSH Terms:noexp]\n",
       " n_articles                                                13274\n",
       " pubmed_ids    2447|5703|13253|17066|23464|30734|32448|35689|...\n",
       " Name: 249, dtype: object,\n",
       " mesh_id                                                 D010291\n",
       " mesh_name                                               Paresis\n",
       " in_hsdn                                                       1\n",
       " term_query                            paresis[MeSH Terms:noexp]\n",
       " n_articles                                                 7657\n",
       " pubmed_ids    165250|182496|192965|195236|268776|389847|3923...\n",
       " Name: 250, dtype: object,\n",
       " mesh_id                                                 D010292\n",
       " mesh_name                                           Paresthesia\n",
       " in_hsdn                                                       1\n",
       " term_query                        paresthesia[MeSH Terms:noexp]\n",
       " n_articles                                                 6327\n",
       " pubmed_ids    7123|11458|48003|48397|51050|51051|55492|56862...\n",
       " Name: 251, dtype: object,\n",
       " mesh_id                                                 D010468\n",
       " mesh_name                                  Perceptual Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query               perceptual disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 6989\n",
       " pubmed_ids    29481|47481|49256|51056|58560|68695|71183|8240...\n",
       " Name: 252, dtype: object,\n",
       " mesh_id                                                 D010591\n",
       " mesh_name                                          Phantom Limb\n",
       " in_hsdn                                                       1\n",
       " term_query                       phantom limb[MeSH Terms:noexp]\n",
       " n_articles                                                 2120\n",
       " pubmed_ids    29536|46747|68483|79303|87841|91726|114819|141...\n",
       " Name: 253, dtype: object,\n",
       " mesh_id                                                 D010842\n",
       " mesh_name                                                  Pica\n",
       " in_hsdn                                                       0\n",
       " term_query                               pica[MeSH Terms:noexp]\n",
       " n_articles                                                 1312\n",
       " pubmed_ids    11141|20458|43539|47481|60544|64850|66562|8560...\n",
       " Name: 254, dtype: object,\n",
       " mesh_id                                                 D010845\n",
       " mesh_name                      Obesity Hypoventilation Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query    obesity hypoventilation syndrome[MeSH Terms:no...\n",
       " n_articles                                                  906\n",
       " pubmed_ids    45501|112012|113749|122063|166266|231120|23279...\n",
       " Name: 255, dtype: object,\n",
       " mesh_id                                                 D011141\n",
       " mesh_name                                              Polyuria\n",
       " in_hsdn                                                       1\n",
       " term_query                           polyuria[MeSH Terms:noexp]\n",
       " n_articles                                                 2365\n",
       " pubmed_ids    48922|50463|65532|72285|72985|78238|79950|9027...\n",
       " Name: 256, dtype: object,\n",
       " mesh_id                                                 D011218\n",
       " mesh_name                                 Prader-Willi Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query              prader-willi syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 3341\n",
       " pubmed_ids    25205|40536|72821|230869|305762|317782|345157|...\n",
       " Name: 257, dtype: object,\n",
       " mesh_id                                                 D011304\n",
       " mesh_name                                           Presbycusis\n",
       " in_hsdn                                                       1\n",
       " term_query                        presbycusis[MeSH Terms:noexp]\n",
       " n_articles                                                 1707\n",
       " pubmed_ids    113738|122983|123939|137290|156774|277814|2873...\n",
       " Name: 258, dtype: object,\n",
       " mesh_id                                                 D011507\n",
       " mesh_name                                           Proteinuria\n",
       " in_hsdn                                                       1\n",
       " term_query                        proteinuria[MeSH Terms:noexp]\n",
       " n_articles                                                26327\n",
       " pubmed_ids    856|973|1625|5816|8228|9230|9368|10152|11015|1...\n",
       " Name: 259, dtype: object,\n",
       " mesh_id                                                 D011537\n",
       " mesh_name                                              Pruritus\n",
       " in_hsdn                                                       1\n",
       " term_query                           pruritus[MeSH Terms:noexp]\n",
       " n_articles                                                14292\n",
       " pubmed_ids    7056|9270|15953|19372|26816|31338|35627|43338|...\n",
       " Name: 260, dtype: object,\n",
       " mesh_id                                                 D011538\n",
       " mesh_name                                          Pruritus Ani\n",
       " in_hsdn                                                       0\n",
       " term_query                       pruritus ani[MeSH Terms:noexp]\n",
       " n_articles                                                  565\n",
       " pubmed_ids    123213|132941|151105|153891|163948|455966|4570...\n",
       " Name: 261, dtype: object,\n",
       " mesh_id                                                 D011539\n",
       " mesh_name                                       Pruritus Vulvae\n",
       " in_hsdn                                                       0\n",
       " term_query                    pruritus vulvae[MeSH Terms:noexp]\n",
       " n_articles                                                  452\n",
       " pubmed_ids    18650|123213|141042|151105|153891|181603|28378...\n",
       " Name: 262, dtype: object,\n",
       " mesh_id                                                 D011595\n",
       " mesh_name                                 Psychomotor Agitation\n",
       " in_hsdn                                                       1\n",
       " term_query              psychomotor agitation[MeSH Terms:noexp]\n",
       " n_articles                                                 5795\n",
       " pubmed_ids    22109|22885|26818|29498|30596|31646|32622|3344...\n",
       " Name: 263, dtype: object,\n",
       " mesh_id                                                 D011596\n",
       " mesh_name                                 Psychomotor Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query              psychomotor disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 5378\n",
       " pubmed_ids    2799|12644|14446|19857|19978|20458|33632|46463...\n",
       " Name: 264, dtype: object,\n",
       " mesh_id                                                 D011602\n",
       " mesh_name                           Psychophysiologic Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query        psychophysiologic disorders[MeSH Terms:noexp]\n",
       " n_articles                                                20045\n",
       " pubmed_ids    725|1078|3030|3086|3309|4885|4893|5382|5384|57...\n",
       " Name: 265, dtype: object,\n",
       " mesh_id                                                 D011681\n",
       " mesh_name                                       Pupil Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                    pupil disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 1238\n",
       " pubmed_ids    1327612|1390424|1392147|1401165|1422101|146940...\n",
       " Name: 266, dtype: object,\n",
       " mesh_id                                                 D011693\n",
       " mesh_name                                               Purpura\n",
       " in_hsdn                                                       1\n",
       " term_query                            purpura[MeSH Terms:noexp]\n",
       " n_articles                                                 7587\n",
       " pubmed_ids    7789|8911|10237|14430|15936|16572|34502|46492|...\n",
       " Name: 267, dtype: object,\n",
       " mesh_id                                                 D011694\n",
       " mesh_name                            Purpura, Hyperglobulinemic\n",
       " in_hsdn                                                       1\n",
       " term_query         purpura, hyperglobulinemic[MeSH Terms:noexp]\n",
       " n_articles                                                  283\n",
       " pubmed_ids    31024|121791|155783|218428|220711|224310|30100...\n",
       " Name: 268, dtype: object,\n",
       " mesh_id                                                 D011695\n",
       " mesh_name                                        IgA Vasculitis\n",
       " in_hsdn                                                       1\n",
       " term_query                     iga vasculitis[MeSH Terms:noexp]\n",
       " n_articles                                                 5052\n",
       " pubmed_ids    11718|15939|16721|17503|20579|22322|24154|2538...\n",
       " Name: 269, dtype: object,\n",
       " mesh_id                                                 D011696\n",
       " mesh_name                             Purpura, Thrombocytopenic\n",
       " in_hsdn                                                       1\n",
       " term_query          purpura, thrombocytopenic[MeSH Terms:noexp]\n",
       " n_articles                                                 6199\n",
       " pubmed_ids    11534|27325|32525|35740|38515|44756|46576|4664...\n",
       " Name: 270, dtype: object,\n",
       " mesh_id                                                 D011697\n",
       " mesh_name                  Purpura, Thrombotic Thrombocytopenic\n",
       " in_hsdn                                                       1\n",
       " term_query    purpura, thrombotic thrombocytopenic[MeSH Term...\n",
       " n_articles                                                 5277\n",
       " pubmed_ids    9526|24154|27206|59334|77387|86782|88388|90841...\n",
       " Name: 271, dtype: object,\n",
       " mesh_id                                                 D011782\n",
       " mesh_name                                          Quadriplegia\n",
       " in_hsdn                                                       1\n",
       " term_query                       quadriplegia[MeSH Terms:noexp]\n",
       " n_articles                                                 8455\n",
       " pubmed_ids    17914|20009|35691|35920|37349|38027|38273|4017...\n",
       " Name: 272, dtype: object,\n",
       " mesh_id                                                 D012001\n",
       " mesh_name                                           Hyperacusis\n",
       " in_hsdn                                                       1\n",
       " term_query                        hyperacusis[MeSH Terms:noexp]\n",
       " n_articles                                                  721\n",
       " pubmed_ids    292147|292154|294676|358060|435151|464893|4898...\n",
       " Name: 273, dtype: object,\n",
       " mesh_id                                                 D012021\n",
       " mesh_name                                      Reflex, Abnormal\n",
       " in_hsdn                                                       1\n",
       " term_query                   reflex, abnormal[MeSH Terms:noexp]\n",
       " n_articles                                                 4985\n",
       " pubmed_ids    20683|30198|33730|37349|40179|45900|52298|5549...\n",
       " Name: 274, dtype: object,\n",
       " mesh_id                                                 D012133\n",
       " mesh_name                                 Respiratory Paralysis\n",
       " in_hsdn                                                       1\n",
       " term_query              respiratory paralysis[MeSH Terms:noexp]\n",
       " n_articles                                                 2036\n",
       " pubmed_ids    20187|78045|78056|82954|122063|122069|147914|1...\n",
       " Name: 275, dtype: object,\n",
       " mesh_id                                                 D012135\n",
       " mesh_name                                    Respiratory Sounds\n",
       " in_hsdn                                                       1\n",
       " term_query                 respiratory sounds[MeSH Terms:noexp]\n",
       " n_articles                                                10250\n",
       " pubmed_ids    92681|93236|114030|116496|117976|233244|292882...\n",
       " Name: 276, dtype: object,\n",
       " mesh_id                                                 D012148\n",
       " mesh_name                                Restless Legs Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query             restless legs syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 4382\n",
       " pubmed_ids    45329|49238|52504|100310|157430|169421|224352|...\n",
       " Name: 277, dtype: object,\n",
       " mesh_id                                                 D012166\n",
       " mesh_name                                    Retinal Hemorrhage\n",
       " in_hsdn                                                       0\n",
       " term_query                 retinal hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                 5694\n",
       " pubmed_ids    11363|47849|52782|61750|68021|87932|92197|9220...\n",
       " Name: 278, dtype: object,\n",
       " mesh_id                                                 D012415\n",
       " mesh_name                             Rubinstein-Taybi Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query          rubinstein-taybi syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  580\n",
       " pubmed_ids    151840|273678|286273|408891|414019|490632|4985...\n",
       " Name: 279, dtype: object,\n",
       " mesh_id                                                 D012585\n",
       " mesh_name                                              Sciatica\n",
       " in_hsdn                                                       1\n",
       " term_query                           sciatica[MeSH Terms:noexp]\n",
       " n_articles                                                 5232\n",
       " pubmed_ids    14381|21068|29536|34814|48685|62163|76856|7738...\n",
       " Name: 280, dtype: object,\n",
       " mesh_id                                                 D012607\n",
       " mesh_name                                               Scotoma\n",
       " in_hsdn                                                       1\n",
       " term_query                            scotoma[MeSH Terms:noexp]\n",
       " n_articles                                                 3253\n",
       " pubmed_ids    68551|71183|76301|87932|133654|135122|141261|1...\n",
       " Name: 281, dtype: object,\n",
       " mesh_id                                                 D012640\n",
       " mesh_name                                              Seizures\n",
       " in_hsdn                                                       1\n",
       " term_query                           seizures[MeSH Terms:noexp]\n",
       " n_articles                                                65111\n",
       " pubmed_ids    1050|1803|2649|3107|4588|5927|6950|7800|7817|8...\n",
       " Name: 282, dtype: object,\n",
       " mesh_id                                                 D012678\n",
       " mesh_name                                   Sensation Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                sensation disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 5377\n",
       " pubmed_ids    1285556|1289734|1291163|1300271|1308972|130919...\n",
       " Name: 283, dtype: object,\n",
       " mesh_id                                               D012817\n",
       " mesh_name                       Signs and Symptoms, Digestive\n",
       " in_hsdn                                                     0\n",
       " term_query    signs and symptoms, digestive[MeSH Terms:noexp]\n",
       " n_articles                                                  0\n",
       " pubmed_ids                                                   \n",
       " Name: 284, dtype: object,\n",
       " mesh_id                                                 D012818\n",
       " mesh_name                       Signs and Symptoms, Respiratory\n",
       " in_hsdn                                                       0\n",
       " term_query    signs and symptoms, respiratory[MeSH Terms:noexp]\n",
       " n_articles                                                    0\n",
       " pubmed_ids                                                     \n",
       " Name: 285, dtype: object,\n",
       " mesh_id                                                 D012877\n",
       " mesh_name                                   Skin Manifestations\n",
       " in_hsdn                                                       1\n",
       " term_query                skin manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                 2723\n",
       " pubmed_ids    4771|15240|15796|16571|17156|18255|18997|21141...\n",
       " Name: 286, dtype: object,\n",
       " mesh_id                                                 D012891\n",
       " mesh_name                                 Sleep Apnea Syndromes\n",
       " in_hsdn                                                       0\n",
       " term_query              sleep apnea syndromes[MeSH Terms:noexp]\n",
       " n_articles                                                16780\n",
       " pubmed_ids    91828|119633|122067|227021|229459|230653|23112...\n",
       " Name: 287, dtype: object,\n",
       " mesh_id                                                 D012892\n",
       " mesh_name                                     Sleep Deprivation\n",
       " in_hsdn                                                       1\n",
       " term_query                  sleep deprivation[MeSH Terms:noexp]\n",
       " n_articles                                                11368\n",
       " pubmed_ids    709|4817|16586|22119|25463|26928|29105|34186|3...\n",
       " Name: 288, dtype: object,\n",
       " mesh_id                                                 D012893\n",
       " mesh_name                                  Sleep Wake Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query               sleep wake disorders[MeSH Terms:noexp]\n",
       " n_articles                                                28060\n",
       " pubmed_ids    1627|1886|2908|3032|4054|4293|6215|9347|9716|1...\n",
       " Name: 289, dtype: object,\n",
       " mesh_id                                                 D012912\n",
       " mesh_name                                              Sneezing\n",
       " in_hsdn                                                       1\n",
       " term_query                           sneezing[MeSH Terms:noexp]\n",
       " n_articles                                                 1023\n",
       " pubmed_ids    665|6392|62367|124893|140400|205151|277420|289...\n",
       " Name: 290, dtype: object,\n",
       " mesh_id                                                 D012913\n",
       " mesh_name                                               Snoring\n",
       " in_hsdn                                                       1\n",
       " term_query                            snoring[MeSH Terms:noexp]\n",
       " n_articles                                                 4759\n",
       " pubmed_ids    45501|211413|216912|254922|446125|452616|46725...\n",
       " Name: 291, dtype: object,\n",
       " mesh_id                                                 D013009\n",
       " mesh_name                                          Somnambulism\n",
       " in_hsdn                                                       0\n",
       " term_query                       somnambulism[MeSH Terms:noexp]\n",
       " n_articles                                                  684\n",
       " pubmed_ids    44211|57711|67478|76558|176105|176558|181607|1...\n",
       " Name: 292, dtype: object,\n",
       " mesh_id                                                 D013035\n",
       " mesh_name                                                 Spasm\n",
       " in_hsdn                                                       1\n",
       " term_query                              spasm[MeSH Terms:noexp]\n",
       " n_articles                                                 7496\n",
       " pubmed_ids    4186|4782|9522|11186|11193|16134|16135|20867|2...\n",
       " Name: 293, dtype: object,\n",
       " mesh_id                                                 D013064\n",
       " mesh_name                                      Speech Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                   speech disorders[MeSH Terms:noexp]\n",
       " n_articles                                                11757\n",
       " pubmed_ids    291|13394|27434|34973|37004|37847|47230|50427|...\n",
       " Name: 294, dtype: object,\n",
       " mesh_id                                                 D013226\n",
       " mesh_name                                    Status Epilepticus\n",
       " in_hsdn                                                       0\n",
       " term_query                 status epilepticus[MeSH Terms:noexp]\n",
       " n_articles                                                 9674\n",
       " pubmed_ids    11555|43112|64874|72273|72651|93071|97072|9707...\n",
       " Name: 295, dtype: object,\n",
       " mesh_id                                                 D013262\n",
       " mesh_name                              Stevens-Johnson Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query           stevens-johnson syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 6134\n",
       " pubmed_ids    972|3900|5694|7134|17904|24335|34242|42243|579...\n",
       " Name: 296, dtype: object,\n",
       " mesh_id                                                 D013342\n",
       " mesh_name                                            Stuttering\n",
       " in_hsdn                                                       1\n",
       " term_query                         stuttering[MeSH Terms:noexp]\n",
       " n_articles                                                 4481\n",
       " pubmed_ids    3524|5103|9926|39200|51758|70761|89683|104321|...\n",
       " Name: 297, dtype: object,\n",
       " mesh_id                                                 D013494\n",
       " mesh_name                       Supranuclear Palsy, Progressive\n",
       " in_hsdn                                                       1\n",
       " term_query    supranuclear palsy, progressive[MeSH Terms:noexp]\n",
       " n_articles                                                 3139\n",
       " pubmed_ids    1301327|1308417|1321966|1321969|1324296|133654...\n",
       " Name: 298, dtype: object,\n",
       " mesh_id                                                 D013575\n",
       " mesh_name                                               Syncope\n",
       " in_hsdn                                                       1\n",
       " term_query                            syncope[MeSH Terms:noexp]\n",
       " n_articles                                                12347\n",
       " pubmed_ids    3965|7050|7817|11767|14792|23595|32675|34679|3...\n",
       " Name: 299, dtype: object,\n",
       " mesh_id                                                 D013651\n",
       " mesh_name                                       Taste Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                    taste disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 2074\n",
       " pubmed_ids    17851|47475|47586|48964|90241|96449|98042|1091...\n",
       " Name: 300, dtype: object,\n",
       " mesh_id                                                 D013746\n",
       " mesh_name                                                Tetany\n",
       " in_hsdn                                                       1\n",
       " term_query                             tetany[MeSH Terms:noexp]\n",
       " n_articles                                                 2518\n",
       " pubmed_ids    3746|4588|7774|10271|10768|15959|35973|45371|4...\n",
       " Name: 301, dtype: object,\n",
       " mesh_id                                                 D013851\n",
       " mesh_name                                              Thinness\n",
       " in_hsdn                                                       1\n",
       " term_query                           thinness[MeSH Terms:noexp]\n",
       " n_articles                                                 8134\n",
       " pubmed_ids    49187|67836|78228|218794|260828|484530|519694|...\n",
       " Name: 302, dtype: object,\n",
       " mesh_id                                                 D014008\n",
       " mesh_name                                           Tinea Pedis\n",
       " in_hsdn                                                       1\n",
       " term_query                        tinea pedis[MeSH Terms:noexp]\n",
       " n_articles                                                 1432\n",
       " pubmed_ids    89246|92017|101790|113370|123886|124247|125094...\n",
       " Name: 303, dtype: object,\n",
       " mesh_id                                                 D014012\n",
       " mesh_name                                              Tinnitus\n",
       " in_hsdn                                                       1\n",
       " term_query                           tinnitus[MeSH Terms:noexp]\n",
       " n_articles                                                 9696\n",
       " pubmed_ids    51064|52695|86841|104108|110565|114919|123940|...\n",
       " Name: 304, dtype: object,\n",
       " mesh_id                                                 D014098\n",
       " mesh_name                                             Toothache\n",
       " in_hsdn                                                       1\n",
       " term_query                          toothache[MeSH Terms:noexp]\n",
       " n_articles                                                 2940\n",
       " pubmed_ids    22103|23328|26722|34046|45013|47620|61220|7049...\n",
       " Name: 305, dtype: object,\n",
       " mesh_id                                                 D014103\n",
       " mesh_name                                           Torticollis\n",
       " in_hsdn                                                       1\n",
       " term_query                        torticollis[MeSH Terms:noexp]\n",
       " n_articles                                                 4027\n",
       " pubmed_ids    13752|21388|34882|50948|75955|79092|94551|9691...\n",
       " Name: 306, dtype: object,\n",
       " mesh_id                                                 D014202\n",
       " mesh_name                                                Tremor\n",
       " in_hsdn                                                       1\n",
       " term_query                             tremor[MeSH Terms:noexp]\n",
       " n_articles                                                11123\n",
       " pubmed_ids    1955|3267|4752|4828|4829|4891|6716|7795|8592|9...\n",
       " Name: 307, dtype: object,\n",
       " mesh_id                                                 D014313\n",
       " mesh_name                                               Trismus\n",
       " in_hsdn                                                       1\n",
       " term_query                            trismus[MeSH Terms:noexp]\n",
       " n_articles                                                 1917\n",
       " pubmed_ids    51912|107132|120858|157508|191553|264734|26534...\n",
       " Name: 308, dtype: object,\n",
       " mesh_id                                                 D014474\n",
       " mesh_name                                       Unconsciousness\n",
       " in_hsdn                                                       1\n",
       " term_query                    unconsciousness[MeSH Terms:noexp]\n",
       " n_articles                                                 4928\n",
       " pubmed_ids    7964|9543|10752|12665|19660|19665|24313|27938|...\n",
       " Name: 309, dtype: object,\n",
       " mesh_id                                                 D014549\n",
       " mesh_name                                  Urinary Incontinence\n",
       " in_hsdn                                                       1\n",
       " term_query               urinary incontinence[MeSH Terms:noexp]\n",
       " n_articles                                                25007\n",
       " pubmed_ids    4915|5343|9724|13031|14876|17938|18862|26451|2...\n",
       " Name: 310, dtype: object,\n",
       " mesh_id                                                 D014550\n",
       " mesh_name                          Urinary Incontinence, Stress\n",
       " in_hsdn                                                       1\n",
       " term_query       urinary incontinence, stress[MeSH Terms:noexp]\n",
       " n_articles                                                13104\n",
       " pubmed_ids    1609|9724|12980|14876|29999|37354|37972|47204|...\n",
       " Name: 311, dtype: object,\n",
       " mesh_id                                                 D014717\n",
       " mesh_name                                               Vertigo\n",
       " in_hsdn                                                       1\n",
       " term_query                            vertigo[MeSH Terms:noexp]\n",
       " n_articles                                                11448\n",
       " pubmed_ids    3634|4752|8363|9552|13936|32758|35998|38524|41...\n",
       " Name: 312, dtype: object,\n",
       " mesh_id                                                 D014770\n",
       " mesh_name                                              Virilism\n",
       " in_hsdn                                                       1\n",
       " term_query                           virilism[MeSH Terms:noexp]\n",
       " n_articles                                                 2363\n",
       " pubmed_ids    16843|39404|57396|68266|91004|102149|119991|12...\n",
       " Name: 313, dtype: object,\n",
       " mesh_id                                                 D014786\n",
       " mesh_name                                      Vision Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                   vision disorders[MeSH Terms:noexp]\n",
       " n_articles                                                31164\n",
       " pubmed_ids    908|3686|14987|34642|34750|35865|38454|40169|4...\n",
       " Name: 314, dtype: object,\n",
       " mesh_id                                                 D014823\n",
       " mesh_name                                   Vitreous Hemorrhage\n",
       " in_hsdn                                                       0\n",
       " term_query                vitreous hemorrhage[MeSH Terms:noexp]\n",
       " n_articles                                                 2148\n",
       " pubmed_ids    318130|1286682|1287361|1299605|1299606|1306495...\n",
       " Name: 315, dtype: object,\n",
       " mesh_id                                                 D014826\n",
       " mesh_name                                  Vocal Cord Paralysis\n",
       " in_hsdn                                                       1\n",
       " term_query               vocal cord paralysis[MeSH Terms:noexp]\n",
       " n_articles                                                 7061\n",
       " pubmed_ids    123626|123993|125822|126321|127047|134203|1344...\n",
       " Name: 316, dtype: object,\n",
       " mesh_id                                                 D014832\n",
       " mesh_name                                       Voice Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query                    voice disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 6336\n",
       " pubmed_ids    112540|116585|155261|159533|160032|161628|1617...\n",
       " Name: 317, dtype: object,\n",
       " mesh_id                                                 D014839\n",
       " mesh_name                                              Vomiting\n",
       " in_hsdn                                                       1\n",
       " term_query                           vomiting[MeSH Terms:noexp]\n",
       " n_articles                                                25802\n",
       " pubmed_ids    127|1136|2377|7774|8837|11869|14273|14394|1489...\n",
       " Name: 318, dtype: object,\n",
       " mesh_id                                                 D014840\n",
       " mesh_name                                Vomiting, Anticipatory\n",
       " in_hsdn                                                       1\n",
       " term_query             vomiting, anticipatory[MeSH Terms:noexp]\n",
       " n_articles                                                  231\n",
       " pubmed_ids    1333617|1419628|1435844|1454956|1454957|155953...\n",
       " Name: 319, dtype: object,\n",
       " mesh_id                                                 D014884\n",
       " mesh_name                      Waterhouse-Friderichsen Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query    waterhouse-friderichsen syndrome[MeSH Terms:no...\n",
       " n_articles                                                  492\n",
       " pubmed_ids    24683|50091|63435|316349|333770|335288|394135|...\n",
       " Name: 320, dtype: object,\n",
       " mesh_id                                                 D014929\n",
       " mesh_name                                      Wolfram Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                   wolfram syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  566\n",
       " pubmed_ids    1383603|1521132|1542564|1568849|1603350|161386...\n",
       " Name: 321, dtype: object,\n",
       " mesh_id                                                 D015160\n",
       " mesh_name                                       Hydrops Fetalis\n",
       " in_hsdn                                                       1\n",
       " term_query                    hydrops fetalis[MeSH Terms:noexp]\n",
       " n_articles                                                 2572\n",
       " pubmed_ids    318464|1279403|1286334|1286427|1287802|1294342...\n",
       " Name: 322, dtype: object,\n",
       " mesh_id                                                 D015325\n",
       " mesh_name     Pyruvate Dehydrogenase Complex Deficiency Disease\n",
       " in_hsdn                                                       0\n",
       " term_query    pyruvate dehydrogenase complex deficiency dise...\n",
       " n_articles                                                  424\n",
       " pubmed_ids    100026|103761|104145|104555|104556|106330|1097...\n",
       " Name: 323, dtype: object,\n",
       " mesh_id                                                 D015354\n",
       " mesh_name                                           Vision, Low\n",
       " in_hsdn                                                       1\n",
       " term_query                        vision, low[MeSH Terms:noexp]\n",
       " n_articles                                                 4162\n",
       " pubmed_ids    1283738|1287173|1299576|1299578|1299581|130386...\n",
       " Name: 324, dtype: object,\n",
       " mesh_id                                                 D015430\n",
       " mesh_name                                           Weight Gain\n",
       " in_hsdn                                                       1\n",
       " term_query                        weight gain[MeSH Terms:noexp]\n",
       " n_articles                                                36589\n",
       " pubmed_ids    1282099|1282387|1284807|1285030|1285261|128609...\n",
       " Name: 325, dtype: object,\n",
       " mesh_id                                                 D015431\n",
       " mesh_name                                           Weight Loss\n",
       " in_hsdn                                                       1\n",
       " term_query                        weight loss[MeSH Terms:noexp]\n",
       " n_articles                                                45180\n",
       " pubmed_ids    162676|1280750|1281395|1284517|1284967|1286136...\n",
       " Name: 326, dtype: object,\n",
       " mesh_id                                                 D015518\n",
       " mesh_name                                         Rett Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                      rett syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 3019\n",
       " pubmed_ids    1283565|1283671|1298942|1308347|1326154|135265...\n",
       " Name: 327, dtype: object,\n",
       " mesh_id                                                 D015746\n",
       " mesh_name                                        Abdominal Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                     abdominal pain[MeSH Terms:noexp]\n",
       " n_articles                                                24757\n",
       " pubmed_ids    95766|1286187|1286949|1287695|1287808|1287938|...\n",
       " Name: 328, dtype: object,\n",
       " mesh_id                                                 D015787\n",
       " mesh_name                            Erythema Chronicum Migrans\n",
       " in_hsdn                                                       0\n",
       " term_query         erythema chronicum migrans[MeSH Terms:noexp]\n",
       " n_articles                                                  789\n",
       " pubmed_ids    1283437|1292852|1313637|1337070|1343019|135789...\n",
       " Name: 329, dtype: object,\n",
       " mesh_id                                                 D015845\n",
       " mesh_name                                           Tonic Pupil\n",
       " in_hsdn                                                       1\n",
       " term_query                        tonic pupil[MeSH Terms:noexp]\n",
       " n_articles                                                  209\n",
       " pubmed_ids    1287177|1300274|1597691|1654342|1827462|183680...\n",
       " Name: 330, dtype: object,\n",
       " mesh_id                                                 D015875\n",
       " mesh_name                                            Anisocoria\n",
       " in_hsdn                                                       1\n",
       " term_query                         anisocoria[MeSH Terms:noexp]\n",
       " n_articles                                                  422\n",
       " pubmed_ids    1304194|1415470|1429141|1477633|1562241|162937...\n",
       " Name: 331, dtype: object,\n",
       " mesh_id                                                 D015877\n",
       " mesh_name                                                Miosis\n",
       " in_hsdn                                                       1\n",
       " term_query                             miosis[MeSH Terms:noexp]\n",
       " n_articles                                                  590\n",
       " pubmed_ids    1414299|1443005|1469625|1483371|1483894|148887...\n",
       " Name: 332, dtype: object,\n",
       " mesh_id                                                 D015878\n",
       " mesh_name                                             Mydriasis\n",
       " in_hsdn                                                       0\n",
       " term_query                          mydriasis[MeSH Terms:noexp]\n",
       " n_articles                                                  860\n",
       " pubmed_ids    1312004|1325920|1344743|1347629|1357615|138469...\n",
       " Name: 333, dtype: object,\n",
       " mesh_id                                                 D016463\n",
       " mesh_name                                        Sweet Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                     sweet syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 1749\n",
       " pubmed_ids    1329174|1350393|1375012|1384410|1404974|141179...\n",
       " Name: 334, dtype: object,\n",
       " mesh_id                                                 D016532\n",
       " mesh_name                              Mucopolysaccharidosis II\n",
       " in_hsdn                                                       0\n",
       " term_query           mucopolysaccharidosis ii[MeSH Terms:noexp]\n",
       " n_articles                                                 1120\n",
       " pubmed_ids    20673|43006|45156|61412|75871|88211|98232|9954...\n",
       " Name: 335, dtype: object,\n",
       " mesh_id                                                 D016534\n",
       " mesh_name                                  Cardiac Output, High\n",
       " in_hsdn                                                       1\n",
       " term_query               cardiac output, high[MeSH Terms:noexp]\n",
       " n_articles                                                  222\n",
       " pubmed_ids    1313653|1315801|1379154|1401800|1415610|145355...\n",
       " Name: 336, dtype: object,\n",
       " mesh_id                                                 D016553\n",
       " mesh_name                 Purpura, Thrombocytopenic, Idiopathic\n",
       " in_hsdn                                                       1\n",
       " term_query    purpura, thrombocytopenic, idiopathic[MeSH Ter...\n",
       " n_articles                                                 7913\n",
       " pubmed_ids    95810|1284746|1293661|1293796|1294972|1294986|...\n",
       " Name: 337, dtype: object,\n",
       " mesh_id                                                 D016731\n",
       " mesh_name                                  Erythema Infectiosum\n",
       " in_hsdn                                                       0\n",
       " term_query               erythema infectiosum[MeSH Terms:noexp]\n",
       " n_articles                                                 1135\n",
       " pubmed_ids    1284951|1287802|1290967|1300262|1308098|132271...\n",
       " Name: 338, dtype: object,\n",
       " mesh_id                                                 D016857\n",
       " mesh_name                                            Hypocapnia\n",
       " in_hsdn                                                       1\n",
       " term_query                         hypocapnia[MeSH Terms:noexp]\n",
       " n_articles                                                 1004\n",
       " pubmed_ids    1288095|1288903|1306935|1307446|1351252|136470...\n",
       " Name: 339, dtype: object,\n",
       " mesh_id                                                 D017036\n",
       " mesh_name                          Epilepsia Partialis Continua\n",
       " in_hsdn                                                       0\n",
       " term_query       epilepsia partialis continua[MeSH Terms:noexp]\n",
       " n_articles                                                  286\n",
       " pubmed_ids    1308422|1527556|1664627|7512914|7554306|760873...\n",
       " Name: 340, dtype: object,\n",
       " mesh_id                                                 D017109\n",
       " mesh_name                               Akathisia, Drug-Induced\n",
       " in_hsdn                                                       1\n",
       " term_query            akathisia, drug-induced[MeSH Terms:noexp]\n",
       " n_articles                                                 1514\n",
       " pubmed_ids    22109|29498|33972|34142|42527|98722|110153|245...\n",
       " Name: 341, dtype: object,\n",
       " mesh_id                                                 D017116\n",
       " mesh_name                                         Low Back Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                      low back pain[MeSH Terms:noexp]\n",
       " n_articles                                                27685\n",
       " pubmed_ids    1285894|1286058|1290548|1290849|1295042|129610...\n",
       " Name: 342, dtype: object,\n",
       " mesh_id                                                 D017246\n",
       " mesh_name         Ophthalmoplegia, Chronic Progressive External\n",
       " in_hsdn                                                       1\n",
       " term_query    ophthalmoplegia, chronic progressive external[...\n",
       " n_articles                                                  632\n",
       " pubmed_ids    1298770|1299529|1300188|1341953|1343860|139213...\n",
       " Name: 343, dtype: object,\n",
       " mesh_id                                                 D017288\n",
       " mesh_name                                        Pain Threshold\n",
       " in_hsdn                                                       0\n",
       " term_query                     pain threshold[MeSH Terms:noexp]\n",
       " n_articles                                                14421\n",
       " pubmed_ids    1280801|1285044|1287573|1288928|1288933|128996...\n",
       " Name: 344, dtype: object,\n",
       " mesh_id                                                 D017566\n",
       " mesh_name                                  Microvascular Angina\n",
       " in_hsdn                                                       0\n",
       " term_query               microvascular angina[MeSH Terms:noexp]\n",
       " n_articles                                                 1149\n",
       " pubmed_ids    1344121|1345329|7486212|7488688|7491175|749521...\n",
       " Name: 345, dtype: object,\n",
       " mesh_id                                                 D017593\n",
       " mesh_name                                 Kleine-Levin Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query              kleine-levin syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  249\n",
       " pubmed_ids    7757600|7963618|7979534|8005368|8006875|814713...\n",
       " Name: 346, dtype: object,\n",
       " mesh_id                                                 D017624\n",
       " mesh_name                                         WAGR Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                      wagr syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  119\n",
       " pubmed_ids    7526938|7527372|7896291|8088833|8282394|840265...\n",
       " Name: 347, dtype: object,\n",
       " mesh_id                                                 D017682\n",
       " mesh_name                                   Myocardial Stunning\n",
       " in_hsdn                                                       0\n",
       " term_query                myocardial stunning[MeSH Terms:noexp]\n",
       " n_articles                                                 2256\n",
       " pubmed_ids    1339791|1339816|1364825|1365940|1366154|747519...\n",
       " Name: 348, dtype: object,\n",
       " mesh_id                                                 D017699\n",
       " mesh_name                                           Pelvic Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                        pelvic pain[MeSH Terms:noexp]\n",
       " n_articles                                                 6883\n",
       " pubmed_ids    1344832|7473437|7482457|7486415|7493693|750178...\n",
       " Name: 349, dtype: object,\n",
       " mesh_id                                                 D017827\n",
       " mesh_name                                Machado-Joseph Disease\n",
       " in_hsdn                                                       0\n",
       " term_query             machado-joseph disease[MeSH Terms:noexp]\n",
       " n_articles                                                 1083\n",
       " pubmed_ids    7485178|7496771|7550335|7561932|7562974|757304...\n",
       " Name: 350, dtype: object,\n",
       " mesh_id                                                 D018437\n",
       " mesh_name                                Brown-Sequard Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query             brown-sequard syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  357\n",
       " pubmed_ids    7475541|7668427|7713991|7716632|7791969|785754...\n",
       " Name: 351, dtype: object,\n",
       " mesh_id                                                 D018458\n",
       " mesh_name                           Persistent Vegetative State\n",
       " in_hsdn                                                       1\n",
       " term_query        persistent vegetative state[MeSH Terms:noexp]\n",
       " n_articles                                                 3210\n",
       " pubmed_ids    1983259|7473638|7494566|7496304|7543150|756190...\n",
       " Name: 352, dtype: object,\n",
       " mesh_id                                                 D018476\n",
       " mesh_name                                           Hypokinesia\n",
       " in_hsdn                                                       1\n",
       " term_query                        hypokinesia[MeSH Terms:noexp]\n",
       " n_articles                                                 1485\n",
       " pubmed_ids    7478462|7483383|7496203|7550907|7565821|758074...\n",
       " Name: 353, dtype: object,\n",
       " mesh_id                                                 D018489\n",
       " mesh_name                                 Space Motion Sickness\n",
       " in_hsdn                                                       1\n",
       " term_query              space motion sickness[MeSH Terms:noexp]\n",
       " n_articles                                                  208\n",
       " pubmed_ids    7550155|7741942|7811217|8563681|8775405|882866...\n",
       " Name: 354, dtype: object,\n",
       " mesh_id                                                 D018496\n",
       " mesh_name                                             Hyperoxia\n",
       " in_hsdn                                                       1\n",
       " term_query                          hyperoxia[MeSH Terms:noexp]\n",
       " n_articles                                                 4496\n",
       " pubmed_ids    5542121|7481108|7485528|7489357|7491979|749464...\n",
       " Name: 355, dtype: object,\n",
       " mesh_id                                                 D018589\n",
       " mesh_name                                         Gastroparesis\n",
       " in_hsdn                                                       1\n",
       " term_query                      gastroparesis[MeSH Terms:noexp]\n",
       " n_articles                                                 2554\n",
       " pubmed_ids    7474464|7475681|7477616|7480968|7481541|748500...\n",
       " Name: 356, dtype: object,\n",
       " mesh_id                                                 D018614\n",
       " mesh_name                                     Sweating Sickness\n",
       " in_hsdn                                                       1\n",
       " term_query                  sweating sickness[MeSH Terms:noexp]\n",
       " n_articles                                                   32\n",
       " pubmed_ids    9023099|9327632|9536626|11284216|11612083|1161...\n",
       " Name: 357, dtype: object,\n",
       " mesh_id                                                 D018771\n",
       " mesh_name                                            Arthralgia\n",
       " in_hsdn                                                       1\n",
       " term_query                         arthralgia[MeSH Terms:noexp]\n",
       " n_articles                                                10175\n",
       " pubmed_ids    1365363|1366307|7481012|7482608|7489265|748926...\n",
       " Name: 358, dtype: object,\n",
       " mesh_id                                                 D018886\n",
       " mesh_name                                   Aphasia, Conduction\n",
       " in_hsdn                                                       1\n",
       " term_query                aphasia, conduction[MeSH Terms:noexp]\n",
       " n_articles                                                   81\n",
       " pubmed_ids    7583186|8564473|8570059|8704297|9126854|956230...\n",
       " Name: 359, dtype: object,\n",
       " mesh_id                                                 D018888\n",
       " mesh_name                          Aphasia, Primary Progressive\n",
       " in_hsdn                                                       1\n",
       " term_query       aphasia, primary progressive[MeSH Terms:noexp]\n",
       " n_articles                                                 1112\n",
       " pubmed_ids    8677717|8738941|8841961|8859072|8921529|892206...\n",
       " Name: 360, dtype: object,\n",
       " mesh_id                                                 D018908\n",
       " mesh_name                                       Muscle Weakness\n",
       " in_hsdn                                                       1\n",
       " term_query                    muscle weakness[MeSH Terms:noexp]\n",
       " n_articles                                                17303\n",
       " pubmed_ids    165250|182496|192965|195236|268776|389847|3923...\n",
       " Name: 361, dtype: object,\n",
       " mesh_id                                                 D018980\n",
       " mesh_name                                     Williams Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                  williams syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                 1950\n",
       " pubmed_ids    7484650|7546456|7547491|7550226|7557968|756996...\n",
       " Name: 362, dtype: object,\n",
       " mesh_id                                                 D019080\n",
       " mesh_name                                    Cafe-au-Lait Spots\n",
       " in_hsdn                                                       1\n",
       " term_query                 cafe-au-lait spots[MeSH Terms:noexp]\n",
       " n_articles                                                  566\n",
       " pubmed_ids    7480286|7490350|7492131|7586657|8537158|854604...\n",
       " Name: 363, dtype: object,\n",
       " mesh_id                                                 D019462\n",
       " mesh_name                                    Syncope, Vasovagal\n",
       " in_hsdn                                                       1\n",
       " term_query                 syncope, vasovagal[MeSH Terms:noexp]\n",
       " n_articles                                                 2288\n",
       " pubmed_ids    8783613|8790955|8803858|8814405|8833492|887686...\n",
       " Name: 364, dtype: object,\n",
       " mesh_id                                                 D019547\n",
       " mesh_name                                             Neck Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                          neck pain[MeSH Terms:noexp]\n",
       " n_articles                                                 8886\n",
       " pubmed_ids    8671132|8715407|8727624|8727627|8783306|879232...\n",
       " Name: 365, dtype: object,\n",
       " mesh_id                                                 D019569\n",
       " mesh_name                                      Hemifacial Spasm\n",
       " in_hsdn                                                       1\n",
       " term_query                   hemifacial spasm[MeSH Terms:noexp]\n",
       " n_articles                                                 1481\n",
       " pubmed_ids    9316041|9339788|9361077|9362139|9367302|938798...\n",
       " Name: 366, dtype: object,\n",
       " mesh_id                                                 D019575\n",
       " mesh_name                                   Blindness, Cortical\n",
       " in_hsdn                                                       1\n",
       " term_query                blindness, cortical[MeSH Terms:noexp]\n",
       " n_articles                                                  646\n",
       " pubmed_ids    9283173|9310919|9310985|9351107|9371947|937348...\n",
       " Name: 367, dtype: object,\n",
       " mesh_id                                                 D019584\n",
       " mesh_name                                           Hot Flashes\n",
       " in_hsdn                                                       1\n",
       " term_query                        hot flashes[MeSH Terms:noexp]\n",
       " n_articles                                                 3707\n",
       " pubmed_ids    9304544|9324185|9332153|9332998|9354042|935704...\n",
       " Name: 368, dtype: object,\n",
       " mesh_id                                                 D019588\n",
       " mesh_name                                      Aging, Premature\n",
       " in_hsdn                                                       1\n",
       " term_query                   aging, premature[MeSH Terms:noexp]\n",
       " n_articles                                                 1326\n",
       " pubmed_ids    9402934|9410852|9428265|9450180|9489217|950437...\n",
       " Name: 369, dtype: object,\n",
       " mesh_id                                                 D019591\n",
       " mesh_name                                          Pseudophakia\n",
       " in_hsdn                                                       1\n",
       " term_query                       pseudophakia[MeSH Terms:noexp]\n",
       " n_articles                                                 2740\n",
       " pubmed_ids    9355187|9368174|9373101|9379383|9379384|937938...\n",
       " Name: 370, dtype: object,\n",
       " mesh_id                                                 D019873\n",
       " mesh_name                                   Schnitzler Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                schnitzler syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  259\n",
       " pubmed_ids    9446924|9638843|9649652|9748880|10074639|10088...\n",
       " Name: 371, dtype: object,\n",
       " mesh_id                                                 D019954\n",
       " mesh_name                        Neurobehavioral Manifestations\n",
       " in_hsdn                                                       1\n",
       " term_query     neurobehavioral manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                  130\n",
       " pubmed_ids    9298400|9330947|9339268|9342204|9342685|934268...\n",
       " Name: 372, dtype: object,\n",
       " mesh_id                                                 D020069\n",
       " mesh_name                                         Shoulder Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                      shoulder pain[MeSH Terms:noexp]\n",
       " n_articles                                                 6119\n",
       " pubmed_ids    9712108|9726482|9741438|9753753|9763237|977615...\n",
       " Name: 373, dtype: object,\n",
       " mesh_id                                                 D020078\n",
       " mesh_name                               Neurogenic Inflammation\n",
       " in_hsdn                                                       0\n",
       " term_query            neurogenic inflammation[MeSH Terms:noexp]\n",
       " n_articles                                                  857\n",
       " pubmed_ids    9746141|9756343|9768840|9779157|9779187|982275...\n",
       " Name: 374, dtype: object,\n",
       " mesh_id                                                 D020150\n",
       " mesh_name                                     Chorea Gravidarum\n",
       " in_hsdn                                                       0\n",
       " term_query                  chorea gravidarum[MeSH Terms:noexp]\n",
       " n_articles                                                   41\n",
       " pubmed_ids    10824060|10967657|12020275|12607770|12772024|1...\n",
       " Name: 375, dtype: object,\n",
       " mesh_id                                                 D020177\n",
       " mesh_name                                Idiopathic Hypersomnia\n",
       " in_hsdn                                                       0\n",
       " term_query             idiopathic hypersomnia[MeSH Terms:noexp]\n",
       " n_articles                                                  187\n",
       " pubmed_ids    10772401|11869432|12655824|12741022|12972686|1...\n",
       " Name: 376, dtype: object,\n",
       " mesh_id                                                 D020178\n",
       " mesh_name                     Sleep Disorders, Circadian Rhythm\n",
       " in_hsdn                                                       0\n",
       " term_query    sleep disorders, circadian rhythm[MeSH Terms:n...\n",
       " n_articles                                                 2222\n",
       " pubmed_ids    9709106|9923220|10498237|10520371|10559705|105...\n",
       " Name: 377, dtype: object,\n",
       " mesh_id                                                 D020179\n",
       " mesh_name                                      Jet Lag Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                   jet lag syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  665\n",
       " pubmed_ids    10477506|10541442|10573331|10582514|10613367|1...\n",
       " Name: 378, dtype: object,\n",
       " mesh_id                                                 D020181\n",
       " mesh_name                              Sleep Apnea, Obstructive\n",
       " in_hsdn                                                       0\n",
       " term_query           sleep apnea, obstructive[MeSH Terms:noexp]\n",
       " n_articles                                                27571\n",
       " pubmed_ids    10334998|10341386|10341387|10448017|10448029|1...\n",
       " Name: 379, dtype: object,\n",
       " mesh_id                                                 D020182\n",
       " mesh_name                                  Sleep Apnea, Central\n",
       " in_hsdn                                                       0\n",
       " term_query               sleep apnea, central[MeSH Terms:noexp]\n",
       " n_articles                                                 1803\n",
       " pubmed_ids    10480208|10508791|10508793|10512956|10522130|1...\n",
       " Name: 380, dtype: object,\n",
       " mesh_id                                                 D020183\n",
       " mesh_name                         Nocturnal Paroxysmal Dystonia\n",
       " in_hsdn                                                       0\n",
       " term_query      nocturnal paroxysmal dystonia[MeSH Terms:noexp]\n",
       " n_articles                                                   49\n",
       " pubmed_ids    10490854|10517062|10996549|11104218|11472389|1...\n",
       " Name: 381, dtype: object,\n",
       " mesh_id                                                 D020184\n",
       " mesh_name                                         Night Terrors\n",
       " in_hsdn                                                       0\n",
       " term_query                      night terrors[MeSH Terms:noexp]\n",
       " n_articles                                                  187\n",
       " pubmed_ids    10544999|10689452|10779247|10802466|10875551|1...\n",
       " Name: 382, dtype: object,\n",
       " mesh_id                                                 D020186\n",
       " mesh_name                                         Sleep Bruxism\n",
       " in_hsdn                                                       0\n",
       " term_query                      sleep bruxism[MeSH Terms:noexp]\n",
       " n_articles                                                  863\n",
       " pubmed_ids    10461163|10495054|10576172|10933561|10973562|1...\n",
       " Name: 383, dtype: object,\n",
       " mesh_id                                                 D020187\n",
       " mesh_name                           REM Sleep Behavior Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query        rem sleep behavior disorder[MeSH Terms:noexp]\n",
       " n_articles                                                 1968\n",
       " pubmed_ids    10563644|10635112|10646174|10648440|10704535|1...\n",
       " Name: 384, dtype: object,\n",
       " mesh_id                                                 D020188\n",
       " mesh_name                                       Sleep Paralysis\n",
       " in_hsdn                                                       0\n",
       " term_query                    sleep paralysis[MeSH Terms:noexp]\n",
       " n_articles                                                  173\n",
       " pubmed_ids    10487786|10646172|10895228|11186082|11285054|1...\n",
       " Name: 385, dtype: object,\n",
       " mesh_id                                                 D020189\n",
       " mesh_name                          Nocturnal Myoclonus Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query       nocturnal myoclonus syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  685\n",
       " pubmed_ids    10566915|10566916|10584676|10634249|10635112|1...\n",
       " Name: 386, dtype: object,\n",
       " mesh_id                                                 D020207\n",
       " mesh_name                                Coma, Post-Head Injury\n",
       " in_hsdn                                                       0\n",
       " term_query             coma, post-head injury[MeSH Terms:noexp]\n",
       " n_articles                                                  130\n",
       " pubmed_ids    10599160|10715976|10715978|10721397|10914642|1...\n",
       " Name: 387, dtype: object,\n",
       " mesh_id                                                 D020233\n",
       " mesh_name                            Gait Disorders, Neurologic\n",
       " in_hsdn                                                       1\n",
       " term_query         gait disorders, neurologic[MeSH Terms:noexp]\n",
       " n_articles                                                 8021\n",
       " pubmed_ids    10467903|10472036|10495043|10499938|10514244|1...\n",
       " Name: 388, dtype: object,\n",
       " mesh_id                                                 D020234\n",
       " mesh_name                                           Gait Ataxia\n",
       " in_hsdn                                                       1\n",
       " term_query                        gait ataxia[MeSH Terms:noexp]\n",
       " n_articles                                                  520\n",
       " pubmed_ids    10536910|10584694|10589796|10593553|10619760|1...\n",
       " Name: 389, dtype: object,\n",
       " mesh_id                                                 D020235\n",
       " mesh_name                                          Gait Apraxia\n",
       " in_hsdn                                                       1\n",
       " term_query                       gait apraxia[MeSH Terms:noexp]\n",
       " n_articles                                                  126\n",
       " pubmed_ids    10668544|10886319|11332785|11347240|11481702|1...\n",
       " Name: 390, dtype: object,\n",
       " mesh_id                                                 D020236\n",
       " mesh_name                             Amnesia, Transient Global\n",
       " in_hsdn                                                       1\n",
       " term_query          amnesia, transient global[MeSH Terms:noexp]\n",
       " n_articles                                                  568\n",
       " pubmed_ids    10362911|10512909|10731904|10744015|10759939|1...\n",
       " Name: 391, dtype: object,\n",
       " mesh_id                                                 D020237\n",
       " mesh_name                                          Alexia, Pure\n",
       " in_hsdn                                                       1\n",
       " term_query                       alexia, pure[MeSH Terms:noexp]\n",
       " n_articles                                                  126\n",
       " pubmed_ids    10953826|11222451|11931940|11954857|12499728|1...\n",
       " Name: 392, dtype: object,\n",
       " mesh_id                                                 D020238\n",
       " mesh_name                                         Prosopagnosia\n",
       " in_hsdn                                                       1\n",
       " term_query                      prosopagnosia[MeSH Terms:noexp]\n",
       " n_articles                                                  680\n",
       " pubmed_ids    10533099|10551026|10574079|10595295|10683834|1...\n",
       " Name: 393, dtype: object,\n",
       " mesh_id                                                 D020240\n",
       " mesh_name                                    Apraxia, Ideomotor\n",
       " in_hsdn                                                       1\n",
       " term_query                 apraxia, ideomotor[MeSH Terms:noexp]\n",
       " n_articles                                                  226\n",
       " pubmed_ids    10577038|10599776|10614158|10622373|10674730|1...\n",
       " Name: 394, dtype: object,\n",
       " mesh_id                                                 D020250\n",
       " mesh_name                     Postoperative Nausea and Vomiting\n",
       " in_hsdn                                                       1\n",
       " term_query    postoperative nausea and vomiting[MeSH Terms:n...\n",
       " n_articles                                                 4844\n",
       " pubmed_ids    9717207|9717590|9742537|9743849|9770086|977313...\n",
       " Name: 395, dtype: object,\n",
       " mesh_id                                                 D020270\n",
       " mesh_name                           Alcohol Withdrawal Seizures\n",
       " in_hsdn                                                       0\n",
       " term_query        alcohol withdrawal seizures[MeSH Terms:noexp]\n",
       " n_articles                                                  286\n",
       " pubmed_ids    10591588|10604976|10627109|10628739|10630609|1...\n",
       " Name: 396, dtype: object,\n",
       " mesh_id                                                 D020323\n",
       " mesh_name                                                  Tics\n",
       " in_hsdn                                                       1\n",
       " term_query                               tics[MeSH Terms:noexp]\n",
       " n_articles                                                 1267\n",
       " pubmed_ids    10489047|10551546|10567498|10567503|10636140|1...\n",
       " Name: 397, dtype: object,\n",
       " mesh_id                                                 D020324\n",
       " mesh_name                                  Amnesia, Anterograde\n",
       " in_hsdn                                                       1\n",
       " term_query               amnesia, anterograde[MeSH Terms:noexp]\n",
       " n_articles                                                  310\n",
       " pubmed_ids    10500274|10509835|10531463|10567496|10583020|1...\n",
       " Name: 398, dtype: object,\n",
       " mesh_id                                                 D020335\n",
       " mesh_name                                           Paraparesis\n",
       " in_hsdn                                                       1\n",
       " term_query                        paraparesis[MeSH Terms:noexp]\n",
       " n_articles                                                  841\n",
       " pubmed_ids    10500256|10544730|10557131|10571762|10598990|1...\n",
       " Name: 399, dtype: object,\n",
       " mesh_id                                                 D020336\n",
       " mesh_name                                  Paraparesis, Spastic\n",
       " in_hsdn                                                       1\n",
       " term_query               paraparesis, spastic[MeSH Terms:noexp]\n",
       " n_articles                                                  466\n",
       " pubmed_ids    10521649|10582615|10585772|10599107|10622457|1...\n",
       " Name: 400, dtype: object,\n",
       " mesh_id                                                 D020385\n",
       " mesh_name                                              Myokymia\n",
       " in_hsdn                                                       1\n",
       " term_query                           myokymia[MeSH Terms:noexp]\n",
       " n_articles                                                  212\n",
       " pubmed_ids    10514588|10514597|10545391|10563654|10567077|1...\n",
       " Name: 401, dtype: object,\n",
       " mesh_id                                                 D020447\n",
       " mesh_name                                           Parasomnias\n",
       " in_hsdn                                                       0\n",
       " term_query                        parasomnias[MeSH Terms:noexp]\n",
       " n_articles                                                  698\n",
       " pubmed_ids    10517062|10619870|10728141|10737339|10740582|1...\n",
       " Name: 402, dtype: object,\n",
       " mesh_id                                                 D020567\n",
       " mesh_name                                          Fetal Weight\n",
       " in_hsdn                                                       1\n",
       " term_query                       fetal weight[MeSH Terms:noexp]\n",
       " n_articles                                                 2289\n",
       " pubmed_ids    10483536|10495409|10495450|10495494|10526258|1...\n",
       " Name: 403, dtype: object,\n",
       " mesh_id                                                 D020754\n",
       " mesh_name                               Spinocerebellar Ataxias\n",
       " in_hsdn                                                       0\n",
       " term_query            spinocerebellar ataxias[MeSH Terms:noexp]\n",
       " n_articles                                                 3096\n",
       " pubmed_ids    10210910|10366652|10369884|10377280|10416231|1...\n",
       " Name: 404, dtype: object,\n",
       " mesh_id                                                 D020757\n",
       " mesh_name                                       Amaurosis Fugax\n",
       " in_hsdn                                                       1\n",
       " term_query                    amaurosis fugax[MeSH Terms:noexp]\n",
       " n_articles                                                  339\n",
       " pubmed_ids    10554788|10565534|10587396|10589802|10603680|1...\n",
       " Name: 405, dtype: object,\n",
       " mesh_id                                                 D020795\n",
       " mesh_name                                           Photophobia\n",
       " in_hsdn                                                       1\n",
       " term_query                        photophobia[MeSH Terms:noexp]\n",
       " n_articles                                                  963\n",
       " pubmed_ids    10209349|10493388|10524659|10524663|10570893|1...\n",
       " Name: 406, dtype: object,\n",
       " mesh_id                                                 D020820\n",
       " mesh_name                                           Dyskinesias\n",
       " in_hsdn                                                       1\n",
       " term_query                        dyskinesias[MeSH Terms:noexp]\n",
       " n_articles                                                 2913\n",
       " pubmed_ids    10493401|10493406|10493407|10495034|10495035|1...\n",
       " Name: 407, dtype: object,\n",
       " mesh_id                                                 D020828\n",
       " mesh_name                                    Pseudobulbar Palsy\n",
       " in_hsdn                                                       1\n",
       " term_query                 pseudobulbar palsy[MeSH Terms:noexp]\n",
       " n_articles                                                  158\n",
       " pubmed_ids    10540005|10587009|10652746|10675156|10726949|1...\n",
       " Name: 408, dtype: object,\n",
       " mesh_id                                              D020879\n",
       " mesh_name                       Neuromuscular Manifestations\n",
       " in_hsdn                                                    0\n",
       " term_query    neuromuscular manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                 0\n",
       " pubmed_ids                                                  \n",
       " Name: 409, dtype: object,\n",
       " mesh_id                                                 D020886\n",
       " mesh_name                               Somatosensory Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query            somatosensory disorders[MeSH Terms:noexp]\n",
       " n_articles                                                 1287\n",
       " pubmed_ids    10501801|10527084|10557198|10567046|10580918|1...\n",
       " Name: 410, dtype: object,\n",
       " mesh_id                                                 D020915\n",
       " mesh_name                                    Korsakoff Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query                 korsakoff syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  566\n",
       " pubmed_ids    10439422|10487391|10516802|10522246|10567496|1...\n",
       " Name: 411, dtype: object,\n",
       " mesh_id                                                 D020919\n",
       " mesh_name                            Sleep Disorders, Intrinsic\n",
       " in_hsdn                                                       0\n",
       " term_query         sleep disorders, intrinsic[MeSH Terms:noexp]\n",
       " n_articles                                                  291\n",
       " pubmed_ids    10577338|10961766|11002615|11007681|11016041|1...\n",
       " Name: 412, dtype: object,\n",
       " mesh_id                                                 D020920\n",
       " mesh_name                                            Dyssomnias\n",
       " in_hsdn                                                       0\n",
       " term_query                         dyssomnias[MeSH Terms:noexp]\n",
       " n_articles                                                  426\n",
       " pubmed_ids    10517062|10522937|10546962|10619870|10630646|1...\n",
       " Name: 413, dtype: object,\n",
       " mesh_id                                                 D020921\n",
       " mesh_name                               Sleep Arousal Disorders\n",
       " in_hsdn                                                       0\n",
       " term_query            sleep arousal disorders[MeSH Terms:noexp]\n",
       " n_articles                                                  179\n",
       " pubmed_ids    10616953|10714338|10714339|10714340|10737339|1...\n",
       " Name: 414, dtype: object,\n",
       " mesh_id                                                 D020922\n",
       " mesh_name                       Sleep-Wake Transition Disorders\n",
       " in_hsdn                                                       0\n",
       " term_query    sleep-wake transition disorders[MeSH Terms:noexp]\n",
       " n_articles                                                  200\n",
       " pubmed_ids    10612149|10778032|10937135|11005200|11104233|1...\n",
       " Name: 415, dtype: object,\n",
       " mesh_id                                                 D020923\n",
       " mesh_name                                 REM Sleep Parasomnias\n",
       " in_hsdn                                                       0\n",
       " term_query              rem sleep parasomnias[MeSH Terms:noexp]\n",
       " n_articles                                                  102\n",
       " pubmed_ids    10728141|10996566|11317618|11383385|11532249|1...\n",
       " Name: 416, dtype: object,\n",
       " mesh_id                                                 D020924\n",
       " mesh_name                             Urological Manifestations\n",
       " in_hsdn                                                       0\n",
       " term_query          urological manifestations[MeSH Terms:noexp]\n",
       " n_articles                                                    7\n",
       " pubmed_ids    13037968|13615375|13940942|13957271|13958840|1...\n",
       " Name: 417, dtype: object,\n",
       " mesh_id                                                 D020925\n",
       " mesh_name                               Hypoxia-Ischemia, Brain\n",
       " in_hsdn                                                       0\n",
       " term_query            hypoxia-ischemia, brain[MeSH Terms:noexp]\n",
       " n_articles                                                 7246\n",
       " pubmed_ids    10375357|10473893|10511343|10513324|10519720|1...\n",
       " Name: 418, dtype: object,\n",
       " mesh_id                                                 D021501\n",
       " mesh_name                                            Flank Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                         flank pain[MeSH Terms:noexp]\n",
       " n_articles                                                  731\n",
       " pubmed_ids    10917391|10958573|10995490|11025378|11037484|1...\n",
       " Name: 419, dtype: object,\n",
       " mesh_id                                                 D023341\n",
       " mesh_name                                                Chills\n",
       " in_hsdn                                                       1\n",
       " term_query                             chills[MeSH Terms:noexp]\n",
       " n_articles                                                  328\n",
       " pubmed_ids    10972914|11073745|11140912|11213566|11249043|1...\n",
       " Name: 420, dtype: object,\n",
       " mesh_id                                                 D034062\n",
       " mesh_name                              Insomnia, Fatal Familial\n",
       " in_hsdn                                                       0\n",
       " term_query           insomnia, fatal familial[MeSH Terms:noexp]\n",
       " n_articles                                                  202\n",
       " pubmed_ids    12109876|12356908|12433271|12464332|12660573|1...\n",
       " Name: 421, dtype: object,\n",
       " mesh_id                                                 D034381\n",
       " mesh_name                                          Hearing Loss\n",
       " in_hsdn                                                       1\n",
       " term_query                       hearing loss[MeSH Terms:noexp]\n",
       " n_articles                                                20772\n",
       " pubmed_ids    81425|83329|83482|84863|91198|92469|95382|1000...\n",
       " Name: 422, dtype: object,\n",
       " mesh_id                                                 D037061\n",
       " mesh_name                                         Metatarsalgia\n",
       " in_hsdn                                                       1\n",
       " term_query                      metatarsalgia[MeSH Terms:noexp]\n",
       " n_articles                                                  343\n",
       " pubmed_ids    12400713|12400714|12500922|12845859|13286518|1...\n",
       " Name: 423, dtype: object,\n",
       " mesh_id                                                 D038901\n",
       " mesh_name                          Mental Retardation, X-Linked\n",
       " in_hsdn                                                       0\n",
       " term_query       mental retardation, x-linked[MeSH Terms:noexp]\n",
       " n_articles                                                  987\n",
       " pubmed_ids    12014383|12087085|12210308|12376095|12428212|1...\n",
       " Name: 424, dtype: object,\n",
       " mesh_id                                                 D038921\n",
       " mesh_name                                 Coffin-Lowry Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query              coffin-lowry syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  108\n",
       " pubmed_ids    12014383|12030896|12210291|12233987|12393804|1...\n",
       " Name: 425, dtype: object,\n",
       " mesh_id                                                 D041781\n",
       " mesh_name                                 Jaundice, Obstructive\n",
       " in_hsdn                                                       1\n",
       " term_query              jaundice, obstructive[MeSH Terms:noexp]\n",
       " n_articles                                                 3888\n",
       " pubmed_ids    11829787|11829824|11832161|11970769|12181756|1...\n",
       " Name: 426, dtype: object,\n",
       " mesh_id                                                 D045262\n",
       " mesh_name                                       Reticulocytosis\n",
       " in_hsdn                                                       1\n",
       " term_query                    reticulocytosis[MeSH Terms:noexp]\n",
       " n_articles                                                  115\n",
       " pubmed_ids    12985908|13003980|13018996|13020258|13020259|1...\n",
       " Name: 427, dtype: object,\n",
       " mesh_id                                                 D046088\n",
       " mesh_name                              Hearing Loss, Unilateral\n",
       " in_hsdn                                                       1\n",
       " term_query           hearing loss, unilateral[MeSH Terms:noexp]\n",
       " n_articles                                                 1073\n",
       " pubmed_ids    13009473|13021686|13121720|13171884|13275295|1...\n",
       " Name: 428, dtype: object,\n",
       " mesh_id                                                 D046089\n",
       " mesh_name          Hearing Loss, Mixed Conductive-Sensorineural\n",
       " in_hsdn                                                       1\n",
       " term_query    hearing loss, mixed conductive-sensorineural[M...\n",
       " n_articles                                                  469\n",
       " pubmed_ids    13611410|14270862|14282770|14403048|15236896|1...\n",
       " Name: 429, dtype: object,\n",
       " mesh_id                                                 D046608\n",
       " mesh_name                                            Synkinesis\n",
       " in_hsdn                                                       1\n",
       " term_query                         synkinesis[MeSH Terms:noexp]\n",
       " n_articles                                                  334\n",
       " pubmed_ids    12979328|12996944|13004623|13064697|13298319|1...\n",
       " Name: 430, dtype: object,\n",
       " mesh_id                                                 D048949\n",
       " mesh_name                                            Labor Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                         labor pain[MeSH Terms:noexp]\n",
       " n_articles                                                 1408\n",
       " pubmed_ids    12411035|12982240|13003246|13003254|13014189|1...\n",
       " Name: 431, dtype: object,\n",
       " mesh_id                                                 D048968\n",
       " mesh_name                                      Morning Sickness\n",
       " in_hsdn                                                       1\n",
       " term_query                   morning sickness[MeSH Terms:noexp]\n",
       " n_articles                                                  216\n",
       " pubmed_ids    14155712|14897076|14992226|15329830|15555170|1...\n",
       " Name: 432, dtype: object,\n",
       " mesh_id                                                 D050177\n",
       " mesh_name                                            Overweight\n",
       " in_hsdn                                                       1\n",
       " term_query                         overweight[MeSH Terms:noexp]\n",
       " n_articles                                                35325\n",
       " pubmed_ids    11590455|12640781|12761436|12869779|13033648|1...\n",
       " Name: 433, dtype: object,\n",
       " mesh_id                                                 D051346\n",
       " mesh_name                                   Mobility Limitation\n",
       " in_hsdn                                                       1\n",
       " term_query                mobility limitation[MeSH Terms:noexp]\n",
       " n_articles                                                 5335\n",
       " pubmed_ids    13534975|13545600|13790260|13906802|14225226|1...\n",
       " Name: 434, dtype: object,\n",
       " mesh_id                                                 D051474\n",
       " mesh_name                               Neuralgia, Postherpetic\n",
       " in_hsdn                                                       1\n",
       " term_query            neuralgia, postherpetic[MeSH Terms:noexp]\n",
       " n_articles                                                 1426\n",
       " pubmed_ids    12466092|12852900|13096930|13211194|13256181|1...\n",
       " Name: 435, dtype: object,\n",
       " mesh_id                                                 D052120\n",
       " mesh_name                     Glycogen Storage Disease Type IIb\n",
       " in_hsdn                                                       0\n",
       " term_query    glycogen storage disease type iib[MeSH Terms:n...\n",
       " n_articles                                                  215\n",
       " pubmed_ids    15505188|15889279|16144992|16217705|16320310|1...\n",
       " Name: 436, dtype: object,\n",
       " mesh_id                                                 D052245\n",
       " mesh_name                                       Usher Syndromes\n",
       " in_hsdn                                                       1\n",
       " term_query                    usher syndromes[MeSH Terms:noexp]\n",
       " n_articles                                                  704\n",
       " pubmed_ids    12976223|13047804|13065180|13105203|13108174|1...\n",
       " Name: 437, dtype: object,\n",
       " mesh_id                                                 D053158\n",
       " mesh_name                                              Nocturia\n",
       " in_hsdn                                                       1\n",
       " term_query                           nocturia[MeSH Terms:noexp]\n",
       " n_articles                                                 1212\n",
       " pubmed_ids    12988592|13006329|13013400|13060160|13214815|1...\n",
       " Name: 438, dtype: object,\n",
       " mesh_id                                                 D053159\n",
       " mesh_name                                               Dysuria\n",
       " in_hsdn                                                       1\n",
       " term_query                            dysuria[MeSH Terms:noexp]\n",
       " n_articles                                                  546\n",
       " pubmed_ids    12981732|13003775|13068526|13086570|13223307|1...\n",
       " Name: 439, dtype: object,\n",
       " mesh_id                                                 D053201\n",
       " mesh_name                           Urinary Bladder, Overactive\n",
       " in_hsdn                                                       1\n",
       " term_query        urinary bladder, overactive[MeSH Terms:noexp]\n",
       " n_articles                                                 6136\n",
       " pubmed_ids    13096355|13684575|13722810|14085775|14087175|1...\n",
       " Name: 440, dtype: object,\n",
       " mesh_id                                                 D053202\n",
       " mesh_name                            Urinary Incontinence, Urge\n",
       " in_hsdn                                                       1\n",
       " term_query         urinary incontinence, urge[MeSH Terms:noexp]\n",
       " n_articles                                                 1185\n",
       " pubmed_ids    13852819|13970523|14232184|16437246|16552618|1...\n",
       " Name: 441, dtype: object,\n",
       " mesh_id                                                 D053448\n",
       " mesh_name                                            Prostatism\n",
       " in_hsdn                                                       1\n",
       " term_query                         prostatism[MeSH Terms:noexp]\n",
       " n_articles                                                  562\n",
       " pubmed_ids    12992300|13044289|13061266|13064714|13084319|1...\n",
       " Name: 442, dtype: object,\n",
       " mesh_id                                                 D053565\n",
       " mesh_name                                        Hypercalciuria\n",
       " in_hsdn                                                       1\n",
       " term_query                     hypercalciuria[MeSH Terms:noexp]\n",
       " n_articles                                                  977\n",
       " pubmed_ids    13103628|13120841|13146861|13187958|13192905|1...\n",
       " Name: 443, dtype: object,\n",
       " mesh_id                                                 D053578\n",
       " mesh_name                         Opsoclonus-Myoclonus Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query      opsoclonus-myoclonus syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  376\n",
       " pubmed_ids    16200567|16652344|16715202|16900484|16939863|1...\n",
       " Name: 444, dtype: object,\n",
       " mesh_id                                                 D053584\n",
       " mesh_name                                               Urinoma\n",
       " in_hsdn                                                       1\n",
       " term_query                            urinoma[MeSH Terms:noexp]\n",
       " n_articles                                                  146\n",
       " pubmed_ids    14217108|16832780|16941574|16965232|17085143|1...\n",
       " Name: 445, dtype: object,\n",
       " mesh_id                                                 D053591\n",
       " mesh_name                                        Pain, Referred\n",
       " in_hsdn                                                       1\n",
       " term_query                     pain, referred[MeSH Terms:noexp]\n",
       " n_articles                                                  381\n",
       " pubmed_ids    13011548|13028744|13095125|13108728|13124482|1...\n",
       " Name: 446, dtype: object,\n",
       " mesh_id                                                 D053608\n",
       " mesh_name                                                Stupor\n",
       " in_hsdn                                                       1\n",
       " term_query                             stupor[MeSH Terms:noexp]\n",
       " n_articles                                                  756\n",
       " pubmed_ids    12982596|12998164|13004942|13008520|13008658|1...\n",
       " Name: 447, dtype: object,\n",
       " mesh_id                                                 D053609\n",
       " mesh_name                                              Lethargy\n",
       " in_hsdn                                                       1\n",
       " term_query                           lethargy[MeSH Terms:noexp]\n",
       " n_articles                                                  508\n",
       " pubmed_ids    12979353|12991839|12998308|13012734|13018500|1...\n",
       " Name: 448, dtype: object,\n",
       " mesh_id                                                 D054062\n",
       " mesh_name                                  Deaf-Blind Disorders\n",
       " in_hsdn                                                       1\n",
       " term_query               deaf-blind disorders[MeSH Terms:noexp]\n",
       " n_articles                                                  175\n",
       " pubmed_ids    14864488|17087444|18003865|18003866|18003867|1...\n",
       " Name: 449, dtype: object,\n",
       " mesh_id                                                 D054068\n",
       " mesh_name                                    Livedo Reticularis\n",
       " in_hsdn                                                       1\n",
       " term_query                 livedo reticularis[MeSH Terms:noexp]\n",
       " n_articles                                                  469\n",
       " pubmed_ids    13214346|13356380|13375166|13384898|13394196|1...\n",
       " Name: 450, dtype: object,\n",
       " mesh_id                                                 D054078\n",
       " mesh_name                          Mevalonate Kinase Deficiency\n",
       " in_hsdn                                                       0\n",
       " term_query       mevalonate kinase deficiency[MeSH Terms:noexp]\n",
       " n_articles                                                  278\n",
       " pubmed_ids    16304362|16871408|17804452|17965046|18008182|1...\n",
       " Name: 451, dtype: object,\n",
       " mesh_id                                                 D054160\n",
       " mesh_name                                      Systolic Murmurs\n",
       " in_hsdn                                                       1\n",
       " term_query                   systolic murmurs[MeSH Terms:noexp]\n",
       " n_articles                                                  226\n",
       " pubmed_ids    13023170|13037085|13069853|13154628|13167205|1...\n",
       " Name: 452, dtype: object,\n",
       " mesh_id                                                 D054221\n",
       " mesh_name     Classical Lissencephalies and Subcortical Band...\n",
       " in_hsdn                                                       0\n",
       " term_query    classical lissencephalies and subcortical band...\n",
       " n_articles                                                  208\n",
       " pubmed_ids    16191320|17028375|17850357|17997972|18021933|1...\n",
       " Name: 453, dtype: object,\n",
       " mesh_id                                                 D054546\n",
       " mesh_name                                   Neuroacanthocytosis\n",
       " in_hsdn                                                       0\n",
       " term_query                neuroacanthocytosis[MeSH Terms:noexp]\n",
       " n_articles                                                  235\n",
       " pubmed_ids    14592625|17277857|17294064|17516458|17627720|1...\n",
       " Name: 454, dtype: object,\n",
       " mesh_id                                                 D054971\n",
       " mesh_name                               Orthostatic Intolerance\n",
       " in_hsdn                                                       1\n",
       " term_query            orthostatic intolerance[MeSH Terms:noexp]\n",
       " n_articles                                                  448\n",
       " pubmed_ids    17254456|18565193|18617843|18757480|18772858|1...\n",
       " Name: 455, dtype: object,\n",
       " mesh_id                                                 D054972\n",
       " mesh_name             Postural Orthostatic Tachycardia Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query    postural orthostatic tachycardia syndrome[MeSH...\n",
       " n_articles                                                  771\n",
       " pubmed_ids    15833184|18392420|18617391|18656847|18704621|1...\n",
       " Name: 456, dtype: object,\n",
       " mesh_id                                                 D055111\n",
       " mesh_name                          Failed Back Surgery Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query       failed back surgery syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  483\n",
       " pubmed_ids    18721177|18806999|18839224|18936878|19006909|1...\n",
       " Name: 457, dtype: object,\n",
       " mesh_id                                                 D055154\n",
       " mesh_name                                             Dysphonia\n",
       " in_hsdn                                                       1\n",
       " term_query                          dysphonia[MeSH Terms:noexp]\n",
       " n_articles                                                 2360\n",
       " pubmed_ids    12852881|13043689|13233670|13268171|13301696|1...\n",
       " Name: 458, dtype: object,\n",
       " mesh_id                                                 D055665\n",
       " mesh_name                                     Purpura Fulminans\n",
       " in_hsdn                                                       1\n",
       " term_query                  purpura fulminans[MeSH Terms:noexp]\n",
       " n_articles                                                  358\n",
       " pubmed_ids    12993516|13002650|13020854|13050035|13094600|1...\n",
       " Name: 459, dtype: object,\n",
       " mesh_id                                                 D055948\n",
       " mesh_name                                            Sarcopenia\n",
       " in_hsdn                                                       1\n",
       " term_query                         sarcopenia[MeSH Terms:noexp]\n",
       " n_articles                                                10589\n",
       " pubmed_ids    18309443|18983905|19341788|19369058|19371777|1...\n",
       " Name: 460, dtype: object,\n",
       " mesh_id                                                 D055954\n",
       " mesh_name                         Corneal Endothelial Cell Loss\n",
       " in_hsdn                                                       0\n",
       " term_query      corneal endothelial cell loss[MeSH Terms:noexp]\n",
       " n_articles                                                  755\n",
       " pubmed_ids    17633472|18949003|19432861|19493251|19628490|1...\n",
       " Name: 461, dtype: object,\n",
       " mesh_id                                                 D055955\n",
       " mesh_name                                        Susac Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query                     susac syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  293\n",
       " pubmed_ids    19403172|19888559|19902818|19953118|20189079|2...\n",
       " Name: 462, dtype: object,\n",
       " mesh_id                                                 D055958\n",
       " mesh_name                            Piriformis Muscle Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query         piriformis muscle syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  184\n",
       " pubmed_ids    19396428|19764421|19918770|19927068|19998490|2...\n",
       " Name: 463, dtype: object,\n",
       " mesh_id                                                 D055964\n",
       " mesh_name                                 Alien Limb Phenomenon\n",
       " in_hsdn                                                       1\n",
       " term_query              alien limb phenomenon[MeSH Terms:noexp]\n",
       " n_articles                                                   72\n",
       " pubmed_ids    19544144|20069502|20220444|20304333|20378359|2...\n",
       " Name: 464, dtype: object,\n",
       " mesh_id                                                 D056124\n",
       " mesh_name                               Slit Ventricle Syndrome\n",
       " in_hsdn                                                       1\n",
       " term_query            slit ventricle syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   47\n",
       " pubmed_ids    20043731|20617320|21039172|21916129|21921577|2...\n",
       " Name: 465, dtype: object,\n",
       " mesh_id                                                 D056128\n",
       " mesh_name                                    Obesity, Abdominal\n",
       " in_hsdn                                                       0\n",
       " term_query                 obesity, abdominal[MeSH Terms:noexp]\n",
       " n_articles                                                 5522\n",
       " pubmed_ids    13186137|13313404|13788503|13840673|14790082|1...\n",
       " Name: 466, dtype: object,\n",
       " mesh_id                                                 D056266\n",
       " mesh_name                        Erythrokeratodermia Variabilis\n",
       " in_hsdn                                                       0\n",
       " term_query     erythrokeratodermia variabilis[MeSH Terms:noexp]\n",
       " n_articles                                                   82\n",
       " pubmed_ids    12996909|13389783|13393794|13447448|13522016|1...\n",
       " Name: 467, dtype: object,\n",
       " mesh_id                                                 D056844\n",
       " mesh_name                                           Renal Colic\n",
       " in_hsdn                                                       1\n",
       " term_query                        renal colic[MeSH Terms:noexp]\n",
       " n_articles                                                  711\n",
       " pubmed_ids    12992385|13125829|13135767|13137835|13170501|1...\n",
       " Name: 468, dtype: object,\n",
       " mesh_id                                                 D056865\n",
       " mesh_name                                     Ideal Body Weight\n",
       " in_hsdn                                                       0\n",
       " term_query                  ideal body weight[MeSH Terms:noexp]\n",
       " n_articles                                                  529\n",
       " pubmed_ids    13278881|13869720|13996280|14480321|19171332|1...\n",
       " Name: 469, dtype: object,\n",
       " mesh_id                                                 D057178\n",
       " mesh_name                 Primary Progressive Nonfluent Aphasia\n",
       " in_hsdn                                                       1\n",
       " term_query    primary progressive nonfluent aphasia[MeSH Ter...\n",
       " n_articles                                                  156\n",
       " pubmed_ids    19696033|19907178|19938681|19938683|19938684|2...\n",
       " Name: 470, dtype: object,\n",
       " mesh_id                                                 D057768\n",
       " mesh_name                    Brief, Resolved, Unexplained Event\n",
       " in_hsdn                                                       1\n",
       " term_query    brief, resolved, unexplained event[MeSH Terms:...\n",
       " n_articles                                                   66\n",
       " pubmed_ids    21140038|21502473|21803779|21903620|22711722|2...\n",
       " Name: 471, dtype: object,\n",
       " mesh_id                                                 D057774\n",
       " mesh_name                             Post-Exercise Hypotension\n",
       " in_hsdn                                                       0\n",
       " term_query          post-exercise hypotension[MeSH Terms:noexp]\n",
       " n_articles                                                  142\n",
       " pubmed_ids    20054347|21358433|21359479|21422379|21430451|2...\n",
       " Name: 472, dtype: object,\n",
       " mesh_id                                                 D057896\n",
       " mesh_name                                      Striae Distensae\n",
       " in_hsdn                                                       1\n",
       " term_query                   striae distensae[MeSH Terms:noexp]\n",
       " n_articles                                                  351\n",
       " pubmed_ids    13125739|13127255|13160182|13251515|13255928|1...\n",
       " Name: 473, dtype: object,\n",
       " mesh_id                                                 D058447\n",
       " mesh_name                                              Eye Pain\n",
       " in_hsdn                                                       1\n",
       " term_query                           eye pain[MeSH Terms:noexp]\n",
       " n_articles                                                  833\n",
       " pubmed_ids    13186007|13221910|13316094|13377809|13532628|1...\n",
       " Name: 474, dtype: object,\n",
       " mesh_id                                                 D058568\n",
       " mesh_name                         Necrolytic Migratory Erythema\n",
       " in_hsdn                                                       1\n",
       " term_query      necrolytic migratory erythema[MeSH Terms:noexp]\n",
       " n_articles                                                   80\n",
       " pubmed_ids    20500495|21034987|21128995|21334267|21416773|2...\n",
       " Name: 475, dtype: object,\n",
       " mesh_id                                                 D058747\n",
       " mesh_name                                       CHARGE Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query                    charge syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                  359\n",
       " pubmed_ids    20363513|20389093|20500074|20584036|20591827|2...\n",
       " Name: 476, dtype: object,\n",
       " mesh_id                                                 D059226\n",
       " mesh_name                                      Nociceptive Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                   nociceptive pain[MeSH Terms:noexp]\n",
       " n_articles                                                  989\n",
       " pubmed_ids    13114531|13221911|13229243|13368820|13724996|1...\n",
       " Name: 477, dtype: object,\n",
       " mesh_id                                                 D059245\n",
       " mesh_name                    Transient Tachypnea of the Newborn\n",
       " in_hsdn                                                       0\n",
       " term_query    transient tachypnea of the newborn[MeSH Terms:...\n",
       " n_articles                                                  162\n",
       " pubmed_ids    20963833|21299397|21658715|21810149|21839467|2...\n",
       " Name: 478, dtype: object,\n",
       " mesh_id                                                 D059246\n",
       " mesh_name                                             Tachypnea\n",
       " in_hsdn                                                       0\n",
       " term_query                          tachypnea[MeSH Terms:noexp]\n",
       " n_articles                                                  326\n",
       " pubmed_ids    13018983|13199031|13334573|13512375|13882058|1...\n",
       " Name: 479, dtype: object,\n",
       " mesh_id                                                 D059265\n",
       " mesh_name                                         Visceral Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                      visceral pain[MeSH Terms:noexp]\n",
       " n_articles                                                  840\n",
       " pubmed_ids    13021503|13101247|13121334|13121335|13121336|1...\n",
       " Name: 480, dtype: object,\n",
       " mesh_id                                                 D059350\n",
       " mesh_name                                          Chronic Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                       chronic pain[MeSH Terms:noexp]\n",
       " n_articles                                                24310\n",
       " pubmed_ids    13072779|13147455|13167528|13188515|13196566|1...\n",
       " Name: 481, dtype: object,\n",
       " mesh_id                                                 D059352\n",
       " mesh_name                                  Musculoskeletal Pain\n",
       " in_hsdn                                                       0\n",
       " term_query               musculoskeletal pain[MeSH Terms:noexp]\n",
       " n_articles                                                 4832\n",
       " pubmed_ids    12979125|12980842|13111481|13146711|13156322|1...\n",
       " Name: 482, dtype: object,\n",
       " mesh_id                                                 D059373\n",
       " mesh_name                                            Mastodynia\n",
       " in_hsdn                                                       0\n",
       " term_query                         mastodynia[MeSH Terms:noexp]\n",
       " n_articles                                                  246\n",
       " pubmed_ids    12982074|13119099|13224017|13280219|13281582|1...\n",
       " Name: 483, dtype: object,\n",
       " mesh_id                                                 D059388\n",
       " mesh_name                                    Pelvic Girdle Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                 pelvic girdle pain[MeSH Terms:noexp]\n",
       " n_articles                                                  231\n",
       " pubmed_ids    21682585|21823869|21871421|21895953|21973126|2...\n",
       " Name: 484, dtype: object,\n",
       " mesh_id                                                 D059390\n",
       " mesh_name                                     Breakthrough Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                  breakthrough pain[MeSH Terms:noexp]\n",
       " n_articles                                                  401\n",
       " pubmed_ids    20580202|20680354|21181210|21208247|21215653|2...\n",
       " Name: 485, dtype: object,\n",
       " mesh_id                                                 D059411\n",
       " mesh_name                          Lower Urinary Tract Symptoms\n",
       " in_hsdn                                                       0\n",
       " term_query       lower urinary tract symptoms[MeSH Terms:noexp]\n",
       " n_articles                                                 4383\n",
       " pubmed_ids    13009502|19804425|21044248|21073697|21112255|2...\n",
       " Name: 486, dtype: object,\n",
       " mesh_id                                                 D059445\n",
       " mesh_name                                             Anhedonia\n",
       " in_hsdn                                                       0\n",
       " term_query                          anhedonia[MeSH Terms:noexp]\n",
       " n_articles                                                 1743\n",
       " pubmed_ids    13792590|18125316|19368847|20176860|20452676|2...\n",
       " Name: 487, dtype: object,\n",
       " mesh_id                                                 D059606\n",
       " mesh_name                                            Polydipsia\n",
       " in_hsdn                                                       0\n",
       " term_query                         polydipsia[MeSH Terms:noexp]\n",
       " n_articles                                                  283\n",
       " pubmed_ids    12985921|13001884|13030757|13050224|13075973|1...\n",
       " Name: 488, dtype: object,\n",
       " mesh_id                                                 D059607\n",
       " mesh_name                               Polydipsia, Psychogenic\n",
       " in_hsdn                                                       0\n",
       " term_query            polydipsia, psychogenic[MeSH Terms:noexp]\n",
       " n_articles                                                   83\n",
       " pubmed_ids    13190426|13202801|13401042|13423317|13658352|1...\n",
       " Name: 489, dtype: object,\n",
       " mesh_id                                                 D059787\n",
       " mesh_name                                            Acute Pain\n",
       " in_hsdn                                                       0\n",
       " term_query                         acute pain[MeSH Terms:noexp]\n",
       " n_articles                                                 3282\n",
       " pubmed_ids    13112408|13430279|13702541|13745301|13940956|1...\n",
       " Name: 490, dtype: object,\n",
       " mesh_id                                                 D060050\n",
       " mesh_name                                        Angina, Stable\n",
       " in_hsdn                                                       0\n",
       " term_query                     angina, stable[MeSH Terms:noexp]\n",
       " n_articles                                                 1666\n",
       " pubmed_ids    15477771|15602433|15699926|17357481|18087560|1...\n",
       " Name: 491, dtype: object,\n",
       " mesh_id                                                 D060486\n",
       " mesh_name                              Ophthalmoplegic Migraine\n",
       " in_hsdn                                                       0\n",
       " term_query           ophthalmoplegic migraine[MeSH Terms:noexp]\n",
       " n_articles                                                   68\n",
       " pubmed_ids    13003244|13012811|13039619|13039647|13073867|1...\n",
       " Name: 492, dtype: object,\n",
       " mesh_id                                                 D060545\n",
       " mesh_name                                    Pudendal Neuralgia\n",
       " in_hsdn                                                       0\n",
       " term_query                 pudendal neuralgia[MeSH Terms:noexp]\n",
       " n_articles                                                  149\n",
       " pubmed_ids    18149416|20727663|20987781|21041801|21056367|2...\n",
       " Name: 493, dtype: object,\n",
       " mesh_id                                                 D060705\n",
       " mesh_name                                           Dyscalculia\n",
       " in_hsdn                                                       0\n",
       " term_query                        dyscalculia[MeSH Terms:noexp]\n",
       " n_articles                                                  293\n",
       " pubmed_ids    12978171|13112326|13167954|13173289|13330514|1...\n",
       " Name: 494, dtype: object,\n",
       " mesh_id                                                 D062026\n",
       " mesh_name                          Alice in Wonderland Syndrome\n",
       " in_hsdn                                                       0\n",
       " term_query       alice in wonderland syndrome[MeSH Terms:noexp]\n",
       " n_articles                                                   73\n",
       " pubmed_ids    22822901|22857942|23037657|23174459|23446681|2...\n",
       " Name: 495, dtype: object,\n",
       " mesh_id                                                 D062706\n",
       " mesh_name                                    Prodromal Symptoms\n",
       " in_hsdn                                                       0\n",
       " term_query                 prodromal symptoms[MeSH Terms:noexp]\n",
       " n_articles                                                 2446\n",
       " pubmed_ids    13037264|13065246|13132963|13162809|13192367|1...\n",
       " Name: 496, dtype: object,\n",
       " mesh_id                                                 D063766\n",
       " mesh_name                                     Pediatric Obesity\n",
       " in_hsdn                                                       0\n",
       " term_query                  pediatric obesity[MeSH Terms:noexp]\n",
       " n_articles                                                14631\n",
       " pubmed_ids    12865679|12985375|13012496|13026325|13068618|1...\n",
       " Name: 497, dtype: object,\n",
       " mesh_id                                                 D063806\n",
       " mesh_name                                               Myalgia\n",
       " in_hsdn                                                       0\n",
       " term_query                            myalgia[MeSH Terms:noexp]\n",
       " n_articles                                                 2859\n",
       " pubmed_ids    12978866|12982209|12986163|13017580|13021382|1...\n",
       " Name: 498, dtype: object,\n",
       " mesh_id                                                 D064250\n",
       " mesh_name                            Hypertriglyceridemic Waist\n",
       " in_hsdn                                                       0\n",
       " term_query         hypertriglyceridemic waist[MeSH Terms:noexp]\n",
       " n_articles                                                   94\n",
       " pubmed_ids    21924777|23336185|23703005|23736857|23758076|2...\n",
       " Name: 499, dtype: object,\n",
       " mesh_id                                                 D065634\n",
       " mesh_name                              Cerebrospinal Fluid Leak\n",
       " in_hsdn                                                       0\n",
       " term_query           cerebrospinal fluid leak[MeSH Terms:noexp]\n",
       " n_articles                                                 2092\n",
       " pubmed_ids    13010347|13997991|14205478|14254367|20443757|2...\n",
       " Name: 500, dtype: object,\n",
       " mesh_id                                                 D065635\n",
       " mesh_name                  Benign Paroxysmal Positional Vertigo\n",
       " in_hsdn                                                       0\n",
       " term_query    benign paroxysmal positional vertigo[MeSH Term...\n",
       " n_articles                                                 1335\n",
       " pubmed_ids    14152207|17702417|18300443|20015792|20053308|2...\n",
       " Name: 501, dtype: object,\n",
       " mesh_id                                                 D065906\n",
       " mesh_name                                       Hyperlactatemia\n",
       " in_hsdn                                                       0\n",
       " term_query                    hyperlactatemia[MeSH Terms:noexp]\n",
       " n_articles                                                  260\n",
       " pubmed_ids    13716482|22321745|23612027|23704758|23995586|2...\n",
       " Name: 502, dtype: object,\n",
       " mesh_id                                                 D066190\n",
       " mesh_name                                           Allesthesia\n",
       " in_hsdn                                                       0\n",
       " term_query                        allesthesia[MeSH Terms:noexp]\n",
       " n_articles                                                   10\n",
       " pubmed_ids    13049863|14257835|14264701|14770594|14959140|1...\n",
       " Name: 503, dtype: object,\n",
       " mesh_id                                                 D066229\n",
       " mesh_name                                 Speech Sound Disorder\n",
       " in_hsdn                                                       0\n",
       " term_query              speech sound disorder[MeSH Terms:noexp]\n",
       " n_articles                                                  371\n",
       " pubmed_ids    22517379|22794277|22815793|23184137|23275415|2...\n",
       " Name: 504, dtype: object]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rows_out"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "validate with the url (open with chrome) https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=adie%20syndrome[MeSH%20Terms%3Anoexp] "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dyspnea[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".......\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for dyspnea[MeSH Terms:noexp]. Results saved in dyspnea_MeSH_Terms_noexp_result.txt\n",
      "25667 articles for Dyspnea\n",
      "edema[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for edema[MeSH Terms:noexp]. Results saved in edema_MeSH_Terms_noexp_result.txt\n",
      "43912 articles for Edema\n",
      "fatigue[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for fatigue[MeSH Terms:noexp]. Results saved in fatigue_MeSH_Terms_noexp_result.txt\n",
      "36458 articles for Fatigue\n",
      "fetal distress[MeSH Terms:noexp]\n",
      "Completed fetching data for fetal distress[MeSH Terms:noexp]. Results saved in fetal_distress_MeSH_Terms_noexp_result.txt\n",
      "3541 articles for Fetal Distress\n"
     ]
    },
    {
     "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>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>in_hsdn</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>D004417</td>\n",
       "      <td>Dyspnea</td>\n",
       "      <td>1</td>\n",
       "      <td>dyspnea[MeSH Terms:noexp]</td>\n",
       "      <td>25667</td>\n",
       "      <td>4751|4753|8819|9881|10809|10813|10814|10820|24...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>136</th>\n",
       "      <td>D004487</td>\n",
       "      <td>Edema</td>\n",
       "      <td>1</td>\n",
       "      <td>edema[MeSH Terms:noexp]</td>\n",
       "      <td>43912</td>\n",
       "      <td>515|657|973|1042|1049|2693|4901|5887|7668|8042...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>152</th>\n",
       "      <td>D005221</td>\n",
       "      <td>Fatigue</td>\n",
       "      <td>1</td>\n",
       "      <td>fatigue[MeSH Terms:noexp]</td>\n",
       "      <td>36458</td>\n",
       "      <td>1333|3032|4054|5019|7710|7923|10321|10513|1714...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>156</th>\n",
       "      <td>D005316</td>\n",
       "      <td>Fetal Distress</td>\n",
       "      <td>1</td>\n",
       "      <td>fetal distress[MeSH Terms:noexp]</td>\n",
       "      <td>3541</td>\n",
       "      <td>480|2544|3546|3899|5585|5894|5895|6366|6505|86...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     mesh_id       mesh_name  in_hsdn                        term_query  \\\n",
       "130  D004417         Dyspnea        1         dyspnea[MeSH Terms:noexp]   \n",
       "136  D004487           Edema        1           edema[MeSH Terms:noexp]   \n",
       "152  D005221         Fatigue        1         fatigue[MeSH Terms:noexp]   \n",
       "156  D005316  Fetal Distress        1  fetal distress[MeSH Terms:noexp]   \n",
       "\n",
       "     n_articles                                         pubmed_ids  \n",
       "130       25667  4751|4753|8819|9881|10809|10813|10814|10820|24...  \n",
       "136       43912  515|657|973|1042|1049|2693|4901|5887|7668|8042...  \n",
       "152       36458  1333|3032|4054|5019|7710|7923|10321|10513|1714...  \n",
       "156        3541  480|2544|3546|3899|5585|5894|5895|6366|6505|86...  "
      ]
     },
     "execution_count": 72,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# rerun case with error\n",
    "error_terms = ['Dyspnea', 'Edema', 'Fatigue', 'Fetal Distress']\n",
    "\n",
    "error_out = list()\n",
    "for i in error_terms:\n",
    "    term_query = '{symptom}[MeSH Terms:noexp]'.format(symptom = i.lower())\n",
    "    print(term_query)\n",
    "    row = symptom_pmids_df.loc[symptom_pmids_df['mesh_name'] == i].squeeze()\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    error_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), i))\n",
    "\n",
    "symptom_error_df = pandas.DataFrame(error_out)\n",
    "symptom_error_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "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",
       "\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>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>in_hsdn</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>D004417</td>\n",
       "      <td>Dyspnea</td>\n",
       "      <td>1</td>\n",
       "      <td>dyspnea[MeSH Terms:noexp]</td>\n",
       "      <td>25604</td>\n",
       "      <td>4751|4753|8819|9881|10809|10813|10814|10820|24...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>136</th>\n",
       "      <td>D004487</td>\n",
       "      <td>Edema</td>\n",
       "      <td>1</td>\n",
       "      <td>edema[MeSH Terms:noexp]</td>\n",
       "      <td>43264</td>\n",
       "      <td>515|657|973|1042|1049|2693|4901|5887|7668|8042...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>152</th>\n",
       "      <td>D005221</td>\n",
       "      <td>Fatigue</td>\n",
       "      <td>1</td>\n",
       "      <td>fatigue[MeSH Terms:noexp]</td>\n",
       "      <td>35781</td>\n",
       "      <td>1333|3032|4054|5019|7710|7923|10321|10513|1714...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>156</th>\n",
       "      <td>D005316</td>\n",
       "      <td>Fetal Distress</td>\n",
       "      <td>1</td>\n",
       "      <td>fetal distress[MeSH Terms:noexp]</td>\n",
       "      <td>3421</td>\n",
       "      <td>480|2544|3546|3899|5585|5894|5895|6366|6505|86...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     mesh_id       mesh_name  in_hsdn                        term_query  \\\n",
       "130  D004417         Dyspnea        1         dyspnea[MeSH Terms:noexp]   \n",
       "136  D004487           Edema        1           edema[MeSH Terms:noexp]   \n",
       "152  D005221         Fatigue        1         fatigue[MeSH Terms:noexp]   \n",
       "156  D005316  Fetal Distress        1  fetal distress[MeSH Terms:noexp]   \n",
       "\n",
       "     n_articles                                         pubmed_ids  \n",
       "130       25604  4751|4753|8819|9881|10809|10813|10814|10820|24...  \n",
       "136       43264  515|657|973|1042|1049|2693|4901|5887|7668|8042...  \n",
       "152       35781  1333|3032|4054|5019|7710|7923|10321|10513|1714...  \n",
       "156        3421  480|2544|3546|3899|5585|5894|5895|6366|6505|86...  "
      ]
     },
     "execution_count": 73,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#validate with first run\n",
    "symptom_pmids_df.loc[symptom_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "\n",
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       "        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>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>in_hsdn</th>\n",
       "      <th>term_query</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>130</th>\n",
       "      <td>D004417</td>\n",
       "      <td>Dyspnea</td>\n",
       "      <td>1</td>\n",
       "      <td>dyspnea[MeSH Terms:noexp]</td>\n",
       "      <td>25667</td>\n",
       "      <td>4751|4753|8819|9881|10809|10813|10814|10820|24...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>136</th>\n",
       "      <td>D004487</td>\n",
       "      <td>Edema</td>\n",
       "      <td>1</td>\n",
       "      <td>edema[MeSH Terms:noexp]</td>\n",
       "      <td>43912</td>\n",
       "      <td>515|657|973|1042|1049|2693|4901|5887|7668|8042...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>152</th>\n",
       "      <td>D005221</td>\n",
       "      <td>Fatigue</td>\n",
       "      <td>1</td>\n",
       "      <td>fatigue[MeSH Terms:noexp]</td>\n",
       "      <td>36458</td>\n",
       "      <td>1333|3032|4054|5019|7710|7923|10321|10513|1714...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>156</th>\n",
       "      <td>D005316</td>\n",
       "      <td>Fetal Distress</td>\n",
       "      <td>1</td>\n",
       "      <td>fetal distress[MeSH Terms:noexp]</td>\n",
       "      <td>3541</td>\n",
       "      <td>480|2544|3546|3899|5585|5894|5895|6366|6505|86...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     mesh_id       mesh_name  in_hsdn                        term_query  \\\n",
       "130  D004417         Dyspnea        1         dyspnea[MeSH Terms:noexp]   \n",
       "136  D004487           Edema        1           edema[MeSH Terms:noexp]   \n",
       "152  D005221         Fatigue        1         fatigue[MeSH Terms:noexp]   \n",
       "156  D005316  Fetal Distress        1  fetal distress[MeSH Terms:noexp]   \n",
       "\n",
       "     n_articles                                         pubmed_ids  \n",
       "130       25667  4751|4753|8819|9881|10809|10813|10814|10820|24...  \n",
       "136       43912  515|657|973|1042|1049|2693|4901|5887|7668|8042...  \n",
       "152       36458  1333|3032|4054|5019|7710|7923|10321|10513|1714...  \n",
       "156        3541  480|2544|3546|3899|5585|5894|5895|6366|6505|86...  "
      ]
     },
     "execution_count": 74,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#update results and check values\n",
    "symptom_pmids_df.loc[symptom_pmids_df.mesh_name.isin(symptom_error_df.mesh_name), ['n_articles', 'pubmed_ids']] = symptom_error_df[['n_articles', 'pubmed_ids']]\n",
    "symptom_pmids_df.loc[symptom_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "with gzip.open(os.path.join(download_dir,'symptom-pmids.tsv.gz'), 'w') as write_file:\n",
    "    write_file = io.TextIOWrapper(write_file)\n",
    "    symptom_pmids_df.to_csv(write_file, sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(505, 6)"
      ]
     },
     "execution_count": 76,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "symptom_pmids_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "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>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>in_hsdn</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D000006</td>\n",
       "      <td>Abdomen, Acute</td>\n",
       "      <td>1</td>\n",
       "      <td>abdomen, acute[MeSH Terms:noexp]</td>\n",
       "      <td>9939</td>\n",
       "      <td>11344|28849|29373|38875|42826|45697|46444|4762...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D000067329</td>\n",
       "      <td>Obesity, Metabolically Benign</td>\n",
       "      <td>0</td>\n",
       "      <td>obesity, metabolically benign[MeSH Terms:noexp]</td>\n",
       "      <td>498</td>\n",
       "      <td>23928805|24670711|25443068|25449143|25515498|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D000067404</td>\n",
       "      <td>Social Communication Disorder</td>\n",
       "      <td>0</td>\n",
       "      <td>social communication disorder[MeSH Terms:noexp]</td>\n",
       "      <td>122</td>\n",
       "      <td>22928858|24659736|24756919|25039503|25240938|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D000067454</td>\n",
       "      <td>Childhood-Onset Fluency Disorder</td>\n",
       "      <td>0</td>\n",
       "      <td>childhood-onset fluency disorder[MeSH Terms:no...</td>\n",
       "      <td>4</td>\n",
       "      <td>26296615|30142643|32013722|32267336</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D000067559</td>\n",
       "      <td>Specific Learning Disorder</td>\n",
       "      <td>0</td>\n",
       "      <td>specific learning disorder[MeSH Terms:noexp]</td>\n",
       "      <td>88</td>\n",
       "      <td>25124507|25243500|25349093|25609675|25807176|2...</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>500</th>\n",
       "      <td>D065634</td>\n",
       "      <td>Cerebrospinal Fluid Leak</td>\n",
       "      <td>0</td>\n",
       "      <td>cerebrospinal fluid leak[MeSH Terms:noexp]</td>\n",
       "      <td>2092</td>\n",
       "      <td>13010347|13997991|14205478|14254367|20443757|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>501</th>\n",
       "      <td>D065635</td>\n",
       "      <td>Benign Paroxysmal Positional Vertigo</td>\n",
       "      <td>0</td>\n",
       "      <td>benign paroxysmal positional vertigo[MeSH Term...</td>\n",
       "      <td>1335</td>\n",
       "      <td>14152207|17702417|18300443|20015792|20053308|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>502</th>\n",
       "      <td>D065906</td>\n",
       "      <td>Hyperlactatemia</td>\n",
       "      <td>0</td>\n",
       "      <td>hyperlactatemia[MeSH Terms:noexp]</td>\n",
       "      <td>260</td>\n",
       "      <td>13716482|22321745|23612027|23704758|23995586|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>503</th>\n",
       "      <td>D066190</td>\n",
       "      <td>Allesthesia</td>\n",
       "      <td>0</td>\n",
       "      <td>allesthesia[MeSH Terms:noexp]</td>\n",
       "      <td>10</td>\n",
       "      <td>13049863|14257835|14264701|14770594|14959140|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>504</th>\n",
       "      <td>D066229</td>\n",
       "      <td>Speech Sound Disorder</td>\n",
       "      <td>0</td>\n",
       "      <td>speech sound disorder[MeSH Terms:noexp]</td>\n",
       "      <td>371</td>\n",
       "      <td>22517379|22794277|22815793|23184137|23275415|2...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>501 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        mesh_id                             mesh_name  in_hsdn  \\\n",
       "0       D000006                        Abdomen, Acute        1   \n",
       "1    D000067329         Obesity, Metabolically Benign        0   \n",
       "2    D000067404         Social Communication Disorder        0   \n",
       "3    D000067454      Childhood-Onset Fluency Disorder        0   \n",
       "4    D000067559            Specific Learning Disorder        0   \n",
       "..          ...                                   ...      ...   \n",
       "500     D065634              Cerebrospinal Fluid Leak        0   \n",
       "501     D065635  Benign Paroxysmal Positional Vertigo        0   \n",
       "502     D065906                       Hyperlactatemia        0   \n",
       "503     D066190                           Allesthesia        0   \n",
       "504     D066229                 Speech Sound Disorder        0   \n",
       "\n",
       "                                            term_query  n_articles  \\\n",
       "0                     abdomen, acute[MeSH Terms:noexp]        9939   \n",
       "1      obesity, metabolically benign[MeSH Terms:noexp]         498   \n",
       "2      social communication disorder[MeSH Terms:noexp]         122   \n",
       "3    childhood-onset fluency disorder[MeSH Terms:no...           4   \n",
       "4         specific learning disorder[MeSH Terms:noexp]          88   \n",
       "..                                                 ...         ...   \n",
       "500         cerebrospinal fluid leak[MeSH Terms:noexp]        2092   \n",
       "501  benign paroxysmal positional vertigo[MeSH Term...        1335   \n",
       "502                  hyperlactatemia[MeSH Terms:noexp]         260   \n",
       "503                      allesthesia[MeSH Terms:noexp]          10   \n",
       "504            speech sound disorder[MeSH Terms:noexp]         371   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "0    11344|28849|29373|38875|42826|45697|46444|4762...  \n",
       "1    23928805|24670711|25443068|25449143|25515498|2...  \n",
       "2    22928858|24659736|24756919|25039503|25240938|2...  \n",
       "3                  26296615|30142643|32013722|32267336  \n",
       "4    25124507|25243500|25349093|25609675|25807176|2...  \n",
       "..                                                 ...  \n",
       "500  13010347|13997991|14205478|14254367|20443757|2...  \n",
       "501  14152207|17702417|18300443|20015792|20053308|2...  \n",
       "502  13716482|22321745|23612027|23704758|23995586|2...  \n",
       "503  13049863|14257835|14264701|14770594|14959140|1...  \n",
       "504  22517379|22794277|22815793|23184137|23275415|2...  \n",
       "\n",
       "[501 rows x 6 columns]"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "symptom_pmids_df[symptom_pmids_df['n_articles']>=1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "#url = 'https://raw.githubusercontent.com/dhimmel/mesh/e561301360e6de2140dedeaa7c7e17ce4714eb7f/data/symptoms.tsv'\n",
    "#check2 = pandas.read_table(url)\n",
    "#check2.shape\n",
    "#check = check2.merge(symptom_pmids_df, on=['mesh_id','mesh_name','in_hsdn'], how='outer', indicator=True)\n",
    "#check['_merge'].unique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cooccurrence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "symptom_df, symptom_to_pmids = read_pmids_tsv(os.path.join(download_dir,'symptom-pmids.tsv.gz'), key='mesh_id')\n",
    "disease_df, disease_to_pmids = read_pmids_tsv(os.path.join(download_dir,'disease-pmids.tsv.gz'), key='doid_code')\n",
    "#disease_df, disease_to_pmids = read_pmids_tsv('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/disease-pmids.tsv.gz', key='doid_code')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2590578"
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "symptom_pmids = set.union(*symptom_to_pmids.values())\n",
    "len(symptom_pmids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4906736"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_pmids = set.union(*disease_to_pmids.values())\n",
    "len(disease_pmids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total articles containing a doid_code: 4906736\n",
      "Total articles containing a mesh_id: 2590578\n",
      "Total articles containing both a doid_code and mesh_id: 541067\n",
      "\n",
      "After removing terms without any cooccurences:\n",
      "+ 121 doid_codes remain\n",
      "+ 488 mesh_ids remain\n",
      "\n",
      "Cooccurrence scores calculated for 59048 doid_code -- mesh_id pairs\n"
     ]
    }
   ],
   "source": [
    "cooc_df = score_pmid_cooccurrence(disease_to_pmids, symptom_to_pmids, 'doid_code', 'mesh_id')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(59048, 11)"
      ]
     },
     "execution_count": 83,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>31772</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D000647</td>\n",
       "      <td>Amnesia</td>\n",
       "      <td>489</td>\n",
       "      <td>19.641482</td>\n",
       "      <td>24.896288</td>\n",
       "      <td>48.294582</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10199</td>\n",
       "      <td>1042</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31834</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D004314</td>\n",
       "      <td>Down Syndrome</td>\n",
       "      <td>1102</td>\n",
       "      <td>56.021580</td>\n",
       "      <td>19.670991</td>\n",
       "      <td>34.268557</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10199</td>\n",
       "      <td>2972</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31902</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D006816</td>\n",
       "      <td>Huntington Disease</td>\n",
       "      <td>397</td>\n",
       "      <td>20.075028</td>\n",
       "      <td>19.775813</td>\n",
       "      <td>32.146898</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10199</td>\n",
       "      <td>1065</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31930</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D008569</td>\n",
       "      <td>Memory Disorders</td>\n",
       "      <td>2856</td>\n",
       "      <td>132.966427</td>\n",
       "      <td>21.479106</td>\n",
       "      <td>48.795618</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10199</td>\n",
       "      <td>7054</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31975</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D011595</td>\n",
       "      <td>Psychomotor Agitation</td>\n",
       "      <td>453</td>\n",
       "      <td>24.994823</td>\n",
       "      <td>18.123753</td>\n",
       "      <td>28.218201</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10199</td>\n",
       "      <td>1326</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code            doid_name  mesh_id              mesh_name  \\\n",
       "31772  DOID:10652  Alzheimer's disease  D000647                Amnesia   \n",
       "31834  DOID:10652  Alzheimer's disease  D004314          Down Syndrome   \n",
       "31902  DOID:10652  Alzheimer's disease  D006816     Huntington Disease   \n",
       "31930  DOID:10652  Alzheimer's disease  D008569       Memory Disorders   \n",
       "31975  DOID:10652  Alzheimer's disease  D011595  Psychomotor Agitation   \n",
       "\n",
       "       cooccurrence    expected  enrichment  odds_ratio  p_fisher  n_source  \\\n",
       "31772           489   19.641482   24.896288   48.294582       0.0     10199   \n",
       "31834          1102   56.021580   19.670991   34.268557       0.0     10199   \n",
       "31902           397   20.075028   19.775813   32.146898       0.0     10199   \n",
       "31930          2856  132.966427   21.479106   48.795618       0.0     10199   \n",
       "31975           453   24.994823   18.123753   28.218201       0.0     10199   \n",
       "\n",
       "       n_target  \n",
       "31772      1042  \n",
       "31834      2972  \n",
       "31902      1065  \n",
       "31930      7054  \n",
       "31975      1326  "
      ]
     },
     "execution_count": 83,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cooc_df = symptom_df[['mesh_id', 'mesh_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = disease_df[['doid_code', 'doid_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = cooc_df.sort_values(by=['doid_name', 'p_fisher'])\n",
    "cooc_df.to_csv(os.path.join(download_dir,'disease-symptom-cooccurrence.tsv'), index=False, sep='\\t')\n",
    "cooc_df.shape\n",
    "cooc_df.head() #59048"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(91, 11)"
      ]
     },
     "execution_count": 84,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "disease_symptom_df = cooc_df\n",
    "disease_symptom_df = disease_symptom_df[disease_symptom_df.p_fisher < 0.005]\n",
    "disease_symptom_df = disease_symptom_df[disease_symptom_df['doid_code'].isin(['DOID:10652','DOID:11949'])]\n",
    "disease_symptom_df.to_csv(os.path.join(download_dir,'symptomManifestationOfDisease.tsv'), index=False, sep='\\t')\n",
    "disease_symptom_df.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Compare with Hetionet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(79, 9)"
      ]
     },
     "execution_count": 85,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#compare with hetionet version  79 rels\n",
    "Dps_hetionet = pandas.read_table('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/disease-symptom-cooccurrence.tsv') \n",
    "Dps_hetionet = Dps_hetionet[Dps_hetionet['doid_code'].isin(['DOID:10652','DOID:11949'])]\n",
    "Dps_hetionet = Dps_hetionet[Dps_hetionet.p_fisher < 0.005]\n",
    "Dps_hetionet.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['both', 'left_only', 'right_only']\n",
       "Categories (3, object): ['left_only', 'right_only', 'both']"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "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>doid_code</th>\n",
       "      <th>doid_name_x</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name_x</th>\n",
       "      <th>cooccurrence_x</th>\n",
       "      <th>expected_x</th>\n",
       "      <th>enrichment_x</th>\n",
       "      <th>odds_ratio_x</th>\n",
       "      <th>p_fisher_x</th>\n",
       "      <th>doid_name_y</th>\n",
       "      <th>mesh_name_y</th>\n",
       "      <th>cooccurrence_y</th>\n",
       "      <th>expected_y</th>\n",
       "      <th>enrichment_y</th>\n",
       "      <th>odds_ratio_y</th>\n",
       "      <th>p_fisher_y</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "      <th>_merge</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D000425</td>\n",
       "      <td>Alcohol Amnestic Disorder</td>\n",
       "      <td>51.0</td>\n",
       "      <td>5.711363</td>\n",
       "      <td>8.929567</td>\n",
       "      <td>10.341223</td>\n",
       "      <td>3.887655e-32</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D020233</td>\n",
       "      <td>Gait Disorders, Neurologic</td>\n",
       "      <td>36.0</td>\n",
       "      <td>17.118001</td>\n",
       "      <td>2.103049</td>\n",
       "      <td>2.148741</td>\n",
       "      <td>3.758550e-05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D009127</td>\n",
       "      <td>Muscle Rigidity</td>\n",
       "      <td>17.0</td>\n",
       "      <td>8.188969</td>\n",
       "      <td>2.075963</td>\n",
       "      <td>2.116383</td>\n",
       "      <td>4.291833e-03</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>D018888</td>\n",
       "      <td>Aphasia, Primary Progressive</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.053046</td>\n",
       "      <td>37.702979</td>\n",
       "      <td>39.306266</td>\n",
       "      <td>1.331623e-03</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>D019569</td>\n",
       "      <td>Hemifacial Spasm</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.100306</td>\n",
       "      <td>19.939075</td>\n",
       "      <td>20.421091</td>\n",
       "      <td>4.655519e-03</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code                doid_name_x  mesh_id  \\\n",
       "19  DOID:10652        Alzheimer's disease  D000425   \n",
       "38  DOID:10652        Alzheimer's disease  D020233   \n",
       "42  DOID:10652        Alzheimer's disease  D009127   \n",
       "70  DOID:11949  Creutzfeldt-Jakob disease  D018888   \n",
       "77  DOID:11949  Creutzfeldt-Jakob disease  D019569   \n",
       "\n",
       "                     mesh_name_x  cooccurrence_x  expected_x  enrichment_x  \\\n",
       "19     Alcohol Amnestic Disorder            51.0    5.711363      8.929567   \n",
       "38    Gait Disorders, Neurologic            36.0   17.118001      2.103049   \n",
       "42               Muscle Rigidity            17.0    8.188969      2.075963   \n",
       "70  Aphasia, Primary Progressive             2.0    0.053046     37.702979   \n",
       "77              Hemifacial Spasm             2.0    0.100306     19.939075   \n",
       "\n",
       "    odds_ratio_x    p_fisher_x doid_name_y mesh_name_y  cooccurrence_y  \\\n",
       "19     10.341223  3.887655e-32         NaN         NaN             NaN   \n",
       "38      2.148741  3.758550e-05         NaN         NaN             NaN   \n",
       "42      2.116383  4.291833e-03         NaN         NaN             NaN   \n",
       "70     39.306266  1.331623e-03         NaN         NaN             NaN   \n",
       "77     20.421091  4.655519e-03         NaN         NaN             NaN   \n",
       "\n",
       "    expected_y  enrichment_y  odds_ratio_y  p_fisher_y  n_source  n_target  \\\n",
       "19         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "38         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "42         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "70         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "77         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "\n",
       "       _merge  \n",
       "19  left_only  \n",
       "38  left_only  \n",
       "42  left_only  \n",
       "70  left_only  \n",
       "77  left_only  "
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "check3 = Dps_hetionet.merge(disease_symptom_df, on=['doid_code','mesh_id'], how='outer', indicator=True)\n",
    "check3['_merge'].unique()\n",
    "check3[(check3['_merge']=='left_only')]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "validate with the url (open with chrome) https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=alzheimer%20disease[MeSH%20Major%20Topic]%26Muscle%20Rigidity[MeSH%20Terms%3Anoexp]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>31939</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D009127</td>\n",
       "      <td>Muscle Rigidity</td>\n",
       "      <td>20</td>\n",
       "      <td>11.856519</td>\n",
       "      <td>1.686836</td>\n",
       "      <td>1.710786</td>\n",
       "      <td>0.018007</td>\n",
       "      <td>10199</td>\n",
       "      <td>629</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32097</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>D020233</td>\n",
       "      <td>Gait Disorders, Neurologic</td>\n",
       "      <td>60</td>\n",
       "      <td>46.860581</td>\n",
       "      <td>1.280394</td>\n",
       "      <td>1.289029</td>\n",
       "      <td>0.034611</td>\n",
       "      <td>10199</td>\n",
       "      <td>2486</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code            doid_name  mesh_id                   mesh_name  \\\n",
       "31939  DOID:10652  Alzheimer's disease  D009127             Muscle Rigidity   \n",
       "32097  DOID:10652  Alzheimer's disease  D020233  Gait Disorders, Neurologic   \n",
       "\n",
       "       cooccurrence   expected  enrichment  odds_ratio  p_fisher  n_source  \\\n",
       "31939            20  11.856519    1.686836    1.710786  0.018007     10199   \n",
       "32097            60  46.860581    1.280394    1.289029  0.034611     10199   \n",
       "\n",
       "       n_target  \n",
       "31939       629  \n",
       "32097      2486  "
      ]
     },
     "execution_count": 92,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#p value larger than 0.005\n",
    "cooc_df[(cooc_df['mesh_id'].isin(['D000425','D020233','D009127']))&(cooc_df['doid_code']=='DOID:10652')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "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>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>in_hsdn</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [mesh_id, mesh_name, in_hsdn, term_query, n_articles]\n",
       "Index: []"
      ]
     },
     "execution_count": 95,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# mesh id does not exists in new version\n",
    "symptom_df[symptom_df['mesh_id']=='D000425'] "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"\\nsymptom_df_hetionet, symptom_to_pmids_hetionet = read_pmids_tsv('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/symptom-pmids.tsv.gz', key='mesh_id')\\ndisease_df_hetionet, disease_to_pmids_hetionet = read_pmids_tsv('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/disease-pmids.tsv.gz', key='doid_code')\\ncooc_df_hetionet =score_pmid_cooccurrence(disease_to_pmids_hetionet, symptom_to_pmids_hetionet, 'doid_code', 'mesh_id')\\ncooc_df_hetionet = symptom_df[['mesh_id', 'mesh_name']].drop_duplicates().merge(cooc_df_hetionet)\\ncooc_df_hetionet = disease_df[['doid_code', 'doid_name']].drop_duplicates().merge(cooc_df_hetionet)\\ncooc_df_hetionet = cooc_df_hetionet.sort_values(by=['doid_name', 'p_fisher'])\\ncooc_df_hetionet['mesh_id'].nunique()\\n\\nchecklist = cooc_df['mesh_id'].tolist()\\ncooc_df_hetionet[~cooc_df_hetionet['mesh_id'].isin(checklist)]['cooccurrence'].unique() #0\\n\""
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\"\"\"\n",
    "symptom_df_hetionet, symptom_to_pmids_hetionet = read_pmids_tsv('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/symptom-pmids.tsv.gz', key='mesh_id')\n",
    "disease_df_hetionet, disease_to_pmids_hetionet = read_pmids_tsv('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/disease-pmids.tsv.gz', key='doid_code')\n",
    "cooc_df_hetionet =score_pmid_cooccurrence(disease_to_pmids_hetionet, symptom_to_pmids_hetionet, 'doid_code', 'mesh_id')\n",
    "cooc_df_hetionet = symptom_df[['mesh_id', 'mesh_name']].drop_duplicates().merge(cooc_df_hetionet)\n",
    "cooc_df_hetionet = disease_df[['doid_code', 'doid_name']].drop_duplicates().merge(cooc_df_hetionet)\n",
    "cooc_df_hetionet = cooc_df_hetionet.sort_values(by=['doid_name', 'p_fisher'])\n",
    "cooc_df_hetionet['mesh_id'].nunique()\n",
    "\n",
    "checklist = cooc_df['mesh_id'].tolist()\n",
    "cooc_df_hetionet[~cooc_df_hetionet['mesh_id'].isin(checklist)]['cooccurrence'].unique() #0\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "import numpy\n",
    "import scipy\n",
    "import seaborn\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sig_df = cooc_df[cooc_df.p_fisher < 0.05]\n",
    "plt.hist(list(numpy.log(sig_df.enrichment)), bins = 50);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tissues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UBERON:0000002</td>\n",
       "      <td>uterine cervix</td>\n",
       "      <td>D002584</td>\n",
       "      <td>Cervix Uteri</td>\n",
       "      <td>BTO:0001421</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UBERON:0000004</td>\n",
       "      <td>nose</td>\n",
       "      <td>D009666</td>\n",
       "      <td>Nose</td>\n",
       "      <td>BTO:0000840</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UBERON:0000006</td>\n",
       "      <td>islet of Langerhans</td>\n",
       "      <td>D007515</td>\n",
       "      <td>Islets of Langerhans</td>\n",
       "      <td>BTO:0000991</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UBERON:0000016</td>\n",
       "      <td>endocrine pancreas</td>\n",
       "      <td>D007515</td>\n",
       "      <td>Islets of Langerhans</td>\n",
       "      <td>BTO:0000650</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBERON:0000007</td>\n",
       "      <td>pituitary gland</td>\n",
       "      <td>D010902</td>\n",
       "      <td>Pituitary Gland</td>\n",
       "      <td>BTO:0001073</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        uberon_id          uberon_name  mesh_id             mesh_name  \\\n",
       "0  UBERON:0000002       uterine cervix  D002584          Cervix Uteri   \n",
       "1  UBERON:0000004                 nose  D009666                  Nose   \n",
       "2  UBERON:0000006  islet of Langerhans  D007515  Islets of Langerhans   \n",
       "3  UBERON:0000016   endocrine pancreas  D007515  Islets of Langerhans   \n",
       "4  UBERON:0000007      pituitary gland  D010902       Pituitary Gland   \n",
       "\n",
       "        bto_id  \n",
       "0  BTO:0001421  \n",
       "1  BTO:0000840  \n",
       "2  BTO:0000991  \n",
       "3  BTO:0000650  \n",
       "4  BTO:0001073  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read MeSH UBERON Anatomical structures\n",
    "url = '../data/Uberon/hetio-slim.tsv'\n",
    "uberon_df = pandas.read_table(url)\n",
    "uberon_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(652, 5)"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uberon_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#validate with the url (open with chrome) \n",
    "#https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=Cervix%20Uteri[MeSH%20Terms%3Anoexp]\n",
    "rows_out = list()\n",
    "\n",
    "for i, row in uberon_df.iterrows():\n",
    "    term_query = '{tissue}[MeSH Terms:noexp]'.format(tissue = row.mesh_name.lower())\n",
    "    print(row.mesh_name)\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    #payload = {'db': 'pubmed', 'term': term_query}\n",
    "    #pmids = eutility.esearch_query(payload, retmax = 5000, sleep=2)\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "\n",
    "uberon_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#run following terms after being interupted\n",
    "#tissues_ls = uberon_df['mesh_name'][548:].tolist()\n",
    "#len(tissues_ls)\n",
    "\n",
    "for i, row in uberon_df[548:].iterrows(): #11:57\n",
    "    term_query = '{tissue}[MeSH Terms:noexp]'.format(tissue = row.mesh_name.lower())\n",
    "    print(row.mesh_name)\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    #payload = {'db': 'pubmed', 'term': term_query}\n",
    "    #pmids = eutility.esearch_query(payload, retmax = 5000, sleep=2)\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "\n",
    "uberon_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Cerebral Crus\n",
      "Completed fetching data for cerebral crus[MeSH Terms:noexp]. Results saved in cerebral_crus_MeSH_Terms_noexp_result.txt\n",
      "9 articles for Cerebral Crus\n",
      "Anterior Hypothalamic Nucleus\n",
      "Completed fetching data for anterior hypothalamic nucleus[MeSH Terms:noexp]. Results saved in anterior_hypothalamic_nucleus_MeSH_Terms_noexp_result.txt\n",
      "260 articles for Anterior Hypothalamic Nucleus\n",
      "Septal Nuclei\n",
      "Completed fetching data for septal nuclei[MeSH Terms:noexp]. Results saved in septal_nuclei_MeSH_Terms_noexp_result.txt\n",
      "3672 articles for Septal Nuclei\n",
      "Vestibular Nuclei\n",
      "Completed fetching data for vestibular nuclei[MeSH Terms:noexp]. Results saved in vestibular_nuclei_MeSH_Terms_noexp_result.txt\n",
      "3458 articles for Vestibular Nuclei\n",
      "Abducens Nucleus\n",
      "Completed fetching data for abducens nucleus[MeSH Terms:noexp]. Results saved in abducens_nucleus_MeSH_Terms_noexp_result.txt\n",
      "12 articles for Abducens Nucleus\n",
      "Nucleus Raphe Obscurus\n",
      "Completed fetching data for nucleus raphe obscurus[MeSH Terms:noexp]. Results saved in nucleus_raphe_obscurus_MeSH_Terms_noexp_result.txt\n",
      "2 articles for Nucleus Raphe Obscurus\n",
      "Ventral Tegmental Area\n",
      "Completed fetching data for ventral tegmental area[MeSH Terms:noexp]. Results saved in ventral_tegmental_area_MeSH_Terms_noexp_result.txt\n",
      "4581 articles for Ventral Tegmental Area\n",
      "Geniculate Bodies\n",
      "Completed fetching data for geniculate bodies[MeSH Terms:noexp]. Results saved in geniculate_bodies_MeSH_Terms_noexp_result.txt\n",
      "8332 articles for Geniculate Bodies\n",
      "Midline Thalamic Nuclei\n",
      "Completed fetching data for midline thalamic nuclei[MeSH Terms:noexp]. Results saved in midline_thalamic_nuclei_MeSH_Terms_noexp_result.txt\n",
      "456 articles for Midline Thalamic Nuclei\n",
      "Pyramidal Tracts\n",
      "Completed fetching data for pyramidal tracts[MeSH Terms:noexp]. Results saved in pyramidal_tracts_MeSH_Terms_noexp_result.txt\n",
      "8499 articles for Pyramidal Tracts\n",
      "Entorhinal Cortex\n",
      "Completed fetching data for entorhinal cortex[MeSH Terms:noexp]. Results saved in entorhinal_cortex_MeSH_Terms_noexp_result.txt\n",
      "3647 articles for Entorhinal Cortex\n",
      "Entorhinal Cortex\n",
      "Completed fetching data for entorhinal cortex[MeSH Terms:noexp]. Results saved in entorhinal_cortex_MeSH_Terms_noexp_result.txt\n",
      "3647 articles for Entorhinal Cortex\n",
      "Intralaminar Thalamic Nuclei\n",
      "Completed fetching data for intralaminar thalamic nuclei[MeSH Terms:noexp]. Results saved in intralaminar_thalamic_nuclei_MeSH_Terms_noexp_result.txt\n",
      "498 articles for Intralaminar Thalamic Nuclei\n",
      "Lateral Thalamic Nuclei\n",
      "Completed fetching data for lateral thalamic nuclei[MeSH Terms:noexp]. Results saved in lateral_thalamic_nuclei_MeSH_Terms_noexp_result.txt\n",
      "128 articles for Lateral Thalamic Nuclei\n",
      "Mediodorsal Thalamic Nucleus\n",
      "Completed fetching data for mediodorsal thalamic nucleus[MeSH Terms:noexp]. Results saved in mediodorsal_thalamic_nucleus_MeSH_Terms_noexp_result.txt\n",
      "370 articles for Mediodorsal Thalamic Nucleus\n",
      "Diagonal Band of Broca\n",
      "Completed fetching data for diagonal band of broca[MeSH Terms:noexp]. Results saved in diagonal_band_of_broca_MeSH_Terms_noexp_result.txt\n",
      "143 articles for Diagonal Band of Broca\n",
      "Basal Forebrain\n",
      "Completed fetching data for basal forebrain[MeSH Terms:noexp]. Results saved in basal_forebrain_MeSH_Terms_noexp_result.txt\n",
      "565 articles for Basal Forebrain\n",
      "Ventral Thalamic Nuclei\n",
      "Completed fetching data for ventral thalamic nuclei[MeSH Terms:noexp]. Results saved in ventral_thalamic_nuclei_MeSH_Terms_noexp_result.txt\n",
      "955 articles for Ventral Thalamic Nuclei\n",
      "Anterior Thalamic Nuclei\n",
      "Completed fetching data for anterior thalamic nuclei[MeSH Terms:noexp]. Results saved in anterior_thalamic_nuclei_MeSH_Terms_noexp_result.txt\n",
      "504 articles for Anterior Thalamic Nuclei\n",
      "Olfactory Cortex\n",
      "Completed fetching data for olfactory cortex[MeSH Terms:noexp]. Results saved in olfactory_cortex_MeSH_Terms_noexp_result.txt\n",
      "328 articles for Olfactory Cortex\n",
      "Trigeminal Nuclei\n",
      "Completed fetching data for trigeminal nuclei[MeSH Terms:noexp]. Results saved in trigeminal_nuclei_MeSH_Terms_noexp_result.txt\n",
      "1765 articles for Trigeminal Nuclei\n",
      "Trapezoid Body\n",
      "Completed fetching data for trapezoid body[MeSH Terms:noexp]. Results saved in trapezoid_body_MeSH_Terms_noexp_result.txt\n",
      "74 articles for Trapezoid Body\n",
      "Spinothalamic Tracts\n",
      "Completed fetching data for spinothalamic tracts[MeSH Terms:noexp]. Results saved in spinothalamic_tracts_MeSH_Terms_noexp_result.txt\n",
      "781 articles for Spinothalamic Tracts\n",
      "Gyrus Cinguli\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for gyrus cinguli[MeSH Terms:noexp]. Results saved in gyrus_cinguli_MeSH_Terms_noexp_result.txt\n",
      "10620 articles for Gyrus Cinguli\n",
      "Parahippocampal Gyrus\n",
      "Completed fetching data for parahippocampal gyrus[MeSH Terms:noexp]. Results saved in parahippocampal_gyrus_MeSH_Terms_noexp_result.txt\n",
      "1190 articles for Parahippocampal Gyrus\n",
      "Pulvinar\n",
      "Completed fetching data for pulvinar[MeSH Terms:noexp]. Results saved in pulvinar_MeSH_Terms_noexp_result.txt\n",
      "406 articles for Pulvinar\n",
      "Substantia Innominata\n",
      "Completed fetching data for substantia innominata[MeSH Terms:noexp]. Results saved in substantia_innominata_MeSH_Terms_noexp_result.txt\n",
      "838 articles for Substantia Innominata\n",
      "Pontine Tegmentum\n",
      "Completed fetching data for pontine tegmentum[MeSH Terms:noexp]. Results saved in pontine_tegmentum_MeSH_Terms_noexp_result.txt\n",
      "131 articles for Pontine Tegmentum\n",
      "Periaqueductal Gray\n",
      "Completed fetching data for periaqueductal gray[MeSH Terms:noexp]. Results saved in periaqueductal_gray_MeSH_Terms_noexp_result.txt\n",
      "3433 articles for Periaqueductal Gray\n",
      "Uncinate Fasciculus\n",
      "Completed fetching data for uncinate fasciculus[MeSH Terms:noexp]. Results saved in uncinate_fasciculus_MeSH_Terms_noexp_result.txt\n",
      "31 articles for Uncinate Fasciculus\n",
      "Organizers, Embryonic\n",
      "Completed fetching data for organizers, embryonic[MeSH Terms:noexp]. Results saved in organizers_embryonic_MeSH_Terms_noexp_result.txt\n",
      "424 articles for Organizers, Embryonic\n",
      "Wolffian Ducts\n",
      "Completed fetching data for wolffian ducts[MeSH Terms:noexp]. Results saved in wolffian_ducts_MeSH_Terms_noexp_result.txt\n",
      "756 articles for Wolffian Ducts\n",
      "Neural Plate\n",
      "Completed fetching data for neural plate[MeSH Terms:noexp]. Results saved in neural_plate_MeSH_Terms_noexp_result.txt\n",
      "577 articles for Neural Plate\n",
      "Ultimobranchial Body\n",
      "Completed fetching data for ultimobranchial body[MeSH Terms:noexp]. Results saved in ultimobranchial_body_MeSH_Terms_noexp_result.txt\n",
      "277 articles for Ultimobranchial Body\n",
      "Chorion\n",
      "Completed fetching data for chorion[MeSH Terms:noexp]. Results saved in chorion_MeSH_Terms_noexp_result.txt\n",
      "4690 articles for Chorion\n",
      "Trachea\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for trachea[MeSH Terms:noexp]. Results saved in trachea_MeSH_Terms_noexp_result.txt\n",
      "38969 articles for Trachea\n",
      "Skull\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for skull[MeSH Terms:noexp]. Results saved in skull_MeSH_Terms_noexp_result.txt\n",
      "38978 articles for Skull\n",
      "Skull\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for skull[MeSH Terms:noexp]. Results saved in skull_MeSH_Terms_noexp_result.txt\n",
      "38978 articles for Skull\n",
      "Palate, Hard\n",
      "Completed fetching data for palate, hard[MeSH Terms:noexp]. Results saved in palate_hard_MeSH_Terms_noexp_result.txt\n",
      "2338 articles for Palate, Hard\n",
      "Cranial Sutures\n",
      "Completed fetching data for cranial sutures[MeSH Terms:noexp]. Results saved in cranial_sutures_MeSH_Terms_noexp_result.txt\n",
      "2458 articles for Cranial Sutures\n",
      "Fallopian Tubes\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".....\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for fallopian tubes[MeSH Terms:noexp]. Results saved in fallopian_tubes_MeSH_Terms_noexp_result.txt\n",
      "12905 articles for Fallopian Tubes\n",
      "Skeleton\n",
      "Completed fetching data for skeleton[MeSH Terms:noexp]. Results saved in skeleton_MeSH_Terms_noexp_result.txt\n",
      "2353 articles for Skeleton\n",
      "Wrist\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".....\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for wrist[MeSH Terms:noexp]. Results saved in wrist_MeSH_Terms_noexp_result.txt\n",
      "20957 articles for Wrist\n",
      "Ankle\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".......\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for ankle[MeSH Terms:noexp]. Results saved in ankle_MeSH_Terms_noexp_result.txt\n",
      "29762 articles for Ankle\n",
      "Cochlear Nerve\n",
      "Completed fetching data for cochlear nerve[MeSH Terms:noexp]. Results saved in cochlear_nerve_MeSH_Terms_noexp_result.txt\n",
      "5522 articles for Cochlear Nerve\n",
      "Diaphyses\n",
      "Completed fetching data for diaphyses[MeSH Terms:noexp]. Results saved in diaphyses_MeSH_Terms_noexp_result.txt\n",
      "2160 articles for Diaphyses\n",
      "Myelencephalon\n",
      "Completed fetching data for myelencephalon[MeSH Terms:noexp]. Results saved in myelencephalon_MeSH_Terms_noexp_result.txt\n",
      "6 articles for Myelencephalon\n",
      "Scapula\n",
      "Completed fetching data for scapula[MeSH Terms:noexp]. Results saved in scapula_MeSH_Terms_noexp_result.txt\n",
      "7589 articles for Scapula\n",
      "Cartilage, Articular\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".........\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for cartilage, articular[MeSH Terms:noexp]. Results saved in cartilage_articular_MeSH_Terms_noexp_result.txt\n",
      "34056 articles for Cartilage, Articular\n"
     ]
    }
   ],
   "source": [
    "#run following terms after being interupted\n",
    "#tissues_ls = uberon_df['mesh_name'][548:].tolist()\n",
    "#len(tissues_ls)\n",
    "\n",
    "for i, row in uberon_df[603:].iterrows(): #internet down at 11:57\n",
    "    term_query = '{tissue}[MeSH Terms:noexp]'.format(tissue = row.mesh_name.lower())\n",
    "    print(row.mesh_name)\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    #payload = {'db': 'pubmed', 'term': term_query}\n",
    "    #pmids = eutility.esearch_query(payload, retmax = 5000, sleep=2)\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "\n",
    "uberon_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(682, 8)"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uberon_pmids_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "renal artery[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".......\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for renal artery[MeSH Terms:noexp]. Results saved in renal_artery_MeSH_Terms_noexp_result.txt\n",
      "18741 articles for Renal Artery\n",
      "gastric mucosa[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "...............\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for gastric mucosa[MeSH Terms:noexp]. Results saved in gastric_mucosa_MeSH_Terms_noexp_result.txt\n",
      "53999 articles for Gastric Mucosa\n",
      "kidney tubules[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".......\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for kidney tubules[MeSH Terms:noexp]. Results saved in kidney_tubules_MeSH_Terms_noexp_result.txt\n",
      "24031 articles for Kidney Tubules\n",
      "intestinal mucosa[MeSH Terms:noexp]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      ".............................\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Completed fetching data for intestinal mucosa[MeSH Terms:noexp]. Results saved in intestinal_mucosa_MeSH_Terms_noexp_result.txt\n",
      "95206 articles for Intestinal Mucosa\n"
     ]
    },
    {
     "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>137</th>\n",
       "      <td>UBERON:0001184</td>\n",
       "      <td>renal artery</td>\n",
       "      <td>D012077</td>\n",
       "      <td>Renal Artery</td>\n",
       "      <td>BTO:0001165</td>\n",
       "      <td>renal artery[MeSH Terms:noexp]</td>\n",
       "      <td>18741</td>\n",
       "      <td>1639|2546|2965|3150|5616|5843|5883|7844|8611|8...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>140</th>\n",
       "      <td>UBERON:0001199</td>\n",
       "      <td>mucosa of stomach</td>\n",
       "      <td>D005753</td>\n",
       "      <td>Gastric Mucosa</td>\n",
       "      <td>BTO:0001308</td>\n",
       "      <td>gastric mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>53999</td>\n",
       "      <td>123|206|290|381|491|612|653|761|807|913|1077|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146</th>\n",
       "      <td>UBERON:0001231</td>\n",
       "      <td>nephron tubule</td>\n",
       "      <td>D007684</td>\n",
       "      <td>Kidney Tubules</td>\n",
       "      <td>BTO:0000343</td>\n",
       "      <td>kidney tubules[MeSH Terms:noexp]</td>\n",
       "      <td>24031</td>\n",
       "      <td>539|856|2016|2153|2771|2900|3111|3114|3258|328...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>151</th>\n",
       "      <td>UBERON:0001242</td>\n",
       "      <td>intestinal mucosa</td>\n",
       "      <td>D007413</td>\n",
       "      <td>Intestinal Mucosa</td>\n",
       "      <td>BTO:0000642</td>\n",
       "      <td>intestinal mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>95206</td>\n",
       "      <td>208|273|781|858|1197|1611|1617|1755|2008|2446|...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          uberon_id        uberon_name  mesh_id          mesh_name  \\\n",
       "137  UBERON:0001184       renal artery  D012077       Renal Artery   \n",
       "140  UBERON:0001199  mucosa of stomach  D005753     Gastric Mucosa   \n",
       "146  UBERON:0001231     nephron tubule  D007684     Kidney Tubules   \n",
       "151  UBERON:0001242  intestinal mucosa  D007413  Intestinal Mucosa   \n",
       "\n",
       "          bto_id                           term_query  n_articles  \\\n",
       "137  BTO:0001165       renal artery[MeSH Terms:noexp]       18741   \n",
       "140  BTO:0001308     gastric mucosa[MeSH Terms:noexp]       53999   \n",
       "146  BTO:0000343     kidney tubules[MeSH Terms:noexp]       24031   \n",
       "151  BTO:0000642  intestinal mucosa[MeSH Terms:noexp]       95206   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "137  1639|2546|2965|3150|5616|5843|5883|7844|8611|8...  \n",
       "140  123|206|290|381|491|612|653|761|807|913|1077|1...  \n",
       "146  539|856|2016|2153|2771|2900|3111|3114|3258|328...  \n",
       "151  208|273|781|858|1197|1611|1617|1755|2008|2446|...  "
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# rerun case with error\n",
    "error_terms = ['Renal Artery', 'Gastric Mucosa', 'Kidney Tubules', 'Intestinal Mucosa']\n",
    "\n",
    "error_out = list()\n",
    "for i in error_terms:\n",
    "    term_query = '{tissue}[MeSH Terms:noexp]'.format(tissue = i.lower())\n",
    "    print(term_query)\n",
    "    row = uberon_pmids_df.loc[uberon_pmids_df['mesh_name'] == i].squeeze()\n",
    "    path = efetch_query(term_query)\n",
    "    path = os.path.join(os.getcwd(), path)\n",
    "    pmids = pandas.read_csv(path, header=None, names=['pmids'])\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids[\"pmids\"].astype(str))\n",
    "    error_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), i))\n",
    "\n",
    "uberon_error_df = pandas.DataFrame(error_out)\n",
    "uberon_error_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>137</th>\n",
       "      <td>UBERON:0001184</td>\n",
       "      <td>renal artery</td>\n",
       "      <td>D012077</td>\n",
       "      <td>Renal Artery</td>\n",
       "      <td>BTO:0001165</td>\n",
       "      <td>renal artery[MeSH Terms:noexp]</td>\n",
       "      <td>18678</td>\n",
       "      <td>1639|2546|2965|3150|5616|5843|5883|7844|8611|8...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>140</th>\n",
       "      <td>UBERON:0001199</td>\n",
       "      <td>mucosa of stomach</td>\n",
       "      <td>D005753</td>\n",
       "      <td>Gastric Mucosa</td>\n",
       "      <td>BTO:0001308</td>\n",
       "      <td>gastric mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>53939</td>\n",
       "      <td>123|206|290|381|491|612|653|761|807|913|1077|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146</th>\n",
       "      <td>UBERON:0001231</td>\n",
       "      <td>nephron tubule</td>\n",
       "      <td>D007684</td>\n",
       "      <td>Kidney Tubules</td>\n",
       "      <td>BTO:0000343</td>\n",
       "      <td>kidney tubules[MeSH Terms:noexp]</td>\n",
       "      <td>23970</td>\n",
       "      <td>539|856|2016|2153|2771|2900|3111|3114|3258|328...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>151</th>\n",
       "      <td>UBERON:0001242</td>\n",
       "      <td>intestinal mucosa</td>\n",
       "      <td>D007413</td>\n",
       "      <td>Intestinal Mucosa</td>\n",
       "      <td>BTO:0000642</td>\n",
       "      <td>intestinal mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>94958</td>\n",
       "      <td>208|273|781|858|1197|1611|1617|1755|2008|2446|...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          uberon_id        uberon_name  mesh_id          mesh_name  \\\n",
       "137  UBERON:0001184       renal artery  D012077       Renal Artery   \n",
       "140  UBERON:0001199  mucosa of stomach  D005753     Gastric Mucosa   \n",
       "146  UBERON:0001231     nephron tubule  D007684     Kidney Tubules   \n",
       "151  UBERON:0001242  intestinal mucosa  D007413  Intestinal Mucosa   \n",
       "\n",
       "          bto_id                           term_query  n_articles  \\\n",
       "137  BTO:0001165       renal artery[MeSH Terms:noexp]       18678   \n",
       "140  BTO:0001308     gastric mucosa[MeSH Terms:noexp]       53939   \n",
       "146  BTO:0000343     kidney tubules[MeSH Terms:noexp]       23970   \n",
       "151  BTO:0000642  intestinal mucosa[MeSH Terms:noexp]       94958   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "137  1639|2546|2965|3150|5616|5843|5883|7844|8611|8...  \n",
       "140  123|206|290|381|491|612|653|761|807|913|1077|1...  \n",
       "146  539|856|2016|2153|2771|2900|3111|3114|3258|328...  \n",
       "151  208|273|781|858|1197|1611|1617|1755|2008|2446|...  "
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#validate with first run\n",
    "uberon_pmids_df.loc[uberon_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>137</th>\n",
       "      <td>UBERON:0001184</td>\n",
       "      <td>renal artery</td>\n",
       "      <td>D012077</td>\n",
       "      <td>Renal Artery</td>\n",
       "      <td>BTO:0001165</td>\n",
       "      <td>renal artery[MeSH Terms:noexp]</td>\n",
       "      <td>18741</td>\n",
       "      <td>1639|2546|2965|3150|5616|5843|5883|7844|8611|8...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>140</th>\n",
       "      <td>UBERON:0001199</td>\n",
       "      <td>mucosa of stomach</td>\n",
       "      <td>D005753</td>\n",
       "      <td>Gastric Mucosa</td>\n",
       "      <td>BTO:0001308</td>\n",
       "      <td>gastric mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>53999</td>\n",
       "      <td>123|206|290|381|491|612|653|761|807|913|1077|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146</th>\n",
       "      <td>UBERON:0001231</td>\n",
       "      <td>nephron tubule</td>\n",
       "      <td>D007684</td>\n",
       "      <td>Kidney Tubules</td>\n",
       "      <td>BTO:0000343</td>\n",
       "      <td>kidney tubules[MeSH Terms:noexp]</td>\n",
       "      <td>24031</td>\n",
       "      <td>539|856|2016|2153|2771|2900|3111|3114|3258|328...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>151</th>\n",
       "      <td>UBERON:0001242</td>\n",
       "      <td>intestinal mucosa</td>\n",
       "      <td>D007413</td>\n",
       "      <td>Intestinal Mucosa</td>\n",
       "      <td>BTO:0000642</td>\n",
       "      <td>intestinal mucosa[MeSH Terms:noexp]</td>\n",
       "      <td>95206</td>\n",
       "      <td>208|273|781|858|1197|1611|1617|1755|2008|2446|...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          uberon_id        uberon_name  mesh_id          mesh_name  \\\n",
       "137  UBERON:0001184       renal artery  D012077       Renal Artery   \n",
       "140  UBERON:0001199  mucosa of stomach  D005753     Gastric Mucosa   \n",
       "146  UBERON:0001231     nephron tubule  D007684     Kidney Tubules   \n",
       "151  UBERON:0001242  intestinal mucosa  D007413  Intestinal Mucosa   \n",
       "\n",
       "          bto_id                           term_query  n_articles  \\\n",
       "137  BTO:0001165       renal artery[MeSH Terms:noexp]       18741   \n",
       "140  BTO:0001308     gastric mucosa[MeSH Terms:noexp]       53999   \n",
       "146  BTO:0000343     kidney tubules[MeSH Terms:noexp]       24031   \n",
       "151  BTO:0000642  intestinal mucosa[MeSH Terms:noexp]       95206   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "137  1639|2546|2965|3150|5616|5843|5883|7844|8611|8...  \n",
       "140  123|206|290|381|491|612|653|761|807|913|1077|1...  \n",
       "146  539|856|2016|2153|2771|2900|3111|3114|3258|328...  \n",
       "151  208|273|781|858|1197|1611|1617|1755|2008|2446|...  "
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#update results and check values\n",
    "uberon_pmids_df.loc[uberon_pmids_df.mesh_name.isin(uberon_error_df.mesh_name), ['n_articles', 'pubmed_ids']] = uberon_error_df[['n_articles', 'pubmed_ids']]\n",
    "uberon_pmids_df.loc[uberon_pmids_df['mesh_name'].isin(error_terms)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>603</th>\n",
       "      <td>UBERON:0002631</td>\n",
       "      <td>cerebral crus</td>\n",
       "      <td>D065843</td>\n",
       "      <td>Cerebral Crus</td>\n",
       "      <td>BTO:0004677</td>\n",
       "      <td>cerebral crus[MeSH Terms:noexp]</td>\n",
       "      <td>9</td>\n",
       "      <td>18900819|24583337|25738471|25835460|27083894|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>604</th>\n",
       "      <td>UBERON:0002634</td>\n",
       "      <td>anterior nucleus of hypothalamus</td>\n",
       "      <td>D007025</td>\n",
       "      <td>Anterior Hypothalamic Nucleus</td>\n",
       "      <td>BTO:0002450</td>\n",
       "      <td>anterior hypothalamic nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>605</th>\n",
       "      <td>UBERON:0002663</td>\n",
       "      <td>septal nuclear complex</td>\n",
       "      <td>D012686</td>\n",
       "      <td>Septal Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>septal nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>606</th>\n",
       "      <td>UBERON:0002673</td>\n",
       "      <td>vestibular nuclear complex</td>\n",
       "      <td>D014726</td>\n",
       "      <td>Vestibular Nuclei</td>\n",
       "      <td>BTO:0004368</td>\n",
       "      <td>vestibular nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>607</th>\n",
       "      <td>UBERON:0002682</td>\n",
       "      <td>abducens nucleus</td>\n",
       "      <td>D065827</td>\n",
       "      <td>Abducens Nucleus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>abducens nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>608</th>\n",
       "      <td>UBERON:0002684</td>\n",
       "      <td>nucleus raphe obscurus</td>\n",
       "      <td>D065849</td>\n",
       "      <td>Nucleus Raphe Obscurus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>nucleus raphe obscurus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>609</th>\n",
       "      <td>UBERON:0002691</td>\n",
       "      <td>ventral tegmental area</td>\n",
       "      <td>D017557</td>\n",
       "      <td>Ventral Tegmental Area</td>\n",
       "      <td>NaN</td>\n",
       "      <td>ventral tegmental area[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>610</th>\n",
       "      <td>UBERON:0002704</td>\n",
       "      <td>metathalamus</td>\n",
       "      <td>D005829</td>\n",
       "      <td>Geniculate Bodies</td>\n",
       "      <td>NaN</td>\n",
       "      <td>geniculate bodies[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>611</th>\n",
       "      <td>UBERON:0002705</td>\n",
       "      <td>midline nuclear group</td>\n",
       "      <td>D020644</td>\n",
       "      <td>Midline Thalamic Nuclei</td>\n",
       "      <td>BTO:0002454</td>\n",
       "      <td>midline thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>612</th>\n",
       "      <td>UBERON:0002707</td>\n",
       "      <td>corticospinal tract</td>\n",
       "      <td>D011712</td>\n",
       "      <td>Pyramidal Tracts</td>\n",
       "      <td>BTO:0006132</td>\n",
       "      <td>pyramidal tracts[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>613</th>\n",
       "      <td>UBERON:0002728</td>\n",
       "      <td>entorhinal cortex</td>\n",
       "      <td>D018728</td>\n",
       "      <td>Entorhinal Cortex</td>\n",
       "      <td>BTO:0002650</td>\n",
       "      <td>entorhinal cortex[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>614</th>\n",
       "      <td>UBERON:0002895</td>\n",
       "      <td>secondary olfactory cortex</td>\n",
       "      <td>D018728</td>\n",
       "      <td>Entorhinal Cortex</td>\n",
       "      <td>BTO:0004345</td>\n",
       "      <td>entorhinal cortex[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615</th>\n",
       "      <td>UBERON:0002733</td>\n",
       "      <td>intralaminar nuclear group</td>\n",
       "      <td>D020646</td>\n",
       "      <td>Intralaminar Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>intralaminar thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>616</th>\n",
       "      <td>UBERON:0002736</td>\n",
       "      <td>lateral nuclear group of thalamus</td>\n",
       "      <td>D020647</td>\n",
       "      <td>Lateral Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>lateral thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>617</th>\n",
       "      <td>UBERON:0002739</td>\n",
       "      <td>medial dorsal nucleus of thalamus</td>\n",
       "      <td>D020645</td>\n",
       "      <td>Mediodorsal Thalamic Nucleus</td>\n",
       "      <td>BTO:0002453</td>\n",
       "      <td>mediodorsal thalamic nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>618</th>\n",
       "      <td>UBERON:0002741</td>\n",
       "      <td>diagonal band of Broca</td>\n",
       "      <td>D020667</td>\n",
       "      <td>Diagonal Band of Broca</td>\n",
       "      <td>BTO:0002445</td>\n",
       "      <td>diagonal band of broca[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>619</th>\n",
       "      <td>UBERON:0002743</td>\n",
       "      <td>basal forebrain</td>\n",
       "      <td>D066187</td>\n",
       "      <td>Basal Forebrain</td>\n",
       "      <td>BTO:0002444</td>\n",
       "      <td>basal forebrain[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>620</th>\n",
       "      <td>UBERON:0002776</td>\n",
       "      <td>ventral nuclear group</td>\n",
       "      <td>D020651</td>\n",
       "      <td>Ventral Thalamic Nuclei</td>\n",
       "      <td>BTO:0002467</td>\n",
       "      <td>ventral thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>621</th>\n",
       "      <td>UBERON:0002788</td>\n",
       "      <td>anterior nuclear group</td>\n",
       "      <td>D020643</td>\n",
       "      <td>Anterior Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>anterior thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>622</th>\n",
       "      <td>UBERON:0002894</td>\n",
       "      <td>olfactory cortex</td>\n",
       "      <td>D066194</td>\n",
       "      <td>Olfactory Cortex</td>\n",
       "      <td>BTO:0001446</td>\n",
       "      <td>olfactory cortex[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>623</th>\n",
       "      <td>UBERON:0002925</td>\n",
       "      <td>trigeminal nucleus</td>\n",
       "      <td>D014278</td>\n",
       "      <td>Trigeminal Nuclei</td>\n",
       "      <td>BTO:0001074</td>\n",
       "      <td>trigeminal nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>624</th>\n",
       "      <td>UBERON:0002932</td>\n",
       "      <td>trapezoid body</td>\n",
       "      <td>D065833</td>\n",
       "      <td>Trapezoid Body</td>\n",
       "      <td>NaN</td>\n",
       "      <td>trapezoid body[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>625</th>\n",
       "      <td>UBERON:0002944</td>\n",
       "      <td>spinothalamic tract of medulla</td>\n",
       "      <td>D013133</td>\n",
       "      <td>Spinothalamic Tracts</td>\n",
       "      <td>NaN</td>\n",
       "      <td>spinothalamic tracts[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>626</th>\n",
       "      <td>UBERON:0002967</td>\n",
       "      <td>cingulate gyrus</td>\n",
       "      <td>D006179</td>\n",
       "      <td>Gyrus Cinguli</td>\n",
       "      <td>BTO:0003976</td>\n",
       "      <td>gyrus cinguli[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>627</th>\n",
       "      <td>UBERON:0002973</td>\n",
       "      <td>parahippocampal gyrus</td>\n",
       "      <td>D020534</td>\n",
       "      <td>Parahippocampal Gyrus</td>\n",
       "      <td>BTO:0004380</td>\n",
       "      <td>parahippocampal gyrus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>628</th>\n",
       "      <td>UBERON:0002981</td>\n",
       "      <td>pulvinar nucleus</td>\n",
       "      <td>D020649</td>\n",
       "      <td>Pulvinar</td>\n",
       "      <td>BTO:0004352</td>\n",
       "      <td>pulvinar[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>629</th>\n",
       "      <td>UBERON:0003017</td>\n",
       "      <td>substantia innominata</td>\n",
       "      <td>D013377</td>\n",
       "      <td>Substantia Innominata</td>\n",
       "      <td>BTO:0002447</td>\n",
       "      <td>substantia innominata[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>630</th>\n",
       "      <td>UBERON:0003023</td>\n",
       "      <td>pontine tegmentum</td>\n",
       "      <td>D065821</td>\n",
       "      <td>Pontine Tegmentum</td>\n",
       "      <td>NaN</td>\n",
       "      <td>pontine tegmentum[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>631</th>\n",
       "      <td>UBERON:0003040</td>\n",
       "      <td>central gray substance of midbrain</td>\n",
       "      <td>D010487</td>\n",
       "      <td>Periaqueductal Gray</td>\n",
       "      <td>BTO:0002701</td>\n",
       "      <td>periaqueductal gray[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>632</th>\n",
       "      <td>UBERON:0003044</td>\n",
       "      <td>uncinate fasciculus</td>\n",
       "      <td>D000083382</td>\n",
       "      <td>Uncinate Fasciculus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>uncinate fasciculus[MeSH Terms:noexp]</td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>603</th>\n",
       "      <td>UBERON:0002631</td>\n",
       "      <td>cerebral crus</td>\n",
       "      <td>D065843</td>\n",
       "      <td>Cerebral Crus</td>\n",
       "      <td>BTO:0004677</td>\n",
       "      <td>cerebral crus[MeSH Terms:noexp]</td>\n",
       "      <td>9</td>\n",
       "      <td>18900819|24583337|25738471|25835460|27083894|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>604</th>\n",
       "      <td>UBERON:0002634</td>\n",
       "      <td>anterior nucleus of hypothalamus</td>\n",
       "      <td>D007025</td>\n",
       "      <td>Anterior Hypothalamic Nucleus</td>\n",
       "      <td>BTO:0002450</td>\n",
       "      <td>anterior hypothalamic nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>260</td>\n",
       "      <td>1430324|1452291|1504850|1539736|1607926|162684...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>605</th>\n",
       "      <td>UBERON:0002663</td>\n",
       "      <td>septal nuclear complex</td>\n",
       "      <td>D012686</td>\n",
       "      <td>Septal Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>septal nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>3672</td>\n",
       "      <td>1503|2943|6117|7798|19788|24720|25363|29156|29...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>606</th>\n",
       "      <td>UBERON:0002673</td>\n",
       "      <td>vestibular nuclear complex</td>\n",
       "      <td>D014726</td>\n",
       "      <td>Vestibular Nuclei</td>\n",
       "      <td>BTO:0004368</td>\n",
       "      <td>vestibular nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>3458</td>\n",
       "      <td>3742|12984|13324|19786|44844|54052|56281|65366...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>607</th>\n",
       "      <td>UBERON:0002682</td>\n",
       "      <td>abducens nucleus</td>\n",
       "      <td>D065827</td>\n",
       "      <td>Abducens Nucleus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>abducens nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>12</td>\n",
       "      <td>14018826|14359296|24478158|24881009|25414191|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>608</th>\n",
       "      <td>UBERON:0002684</td>\n",
       "      <td>nucleus raphe obscurus</td>\n",
       "      <td>D065849</td>\n",
       "      <td>Nucleus Raphe Obscurus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>nucleus raphe obscurus[MeSH Terms:noexp]</td>\n",
       "      <td>2</td>\n",
       "      <td>25107878|32961215</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>609</th>\n",
       "      <td>UBERON:0002691</td>\n",
       "      <td>ventral tegmental area</td>\n",
       "      <td>D017557</td>\n",
       "      <td>Ventral Tegmental Area</td>\n",
       "      <td>NaN</td>\n",
       "      <td>ventral tegmental area[MeSH Terms:noexp]</td>\n",
       "      <td>4581</td>\n",
       "      <td>1285292|1365637|7477962|7480515|7493614|749679...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>610</th>\n",
       "      <td>UBERON:0002704</td>\n",
       "      <td>metathalamus</td>\n",
       "      <td>D005829</td>\n",
       "      <td>Geniculate Bodies</td>\n",
       "      <td>NaN</td>\n",
       "      <td>geniculate bodies[MeSH Terms:noexp]</td>\n",
       "      <td>8332</td>\n",
       "      <td>3423|5977|6784|10535|12250|14768|18872|19781|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>611</th>\n",
       "      <td>UBERON:0002705</td>\n",
       "      <td>midline nuclear group</td>\n",
       "      <td>D020644</td>\n",
       "      <td>Midline Thalamic Nuclei</td>\n",
       "      <td>BTO:0002454</td>\n",
       "      <td>midline thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>456</td>\n",
       "      <td>10603291|10627313|10640708|10642829|10654626|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>612</th>\n",
       "      <td>UBERON:0002707</td>\n",
       "      <td>corticospinal tract</td>\n",
       "      <td>D011712</td>\n",
       "      <td>Pyramidal Tracts</td>\n",
       "      <td>BTO:0006132</td>\n",
       "      <td>pyramidal tracts[MeSH Terms:noexp]</td>\n",
       "      <td>8499</td>\n",
       "      <td>6297|11491|11492|15338|26879|29526|51729|52225...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>613</th>\n",
       "      <td>UBERON:0002728</td>\n",
       "      <td>entorhinal cortex</td>\n",
       "      <td>D018728</td>\n",
       "      <td>Entorhinal Cortex</td>\n",
       "      <td>BTO:0002650</td>\n",
       "      <td>entorhinal cortex[MeSH Terms:noexp]</td>\n",
       "      <td>3647</td>\n",
       "      <td>7472334|7472396|7472444|7478170|7491048|749952...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>614</th>\n",
       "      <td>UBERON:0002895</td>\n",
       "      <td>secondary olfactory cortex</td>\n",
       "      <td>D018728</td>\n",
       "      <td>Entorhinal Cortex</td>\n",
       "      <td>BTO:0004345</td>\n",
       "      <td>entorhinal cortex[MeSH Terms:noexp]</td>\n",
       "      <td>3647</td>\n",
       "      <td>7472334|7472396|7472444|7478170|7491048|749952...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615</th>\n",
       "      <td>UBERON:0002733</td>\n",
       "      <td>intralaminar nuclear group</td>\n",
       "      <td>D020646</td>\n",
       "      <td>Intralaminar Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>intralaminar thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>498</td>\n",
       "      <td>10502314|10527369|10578450|10638434|10708697|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>616</th>\n",
       "      <td>UBERON:0002736</td>\n",
       "      <td>lateral nuclear group of thalamus</td>\n",
       "      <td>D020647</td>\n",
       "      <td>Lateral Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>lateral thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>128</td>\n",
       "      <td>10501458|10581467|10584691|10596786|10657525|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>617</th>\n",
       "      <td>UBERON:0002739</td>\n",
       "      <td>medial dorsal nucleus of thalamus</td>\n",
       "      <td>D020645</td>\n",
       "      <td>Mediodorsal Thalamic Nucleus</td>\n",
       "      <td>BTO:0002453</td>\n",
       "      <td>mediodorsal thalamic nucleus[MeSH Terms:noexp]</td>\n",
       "      <td>370</td>\n",
       "      <td>10501458|10502314|10511452|10642841|10711294|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>618</th>\n",
       "      <td>UBERON:0002741</td>\n",
       "      <td>diagonal band of Broca</td>\n",
       "      <td>D020667</td>\n",
       "      <td>Diagonal Band of Broca</td>\n",
       "      <td>BTO:0002445</td>\n",
       "      <td>diagonal band of broca[MeSH Terms:noexp]</td>\n",
       "      <td>143</td>\n",
       "      <td>10507467|10529618|10536201|10579569|10614664|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>619</th>\n",
       "      <td>UBERON:0002743</td>\n",
       "      <td>basal forebrain</td>\n",
       "      <td>D066187</td>\n",
       "      <td>Basal Forebrain</td>\n",
       "      <td>BTO:0002444</td>\n",
       "      <td>basal forebrain[MeSH Terms:noexp]</td>\n",
       "      <td>565</td>\n",
       "      <td>13495468|13916975|13916976|14021689|14287781|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>620</th>\n",
       "      <td>UBERON:0002776</td>\n",
       "      <td>ventral nuclear group</td>\n",
       "      <td>D020651</td>\n",
       "      <td>Ventral Thalamic Nuclei</td>\n",
       "      <td>BTO:0002467</td>\n",
       "      <td>ventral thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>955</td>\n",
       "      <td>10495039|10495050|10500254|10501458|10515975|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>621</th>\n",
       "      <td>UBERON:0002788</td>\n",
       "      <td>anterior nuclear group</td>\n",
       "      <td>D020643</td>\n",
       "      <td>Anterior Thalamic Nuclei</td>\n",
       "      <td>NaN</td>\n",
       "      <td>anterior thalamic nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>504</td>\n",
       "      <td>10501458|10507474|10532632|10571478|10582992|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>622</th>\n",
       "      <td>UBERON:0002894</td>\n",
       "      <td>olfactory cortex</td>\n",
       "      <td>D066194</td>\n",
       "      <td>Olfactory Cortex</td>\n",
       "      <td>BTO:0001446</td>\n",
       "      <td>olfactory cortex[MeSH Terms:noexp]</td>\n",
       "      <td>328</td>\n",
       "      <td>12980169|12988917|13011534|13012415|13033297|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>623</th>\n",
       "      <td>UBERON:0002925</td>\n",
       "      <td>trigeminal nucleus</td>\n",
       "      <td>D014278</td>\n",
       "      <td>Trigeminal Nuclei</td>\n",
       "      <td>BTO:0001074</td>\n",
       "      <td>trigeminal nuclei[MeSH Terms:noexp]</td>\n",
       "      <td>1765</td>\n",
       "      <td>42868|95614|121306|158427|296267|316000|401235...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>624</th>\n",
       "      <td>UBERON:0002932</td>\n",
       "      <td>trapezoid body</td>\n",
       "      <td>D065833</td>\n",
       "      <td>Trapezoid Body</td>\n",
       "      <td>NaN</td>\n",
       "      <td>trapezoid body[MeSH Terms:noexp]</td>\n",
       "      <td>74</td>\n",
       "      <td>12991253|13062245|13109749|13252605|14080311|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>625</th>\n",
       "      <td>UBERON:0002944</td>\n",
       "      <td>spinothalamic tract of medulla</td>\n",
       "      <td>D013133</td>\n",
       "      <td>Spinothalamic Tracts</td>\n",
       "      <td>NaN</td>\n",
       "      <td>spinothalamic tracts[MeSH Terms:noexp]</td>\n",
       "      <td>781</td>\n",
       "      <td>24487|29526|54206|71228|74048|75893|83245|8400...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>626</th>\n",
       "      <td>UBERON:0002967</td>\n",
       "      <td>cingulate gyrus</td>\n",
       "      <td>D006179</td>\n",
       "      <td>Gyrus Cinguli</td>\n",
       "      <td>BTO:0003976</td>\n",
       "      <td>gyrus cinguli[MeSH Terms:noexp]</td>\n",
       "      <td>10620</td>\n",
       "      <td>24492|31230|33749|34469|45898|46163|50205|6276...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>627</th>\n",
       "      <td>UBERON:0002973</td>\n",
       "      <td>parahippocampal gyrus</td>\n",
       "      <td>D020534</td>\n",
       "      <td>Parahippocampal Gyrus</td>\n",
       "      <td>BTO:0004380</td>\n",
       "      <td>parahippocampal gyrus[MeSH Terms:noexp]</td>\n",
       "      <td>1190</td>\n",
       "      <td>10490938|10505430|10510193|10526199|10531459|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>628</th>\n",
       "      <td>UBERON:0002981</td>\n",
       "      <td>pulvinar nucleus</td>\n",
       "      <td>D020649</td>\n",
       "      <td>Pulvinar</td>\n",
       "      <td>BTO:0004352</td>\n",
       "      <td>pulvinar[MeSH Terms:noexp]</td>\n",
       "      <td>406</td>\n",
       "      <td>10501458|10507560|10631787|10666560|10716200|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>629</th>\n",
       "      <td>UBERON:0003017</td>\n",
       "      <td>substantia innominata</td>\n",
       "      <td>D013377</td>\n",
       "      <td>Substantia Innominata</td>\n",
       "      <td>BTO:0002447</td>\n",
       "      <td>substantia innominata[MeSH Terms:noexp]</td>\n",
       "      <td>838</td>\n",
       "      <td>1282013|1300505|1304338|1317181|1319789|132136...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>630</th>\n",
       "      <td>UBERON:0003023</td>\n",
       "      <td>pontine tegmentum</td>\n",
       "      <td>D065821</td>\n",
       "      <td>Pontine Tegmentum</td>\n",
       "      <td>NaN</td>\n",
       "      <td>pontine tegmentum[MeSH Terms:noexp]</td>\n",
       "      <td>131</td>\n",
       "      <td>13064513|13338960|13501155|13721895|13770384|1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>631</th>\n",
       "      <td>UBERON:0003040</td>\n",
       "      <td>central gray substance of midbrain</td>\n",
       "      <td>D010487</td>\n",
       "      <td>Periaqueductal Gray</td>\n",
       "      <td>BTO:0002701</td>\n",
       "      <td>periaqueductal gray[MeSH Terms:noexp]</td>\n",
       "      <td>3433</td>\n",
       "      <td>1282709|1282765|1295034|1311108|1330145|133322...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>632</th>\n",
       "      <td>UBERON:0003044</td>\n",
       "      <td>uncinate fasciculus</td>\n",
       "      <td>D000083382</td>\n",
       "      <td>Uncinate Fasciculus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>uncinate fasciculus[MeSH Terms:noexp]</td>\n",
       "      <td>31</td>\n",
       "      <td>29122609|29454977|31604519|32107139|32182577|3...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          uberon_id                         uberon_name     mesh_id  \\\n",
       "603  UBERON:0002631                       cerebral crus     D065843   \n",
       "604  UBERON:0002634    anterior nucleus of hypothalamus     D007025   \n",
       "605  UBERON:0002663              septal nuclear complex     D012686   \n",
       "606  UBERON:0002673          vestibular nuclear complex     D014726   \n",
       "607  UBERON:0002682                    abducens nucleus     D065827   \n",
       "608  UBERON:0002684              nucleus raphe obscurus     D065849   \n",
       "609  UBERON:0002691              ventral tegmental area     D017557   \n",
       "610  UBERON:0002704                        metathalamus     D005829   \n",
       "611  UBERON:0002705               midline nuclear group     D020644   \n",
       "612  UBERON:0002707                 corticospinal tract     D011712   \n",
       "613  UBERON:0002728                   entorhinal cortex     D018728   \n",
       "614  UBERON:0002895          secondary olfactory cortex     D018728   \n",
       "615  UBERON:0002733          intralaminar nuclear group     D020646   \n",
       "616  UBERON:0002736   lateral nuclear group of thalamus     D020647   \n",
       "617  UBERON:0002739   medial dorsal nucleus of thalamus     D020645   \n",
       "618  UBERON:0002741              diagonal band of Broca     D020667   \n",
       "619  UBERON:0002743                     basal forebrain     D066187   \n",
       "620  UBERON:0002776               ventral nuclear group     D020651   \n",
       "621  UBERON:0002788              anterior nuclear group     D020643   \n",
       "622  UBERON:0002894                    olfactory cortex     D066194   \n",
       "623  UBERON:0002925                  trigeminal nucleus     D014278   \n",
       "624  UBERON:0002932                      trapezoid body     D065833   \n",
       "625  UBERON:0002944      spinothalamic tract of medulla     D013133   \n",
       "626  UBERON:0002967                     cingulate gyrus     D006179   \n",
       "627  UBERON:0002973               parahippocampal gyrus     D020534   \n",
       "628  UBERON:0002981                    pulvinar nucleus     D020649   \n",
       "629  UBERON:0003017               substantia innominata     D013377   \n",
       "630  UBERON:0003023                   pontine tegmentum     D065821   \n",
       "631  UBERON:0003040  central gray substance of midbrain     D010487   \n",
       "632  UBERON:0003044                 uncinate fasciculus  D000083382   \n",
       "603  UBERON:0002631                       cerebral crus     D065843   \n",
       "604  UBERON:0002634    anterior nucleus of hypothalamus     D007025   \n",
       "605  UBERON:0002663              septal nuclear complex     D012686   \n",
       "606  UBERON:0002673          vestibular nuclear complex     D014726   \n",
       "607  UBERON:0002682                    abducens nucleus     D065827   \n",
       "608  UBERON:0002684              nucleus raphe obscurus     D065849   \n",
       "609  UBERON:0002691              ventral tegmental area     D017557   \n",
       "610  UBERON:0002704                        metathalamus     D005829   \n",
       "611  UBERON:0002705               midline nuclear group     D020644   \n",
       "612  UBERON:0002707                 corticospinal tract     D011712   \n",
       "613  UBERON:0002728                   entorhinal cortex     D018728   \n",
       "614  UBERON:0002895          secondary olfactory cortex     D018728   \n",
       "615  UBERON:0002733          intralaminar nuclear group     D020646   \n",
       "616  UBERON:0002736   lateral nuclear group of thalamus     D020647   \n",
       "617  UBERON:0002739   medial dorsal nucleus of thalamus     D020645   \n",
       "618  UBERON:0002741              diagonal band of Broca     D020667   \n",
       "619  UBERON:0002743                     basal forebrain     D066187   \n",
       "620  UBERON:0002776               ventral nuclear group     D020651   \n",
       "621  UBERON:0002788              anterior nuclear group     D020643   \n",
       "622  UBERON:0002894                    olfactory cortex     D066194   \n",
       "623  UBERON:0002925                  trigeminal nucleus     D014278   \n",
       "624  UBERON:0002932                      trapezoid body     D065833   \n",
       "625  UBERON:0002944      spinothalamic tract of medulla     D013133   \n",
       "626  UBERON:0002967                     cingulate gyrus     D006179   \n",
       "627  UBERON:0002973               parahippocampal gyrus     D020534   \n",
       "628  UBERON:0002981                    pulvinar nucleus     D020649   \n",
       "629  UBERON:0003017               substantia innominata     D013377   \n",
       "630  UBERON:0003023                   pontine tegmentum     D065821   \n",
       "631  UBERON:0003040  central gray substance of midbrain     D010487   \n",
       "632  UBERON:0003044                 uncinate fasciculus  D000083382   \n",
       "\n",
       "                         mesh_name       bto_id  \\\n",
       "603                  Cerebral Crus  BTO:0004677   \n",
       "604  Anterior Hypothalamic Nucleus  BTO:0002450   \n",
       "605                  Septal Nuclei          NaN   \n",
       "606              Vestibular Nuclei  BTO:0004368   \n",
       "607               Abducens Nucleus          NaN   \n",
       "608         Nucleus Raphe Obscurus          NaN   \n",
       "609         Ventral Tegmental Area          NaN   \n",
       "610              Geniculate Bodies          NaN   \n",
       "611        Midline Thalamic Nuclei  BTO:0002454   \n",
       "612               Pyramidal Tracts  BTO:0006132   \n",
       "613              Entorhinal Cortex  BTO:0002650   \n",
       "614              Entorhinal Cortex  BTO:0004345   \n",
       "615   Intralaminar Thalamic Nuclei          NaN   \n",
       "616        Lateral Thalamic Nuclei          NaN   \n",
       "617   Mediodorsal Thalamic Nucleus  BTO:0002453   \n",
       "618         Diagonal Band of Broca  BTO:0002445   \n",
       "619                Basal Forebrain  BTO:0002444   \n",
       "620        Ventral Thalamic Nuclei  BTO:0002467   \n",
       "621       Anterior Thalamic Nuclei          NaN   \n",
       "622               Olfactory Cortex  BTO:0001446   \n",
       "623              Trigeminal Nuclei  BTO:0001074   \n",
       "624                 Trapezoid Body          NaN   \n",
       "625           Spinothalamic Tracts          NaN   \n",
       "626                  Gyrus Cinguli  BTO:0003976   \n",
       "627          Parahippocampal Gyrus  BTO:0004380   \n",
       "628                       Pulvinar  BTO:0004352   \n",
       "629          Substantia Innominata  BTO:0002447   \n",
       "630              Pontine Tegmentum          NaN   \n",
       "631            Periaqueductal Gray  BTO:0002701   \n",
       "632            Uncinate Fasciculus          NaN   \n",
       "603                  Cerebral Crus  BTO:0004677   \n",
       "604  Anterior Hypothalamic Nucleus  BTO:0002450   \n",
       "605                  Septal Nuclei          NaN   \n",
       "606              Vestibular Nuclei  BTO:0004368   \n",
       "607               Abducens Nucleus          NaN   \n",
       "608         Nucleus Raphe Obscurus          NaN   \n",
       "609         Ventral Tegmental Area          NaN   \n",
       "610              Geniculate Bodies          NaN   \n",
       "611        Midline Thalamic Nuclei  BTO:0002454   \n",
       "612               Pyramidal Tracts  BTO:0006132   \n",
       "613              Entorhinal Cortex  BTO:0002650   \n",
       "614              Entorhinal Cortex  BTO:0004345   \n",
       "615   Intralaminar Thalamic Nuclei          NaN   \n",
       "616        Lateral Thalamic Nuclei          NaN   \n",
       "617   Mediodorsal Thalamic Nucleus  BTO:0002453   \n",
       "618         Diagonal Band of Broca  BTO:0002445   \n",
       "619                Basal Forebrain  BTO:0002444   \n",
       "620        Ventral Thalamic Nuclei  BTO:0002467   \n",
       "621       Anterior Thalamic Nuclei          NaN   \n",
       "622               Olfactory Cortex  BTO:0001446   \n",
       "623              Trigeminal Nuclei  BTO:0001074   \n",
       "624                 Trapezoid Body          NaN   \n",
       "625           Spinothalamic Tracts          NaN   \n",
       "626                  Gyrus Cinguli  BTO:0003976   \n",
       "627          Parahippocampal Gyrus  BTO:0004380   \n",
       "628                       Pulvinar  BTO:0004352   \n",
       "629          Substantia Innominata  BTO:0002447   \n",
       "630              Pontine Tegmentum          NaN   \n",
       "631            Periaqueductal Gray  BTO:0002701   \n",
       "632            Uncinate Fasciculus          NaN   \n",
       "\n",
       "                                          term_query  n_articles  \\\n",
       "603                  cerebral crus[MeSH Terms:noexp]           9   \n",
       "604  anterior hypothalamic nucleus[MeSH Terms:noexp]           0   \n",
       "605                  septal nuclei[MeSH Terms:noexp]           0   \n",
       "606              vestibular nuclei[MeSH Terms:noexp]           0   \n",
       "607               abducens nucleus[MeSH Terms:noexp]           0   \n",
       "608         nucleus raphe obscurus[MeSH Terms:noexp]           0   \n",
       "609         ventral tegmental area[MeSH Terms:noexp]           0   \n",
       "610              geniculate bodies[MeSH Terms:noexp]           0   \n",
       "611        midline thalamic nuclei[MeSH Terms:noexp]           0   \n",
       "612               pyramidal tracts[MeSH Terms:noexp]           0   \n",
       "613              entorhinal cortex[MeSH Terms:noexp]           0   \n",
       "614              entorhinal cortex[MeSH Terms:noexp]           0   \n",
       "615   intralaminar thalamic nuclei[MeSH Terms:noexp]           0   \n",
       "616        lateral thalamic nuclei[MeSH Terms:noexp]           0   \n",
       "617   mediodorsal thalamic nucleus[MeSH Terms:noexp]           0   \n",
       "618         diagonal band of broca[MeSH Terms:noexp]           0   \n",
       "619                basal forebrain[MeSH Terms:noexp]           0   \n",
       "620        ventral thalamic nuclei[MeSH Terms:noexp]           0   \n",
       "621       anterior thalamic nuclei[MeSH Terms:noexp]           0   \n",
       "622               olfactory cortex[MeSH Terms:noexp]           0   \n",
       "623              trigeminal nuclei[MeSH Terms:noexp]           0   \n",
       "624                 trapezoid body[MeSH Terms:noexp]           0   \n",
       "625           spinothalamic tracts[MeSH Terms:noexp]           0   \n",
       "626                  gyrus cinguli[MeSH Terms:noexp]           0   \n",
       "627          parahippocampal gyrus[MeSH Terms:noexp]           0   \n",
       "628                       pulvinar[MeSH Terms:noexp]           0   \n",
       "629          substantia innominata[MeSH Terms:noexp]           0   \n",
       "630              pontine tegmentum[MeSH Terms:noexp]           0   \n",
       "631            periaqueductal gray[MeSH Terms:noexp]           0   \n",
       "632            uncinate fasciculus[MeSH Terms:noexp]           0   \n",
       "603                  cerebral crus[MeSH Terms:noexp]           9   \n",
       "604  anterior hypothalamic nucleus[MeSH Terms:noexp]         260   \n",
       "605                  septal nuclei[MeSH Terms:noexp]        3672   \n",
       "606              vestibular nuclei[MeSH Terms:noexp]        3458   \n",
       "607               abducens nucleus[MeSH Terms:noexp]          12   \n",
       "608         nucleus raphe obscurus[MeSH Terms:noexp]           2   \n",
       "609         ventral tegmental area[MeSH Terms:noexp]        4581   \n",
       "610              geniculate bodies[MeSH Terms:noexp]        8332   \n",
       "611        midline thalamic nuclei[MeSH Terms:noexp]         456   \n",
       "612               pyramidal tracts[MeSH Terms:noexp]        8499   \n",
       "613              entorhinal cortex[MeSH Terms:noexp]        3647   \n",
       "614              entorhinal cortex[MeSH Terms:noexp]        3647   \n",
       "615   intralaminar thalamic nuclei[MeSH Terms:noexp]         498   \n",
       "616        lateral thalamic nuclei[MeSH Terms:noexp]         128   \n",
       "617   mediodorsal thalamic nucleus[MeSH Terms:noexp]         370   \n",
       "618         diagonal band of broca[MeSH Terms:noexp]         143   \n",
       "619                basal forebrain[MeSH Terms:noexp]         565   \n",
       "620        ventral thalamic nuclei[MeSH Terms:noexp]         955   \n",
       "621       anterior thalamic nuclei[MeSH Terms:noexp]         504   \n",
       "622               olfactory cortex[MeSH Terms:noexp]         328   \n",
       "623              trigeminal nuclei[MeSH Terms:noexp]        1765   \n",
       "624                 trapezoid body[MeSH Terms:noexp]          74   \n",
       "625           spinothalamic tracts[MeSH Terms:noexp]         781   \n",
       "626                  gyrus cinguli[MeSH Terms:noexp]       10620   \n",
       "627          parahippocampal gyrus[MeSH Terms:noexp]        1190   \n",
       "628                       pulvinar[MeSH Terms:noexp]         406   \n",
       "629          substantia innominata[MeSH Terms:noexp]         838   \n",
       "630              pontine tegmentum[MeSH Terms:noexp]         131   \n",
       "631            periaqueductal gray[MeSH Terms:noexp]        3433   \n",
       "632            uncinate fasciculus[MeSH Terms:noexp]          31   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "603  18900819|24583337|25738471|25835460|27083894|2...  \n",
       "604                                                     \n",
       "605                                                     \n",
       "606                                                     \n",
       "607                                                     \n",
       "608                                                     \n",
       "609                                                     \n",
       "610                                                     \n",
       "611                                                     \n",
       "612                                                     \n",
       "613                                                     \n",
       "614                                                     \n",
       "615                                                     \n",
       "616                                                     \n",
       "617                                                     \n",
       "618                                                     \n",
       "619                                                     \n",
       "620                                                     \n",
       "621                                                     \n",
       "622                                                     \n",
       "623                                                     \n",
       "624                                                     \n",
       "625                                                     \n",
       "626                                                     \n",
       "627                                                     \n",
       "628                                                     \n",
       "629                                                     \n",
       "630                                                     \n",
       "631                                                     \n",
       "632                                                     \n",
       "603  18900819|24583337|25738471|25835460|27083894|2...  \n",
       "604  1430324|1452291|1504850|1539736|1607926|162684...  \n",
       "605  1503|2943|6117|7798|19788|24720|25363|29156|29...  \n",
       "606  3742|12984|13324|19786|44844|54052|56281|65366...  \n",
       "607  14018826|14359296|24478158|24881009|25414191|2...  \n",
       "608                                  25107878|32961215  \n",
       "609  1285292|1365637|7477962|7480515|7493614|749679...  \n",
       "610  3423|5977|6784|10535|12250|14768|18872|19781|1...  \n",
       "611  10603291|10627313|10640708|10642829|10654626|1...  \n",
       "612  6297|11491|11492|15338|26879|29526|51729|52225...  \n",
       "613  7472334|7472396|7472444|7478170|7491048|749952...  \n",
       "614  7472334|7472396|7472444|7478170|7491048|749952...  \n",
       "615  10502314|10527369|10578450|10638434|10708697|1...  \n",
       "616  10501458|10581467|10584691|10596786|10657525|1...  \n",
       "617  10501458|10502314|10511452|10642841|10711294|1...  \n",
       "618  10507467|10529618|10536201|10579569|10614664|1...  \n",
       "619  13495468|13916975|13916976|14021689|14287781|2...  \n",
       "620  10495039|10495050|10500254|10501458|10515975|1...  \n",
       "621  10501458|10507474|10532632|10571478|10582992|1...  \n",
       "622  12980169|12988917|13011534|13012415|13033297|1...  \n",
       "623  42868|95614|121306|158427|296267|316000|401235...  \n",
       "624  12991253|13062245|13109749|13252605|14080311|1...  \n",
       "625  24487|29526|54206|71228|74048|75893|83245|8400...  \n",
       "626  24492|31230|33749|34469|45898|46163|50205|6276...  \n",
       "627  10490938|10505430|10510193|10526199|10531459|1...  \n",
       "628  10501458|10507560|10631787|10666560|10716200|1...  \n",
       "629  1282013|1300505|1304338|1317181|1319789|132136...  \n",
       "630  13064513|13338960|13501155|13721895|13770384|1...  \n",
       "631  1282709|1282765|1295034|1311108|1330145|133322...  \n",
       "632  29122609|29454977|31604519|32107139|32182577|3...  "
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#check duplicated rows\n",
    "#duplicated terms = uberon_df['mesh_name'][603:633]\n",
    "uberon_pmids_df[uberon_pmids_df.duplicated(['uberon_id','uberon_name','mesh_id','mesh_name','bto_id'],keep=False)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(682, 8)"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uberon_pmids_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(652, 8)"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#remove duplicated rows\n",
    "uberon_pmids_df = uberon_pmids_df.sort_index().drop_duplicates(['uberon_id','uberon_name','mesh_id','mesh_name','bto_id'], keep='last')\n",
    "uberon_pmids_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [uberon_id, uberon_name, mesh_id, mesh_name, bto_id, term_query, n_articles, pubmed_ids]\n",
       "Index: []"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uberon_pmids_df[uberon_pmids_df.duplicated(['uberon_id','uberon_name','mesh_id','mesh_name','bto_id'],keep=False)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>603</th>\n",
       "      <td>UBERON:0002631</td>\n",
       "      <td>cerebral crus</td>\n",
       "      <td>D065843</td>\n",
       "      <td>Cerebral Crus</td>\n",
       "      <td>BTO:0004677</td>\n",
       "      <td>cerebral crus[MeSH Terms:noexp]</td>\n",
       "      <td>9</td>\n",
       "      <td>18900819|24583337|25738471|25835460|27083894|2...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          uberon_id    uberon_name  mesh_id      mesh_name       bto_id  \\\n",
       "603  UBERON:0002631  cerebral crus  D065843  Cerebral Crus  BTO:0004677   \n",
       "\n",
       "                          term_query  n_articles  \\\n",
       "603  cerebral crus[MeSH Terms:noexp]           9   \n",
       "\n",
       "                                            pubmed_ids  \n",
       "603  18900819|24583337|25738471|25835460|27083894|2...  "
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uberon_pmids_df[uberon_pmids_df['mesh_name']=='Cerebral Crus'] "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "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>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UBERON:0000002</td>\n",
       "      <td>uterine cervix</td>\n",
       "      <td>D002584</td>\n",
       "      <td>Cervix Uteri</td>\n",
       "      <td>BTO:0001421</td>\n",
       "      <td>cervix uteri[MeSH Terms:noexp]</td>\n",
       "      <td>29638</td>\n",
       "      <td>2135|12122|13010|13018|15040|15694|15911|15912...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UBERON:0000004</td>\n",
       "      <td>nose</td>\n",
       "      <td>D009666</td>\n",
       "      <td>Nose</td>\n",
       "      <td>BTO:0000840</td>\n",
       "      <td>nose[MeSH Terms:noexp]</td>\n",
       "      <td>27243</td>\n",
       "      <td>2067|5220|18131|18962|19546|21298|25090|27057|...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UBERON:0000006</td>\n",
       "      <td>islet of Langerhans</td>\n",
       "      <td>D007515</td>\n",
       "      <td>Islets of Langerhans</td>\n",
       "      <td>BTO:0000991</td>\n",
       "      <td>islets of langerhans[MeSH Terms:noexp]</td>\n",
       "      <td>38235</td>\n",
       "      <td>1320|1687|2929|4295|4298|6851|9188|9697|11432|...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UBERON:0000016</td>\n",
       "      <td>endocrine pancreas</td>\n",
       "      <td>D007515</td>\n",
       "      <td>Islets of Langerhans</td>\n",
       "      <td>BTO:0000650</td>\n",
       "      <td>islets of langerhans[MeSH Terms:noexp]</td>\n",
       "      <td>38235</td>\n",
       "      <td>1320|1687|2929|4295|4298|6851|9188|9697|11432|...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBERON:0000007</td>\n",
       "      <td>pituitary gland</td>\n",
       "      <td>D010902</td>\n",
       "      <td>Pituitary Gland</td>\n",
       "      <td>BTO:0001073</td>\n",
       "      <td>pituitary gland[MeSH Terms:noexp]</td>\n",
       "      <td>50175</td>\n",
       "      <td>226|227|662|1780|2025|2577|2938|3355|3617|4162...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        uberon_id          uberon_name  mesh_id             mesh_name  \\\n",
       "0  UBERON:0000002       uterine cervix  D002584          Cervix Uteri   \n",
       "1  UBERON:0000004                 nose  D009666                  Nose   \n",
       "2  UBERON:0000006  islet of Langerhans  D007515  Islets of Langerhans   \n",
       "3  UBERON:0000016   endocrine pancreas  D007515  Islets of Langerhans   \n",
       "4  UBERON:0000007      pituitary gland  D010902       Pituitary Gland   \n",
       "\n",
       "        bto_id                              term_query  n_articles  \\\n",
       "0  BTO:0001421          cervix uteri[MeSH Terms:noexp]       29638   \n",
       "1  BTO:0000840                  nose[MeSH Terms:noexp]       27243   \n",
       "2  BTO:0000991  islets of langerhans[MeSH Terms:noexp]       38235   \n",
       "3  BTO:0000650  islets of langerhans[MeSH Terms:noexp]       38235   \n",
       "4  BTO:0001073       pituitary gland[MeSH Terms:noexp]       50175   \n",
       "\n",
       "                                          pubmed_ids  \n",
       "0  2135|12122|13010|13018|15040|15694|15911|15912...  \n",
       "1  2067|5220|18131|18962|19546|21298|25090|27057|...  \n",
       "2  1320|1687|2929|4295|4298|6851|9188|9697|11432|...  \n",
       "3  1320|1687|2929|4295|4298|6851|9188|9697|11432|...  \n",
       "4  226|227|662|1780|2025|2577|2938|3355|3617|4162...  "
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "download_dir = '../data/MEDLINE'\n",
    "\n",
    "with gzip.open(os.path.join(download_dir,'uberon-pmids.tsv.gz'),'w') as write_file:\n",
    "    write_file = io.TextIOWrapper(write_file)\n",
    "    uberon_pmids_df.to_csv(write_file, sep='\\t', index=False)\n",
    "               \n",
    "uberon_pmids_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Tissue-Disease Cooccurrence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "download_dir = '../data/MEDLINE'\n",
    "\n",
    "uberon_df, uberon_to_pmids = read_pmids_tsv(os.path.join(download_dir,'uberon-pmids.tsv.gz'), key='uberon_id')\n",
    "disease_df, disease_to_pmids = read_pmids_tsv(os.path.join(download_dir,'disease-pmids.tsv.gz'), key='doid_code')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total articles containing a doid_code: 4906736\n",
      "Total articles containing a uberon_id: 6720887\n",
      "Total articles containing both a doid_code and uberon_id: 980317\n",
      "\n",
      "After removing terms without any cooccurences:\n",
      "+ 121 doid_codes remain\n",
      "+ 554 uberon_ids remain\n",
      "\n",
      "Cooccurrence scores calculated for 67034 doid_code -- uberon_id pairs\n"
     ]
    }
   ],
   "source": [
    "cooc_df = score_pmid_cooccurrence(disease_to_pmids, uberon_to_pmids, 'doid_code', 'uberon_id')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(67034, 11)"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36046</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000955</td>\n",
       "      <td>brain</td>\n",
       "      <td>21745</td>\n",
       "      <td>3071.649615</td>\n",
       "      <td>7.079258</td>\n",
       "      <td>27.695942</td>\n",
       "      <td>0.0</td>\n",
       "      <td>30744</td>\n",
       "      <td>97944</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36047</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000956</td>\n",
       "      <td>cerebral cortex</td>\n",
       "      <td>3590</td>\n",
       "      <td>594.986283</td>\n",
       "      <td>6.033753</td>\n",
       "      <td>8.029408</td>\n",
       "      <td>0.0</td>\n",
       "      <td>30744</td>\n",
       "      <td>18972</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36347</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001870</td>\n",
       "      <td>frontal cortex</td>\n",
       "      <td>1212</td>\n",
       "      <td>274.191707</td>\n",
       "      <td>4.420265</td>\n",
       "      <td>5.133663</td>\n",
       "      <td>0.0</td>\n",
       "      <td>30744</td>\n",
       "      <td>8743</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36348</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001871</td>\n",
       "      <td>temporal lobe</td>\n",
       "      <td>1517</td>\n",
       "      <td>325.749659</td>\n",
       "      <td>4.656950</td>\n",
       "      <td>5.504657</td>\n",
       "      <td>0.0</td>\n",
       "      <td>30744</td>\n",
       "      <td>10387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36535</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002895</td>\n",
       "      <td>secondary olfactory cortex</td>\n",
       "      <td>492</td>\n",
       "      <td>26.029866</td>\n",
       "      <td>18.901365</td>\n",
       "      <td>45.673895</td>\n",
       "      <td>0.0</td>\n",
       "      <td>30744</td>\n",
       "      <td>830</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code            doid_name       uberon_id  \\\n",
       "36046  DOID:10652  Alzheimer's disease  UBERON:0000955   \n",
       "36047  DOID:10652  Alzheimer's disease  UBERON:0000956   \n",
       "36347  DOID:10652  Alzheimer's disease  UBERON:0001870   \n",
       "36348  DOID:10652  Alzheimer's disease  UBERON:0001871   \n",
       "36535  DOID:10652  Alzheimer's disease  UBERON:0002895   \n",
       "\n",
       "                      uberon_name  cooccurrence     expected  enrichment  \\\n",
       "36046                       brain         21745  3071.649615    7.079258   \n",
       "36047             cerebral cortex          3590   594.986283    6.033753   \n",
       "36347              frontal cortex          1212   274.191707    4.420265   \n",
       "36348               temporal lobe          1517   325.749659    4.656950   \n",
       "36535  secondary olfactory cortex           492    26.029866   18.901365   \n",
       "\n",
       "       odds_ratio  p_fisher  n_source  n_target  \n",
       "36046   27.695942       0.0     30744     97944  \n",
       "36047    8.029408       0.0     30744     18972  \n",
       "36347    5.133663       0.0     30744      8743  \n",
       "36348    5.504657       0.0     30744     10387  \n",
       "36535   45.673895       0.0     30744       830  "
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cooc_df = uberon_df[['uberon_id', 'uberon_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = disease_df[['doid_code', 'doid_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = cooc_df.sort_values(by=['doid_name', 'p_fisher'])\n",
    "cooc_df.shape\n",
    "cooc_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "cooc_df.to_csv(os.path.join(download_dir,'disease-uberon-cooccurrence.tsv'), index=False, sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(50, 11)"
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alzkb_dla = cooc_df[(cooc_df['doid_code'].isin(['DOID:10652','DOID:11949']))&(cooc_df['p_fisher']<0.005)&(cooc_df['uberon_id'].isin(uberon_df['uberon_id']))]\n",
    "alzkb_dla.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(29, 9)"
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#compare with previous version\n",
    "dla_hetionet = pandas.read_table('https://raw.githubusercontent.com/dhimmel/medline/gh-pages/data/disease-uberon-cooccurrence.tsv') \n",
    "dla_hetionet = dla_hetionet[dla_hetionet['doid_code'].isin(['DOID:10652','DOID:11949'])]\n",
    "dla_hetionet = dla_hetionet[dla_hetionet.p_fisher < 0.005]\n",
    "dla_hetionet.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36046</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000955</td>\n",
       "      <td>brain</td>\n",
       "      <td>21745</td>\n",
       "      <td>3071.649615</td>\n",
       "      <td>7.079258</td>\n",
       "      <td>27.695942</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30744</td>\n",
       "      <td>97944</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36047</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000956</td>\n",
       "      <td>cerebral cortex</td>\n",
       "      <td>3590</td>\n",
       "      <td>594.986283</td>\n",
       "      <td>6.033753</td>\n",
       "      <td>8.029408</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30744</td>\n",
       "      <td>18972</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36347</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001870</td>\n",
       "      <td>frontal cortex</td>\n",
       "      <td>1212</td>\n",
       "      <td>274.191707</td>\n",
       "      <td>4.420265</td>\n",
       "      <td>5.133663</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30744</td>\n",
       "      <td>8743</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36348</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001871</td>\n",
       "      <td>temporal lobe</td>\n",
       "      <td>1517</td>\n",
       "      <td>325.749659</td>\n",
       "      <td>4.656950</td>\n",
       "      <td>5.504657</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30744</td>\n",
       "      <td>10387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36535</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002895</td>\n",
       "      <td>secondary olfactory cortex</td>\n",
       "      <td>492</td>\n",
       "      <td>26.029866</td>\n",
       "      <td>18.901365</td>\n",
       "      <td>45.673895</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>30744</td>\n",
       "      <td>830</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36439</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002316</td>\n",
       "      <td>white matter</td>\n",
       "      <td>655</td>\n",
       "      <td>130.306136</td>\n",
       "      <td>5.026624</td>\n",
       "      <td>5.884237</td>\n",
       "      <td>1.900170e-251</td>\n",
       "      <td>30744</td>\n",
       "      <td>4155</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36349</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001872</td>\n",
       "      <td>parietal lobe</td>\n",
       "      <td>533</td>\n",
       "      <td>104.997579</td>\n",
       "      <td>5.076308</td>\n",
       "      <td>5.933660</td>\n",
       "      <td>9.777043e-207</td>\n",
       "      <td>30744</td>\n",
       "      <td>3348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36543</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0003017</td>\n",
       "      <td>substantia innominata</td>\n",
       "      <td>139</td>\n",
       "      <td>5.300057</td>\n",
       "      <td>26.226133</td>\n",
       "      <td>143.752630</td>\n",
       "      <td>4.794031e-177</td>\n",
       "      <td>30744</td>\n",
       "      <td>169</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36400</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002148</td>\n",
       "      <td>locus ceruleus</td>\n",
       "      <td>204</td>\n",
       "      <td>19.161745</td>\n",
       "      <td>10.646212</td>\n",
       "      <td>15.577900</td>\n",
       "      <td>8.877886e-146</td>\n",
       "      <td>30744</td>\n",
       "      <td>611</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36358</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001885</td>\n",
       "      <td>dentate gyrus of hippocampal formation</td>\n",
       "      <td>219</td>\n",
       "      <td>31.518091</td>\n",
       "      <td>6.948390</td>\n",
       "      <td>8.660334</td>\n",
       "      <td>8.555847e-114</td>\n",
       "      <td>30744</td>\n",
       "      <td>1005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36361</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001890</td>\n",
       "      <td>forebrain</td>\n",
       "      <td>140</td>\n",
       "      <td>13.297184</td>\n",
       "      <td>10.528545</td>\n",
       "      <td>15.290791</td>\n",
       "      <td>7.857538e-100</td>\n",
       "      <td>30744</td>\n",
       "      <td>424</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36428</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002264</td>\n",
       "      <td>olfactory bulb</td>\n",
       "      <td>139</td>\n",
       "      <td>16.558758</td>\n",
       "      <td>8.394349</td>\n",
       "      <td>11.082130</td>\n",
       "      <td>2.111415e-84</td>\n",
       "      <td>30744</td>\n",
       "      <td>528</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36536</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002743</td>\n",
       "      <td>basal forebrain</td>\n",
       "      <td>77</td>\n",
       "      <td>3.826077</td>\n",
       "      <td>20.125054</td>\n",
       "      <td>52.980334</td>\n",
       "      <td>2.108781e-83</td>\n",
       "      <td>30744</td>\n",
       "      <td>122</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36541</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002967</td>\n",
       "      <td>cingulate gyrus</td>\n",
       "      <td>290</td>\n",
       "      <td>87.780234</td>\n",
       "      <td>3.303705</td>\n",
       "      <td>3.594449</td>\n",
       "      <td>1.545982e-68</td>\n",
       "      <td>30744</td>\n",
       "      <td>2799</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36083</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001017</td>\n",
       "      <td>central nervous system</td>\n",
       "      <td>336</td>\n",
       "      <td>144.105101</td>\n",
       "      <td>2.331632</td>\n",
       "      <td>2.452561</td>\n",
       "      <td>1.969408e-44</td>\n",
       "      <td>30744</td>\n",
       "      <td>4595</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36016</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000011</td>\n",
       "      <td>parasympathetic nervous system</td>\n",
       "      <td>108</td>\n",
       "      <td>23.583686</td>\n",
       "      <td>4.579437</td>\n",
       "      <td>5.194450</td>\n",
       "      <td>5.497682e-39</td>\n",
       "      <td>30744</td>\n",
       "      <td>752</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36353</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001876</td>\n",
       "      <td>amygdala</td>\n",
       "      <td>262</td>\n",
       "      <td>112.273397</td>\n",
       "      <td>2.333589</td>\n",
       "      <td>2.451261</td>\n",
       "      <td>4.465622e-35</td>\n",
       "      <td>30744</td>\n",
       "      <td>3580</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36525</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002606</td>\n",
       "      <td>neuropil</td>\n",
       "      <td>42</td>\n",
       "      <td>4.955083</td>\n",
       "      <td>8.476145</td>\n",
       "      <td>11.196955</td>\n",
       "      <td>7.290708e-27</td>\n",
       "      <td>30744</td>\n",
       "      <td>158</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36391</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002129</td>\n",
       "      <td>cerebellar cortex</td>\n",
       "      <td>53</td>\n",
       "      <td>10.882366</td>\n",
       "      <td>4.870265</td>\n",
       "      <td>5.575854</td>\n",
       "      <td>3.156373e-21</td>\n",
       "      <td>30744</td>\n",
       "      <td>347</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36177</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001359</td>\n",
       "      <td>cerebrospinal fluid</td>\n",
       "      <td>154</td>\n",
       "      <td>71.911425</td>\n",
       "      <td>2.141523</td>\n",
       "      <td>2.229869</td>\n",
       "      <td>6.029588e-18</td>\n",
       "      <td>30744</td>\n",
       "      <td>2293</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36035</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000922</td>\n",
       "      <td>embryo</td>\n",
       "      <td>94</td>\n",
       "      <td>40.581502</td>\n",
       "      <td>2.316326</td>\n",
       "      <td>2.423792</td>\n",
       "      <td>1.747443e-13</td>\n",
       "      <td>30744</td>\n",
       "      <td>1294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36359</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001886</td>\n",
       "      <td>choroid plexus</td>\n",
       "      <td>77</td>\n",
       "      <td>30.295000</td>\n",
       "      <td>2.541674</td>\n",
       "      <td>2.679410</td>\n",
       "      <td>2.704534e-13</td>\n",
       "      <td>30744</td>\n",
       "      <td>966</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36350</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001873</td>\n",
       "      <td>caudate nucleus</td>\n",
       "      <td>98</td>\n",
       "      <td>46.101088</td>\n",
       "      <td>2.125763</td>\n",
       "      <td>2.210032</td>\n",
       "      <td>7.639637e-12</td>\n",
       "      <td>30744</td>\n",
       "      <td>1470</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36444</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002336</td>\n",
       "      <td>corpus callosum</td>\n",
       "      <td>155</td>\n",
       "      <td>86.651228</td>\n",
       "      <td>1.788780</td>\n",
       "      <td>1.839894</td>\n",
       "      <td>9.401869e-12</td>\n",
       "      <td>30744</td>\n",
       "      <td>2763</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36351</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001874</td>\n",
       "      <td>putamen</td>\n",
       "      <td>84</td>\n",
       "      <td>38.041238</td>\n",
       "      <td>2.208130</td>\n",
       "      <td>2.301574</td>\n",
       "      <td>3.514023e-11</td>\n",
       "      <td>30744</td>\n",
       "      <td>1213</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36414</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002206</td>\n",
       "      <td>mammillary body</td>\n",
       "      <td>15</td>\n",
       "      <td>2.571625</td>\n",
       "      <td>5.832887</td>\n",
       "      <td>6.917764</td>\n",
       "      <td>3.791430e-08</td>\n",
       "      <td>30744</td>\n",
       "      <td>82</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36432</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002285</td>\n",
       "      <td>telencephalic ventricle</td>\n",
       "      <td>50</td>\n",
       "      <td>21.952899</td>\n",
       "      <td>2.277604</td>\n",
       "      <td>2.378122</td>\n",
       "      <td>1.094974e-07</td>\n",
       "      <td>30744</td>\n",
       "      <td>700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36374</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001908</td>\n",
       "      <td>optic tract</td>\n",
       "      <td>66</td>\n",
       "      <td>34.152438</td>\n",
       "      <td>1.932512</td>\n",
       "      <td>1.994810</td>\n",
       "      <td>5.286643e-07</td>\n",
       "      <td>30744</td>\n",
       "      <td>1089</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36363</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001893</td>\n",
       "      <td>telencephalon</td>\n",
       "      <td>23</td>\n",
       "      <td>7.024928</td>\n",
       "      <td>3.274055</td>\n",
       "      <td>3.536168</td>\n",
       "      <td>8.017514e-07</td>\n",
       "      <td>30744</td>\n",
       "      <td>224</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36082</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001016</td>\n",
       "      <td>nervous system</td>\n",
       "      <td>76</td>\n",
       "      <td>44.438940</td>\n",
       "      <td>1.710212</td>\n",
       "      <td>1.752322</td>\n",
       "      <td>7.118732e-06</td>\n",
       "      <td>30744</td>\n",
       "      <td>1417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36220</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001579</td>\n",
       "      <td>olfactory nerve</td>\n",
       "      <td>14</td>\n",
       "      <td>4.421941</td>\n",
       "      <td>3.166030</td>\n",
       "      <td>3.405901</td>\n",
       "      <td>1.533381e-04</td>\n",
       "      <td>30744</td>\n",
       "      <td>141</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36533</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002704</td>\n",
       "      <td>metathalamus</td>\n",
       "      <td>14</td>\n",
       "      <td>5.864560</td>\n",
       "      <td>2.387221</td>\n",
       "      <td>2.500165</td>\n",
       "      <td>2.500189e-03</td>\n",
       "      <td>30744</td>\n",
       "      <td>187</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36182</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001393</td>\n",
       "      <td>auditory cortex</td>\n",
       "      <td>25</td>\n",
       "      <td>13.987133</td>\n",
       "      <td>1.787357</td>\n",
       "      <td>1.834791</td>\n",
       "      <td>4.306279e-03</td>\n",
       "      <td>30744</td>\n",
       "      <td>446</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48234</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0000955</td>\n",
       "      <td>brain</td>\n",
       "      <td>1370</td>\n",
       "      <td>199.221615</td>\n",
       "      <td>6.876764</td>\n",
       "      <td>20.045677</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>1994</td>\n",
       "      <td>97944</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48235</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0000956</td>\n",
       "      <td>cerebral cortex</td>\n",
       "      <td>288</td>\n",
       "      <td>38.589730</td>\n",
       "      <td>7.463126</td>\n",
       "      <td>8.670647</td>\n",
       "      <td>2.660713e-153</td>\n",
       "      <td>1994</td>\n",
       "      <td>18972</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48646</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002363</td>\n",
       "      <td>dura mater</td>\n",
       "      <td>106</td>\n",
       "      <td>4.289782</td>\n",
       "      <td>24.709882</td>\n",
       "      <td>27.366239</td>\n",
       "      <td>8.296144e-108</td>\n",
       "      <td>1994</td>\n",
       "      <td>2109</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48655</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002372</td>\n",
       "      <td>tonsil</td>\n",
       "      <td>45</td>\n",
       "      <td>2.453047</td>\n",
       "      <td>18.344530</td>\n",
       "      <td>19.432784</td>\n",
       "      <td>7.933935e-41</td>\n",
       "      <td>1994</td>\n",
       "      <td>1206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48656</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002373</td>\n",
       "      <td>palatine tonsil</td>\n",
       "      <td>45</td>\n",
       "      <td>2.453047</td>\n",
       "      <td>18.344530</td>\n",
       "      <td>19.432784</td>\n",
       "      <td>7.933935e-41</td>\n",
       "      <td>1994</td>\n",
       "      <td>1206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48579</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002129</td>\n",
       "      <td>cerebellar cortex</td>\n",
       "      <td>29</td>\n",
       "      <td>0.705810</td>\n",
       "      <td>41.087518</td>\n",
       "      <td>45.388873</td>\n",
       "      <td>6.113355e-37</td>\n",
       "      <td>1994</td>\n",
       "      <td>347</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48730</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002981</td>\n",
       "      <td>pulvinar nucleus</td>\n",
       "      <td>19</td>\n",
       "      <td>0.146451</td>\n",
       "      <td>129.736592</td>\n",
       "      <td>177.569907</td>\n",
       "      <td>7.053657e-35</td>\n",
       "      <td>1994</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48538</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001873</td>\n",
       "      <td>caudate nucleus</td>\n",
       "      <td>27</td>\n",
       "      <td>2.990033</td>\n",
       "      <td>9.030001</td>\n",
       "      <td>9.292537</td>\n",
       "      <td>2.588297e-17</td>\n",
       "      <td>1994</td>\n",
       "      <td>1470</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48535</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001870</td>\n",
       "      <td>frontal cortex</td>\n",
       "      <td>60</td>\n",
       "      <td>17.783576</td>\n",
       "      <td>3.373900</td>\n",
       "      <td>3.464460</td>\n",
       "      <td>1.851998e-15</td>\n",
       "      <td>1994</td>\n",
       "      <td>8743</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48481</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001744</td>\n",
       "      <td>lymphoid tissue</td>\n",
       "      <td>20</td>\n",
       "      <td>2.396094</td>\n",
       "      <td>8.346917</td>\n",
       "      <td>8.549529</td>\n",
       "      <td>1.345051e-12</td>\n",
       "      <td>1994</td>\n",
       "      <td>1178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48539</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001874</td>\n",
       "      <td>putamen</td>\n",
       "      <td>20</td>\n",
       "      <td>2.467286</td>\n",
       "      <td>8.106074</td>\n",
       "      <td>8.298407</td>\n",
       "      <td>2.270103e-12</td>\n",
       "      <td>1994</td>\n",
       "      <td>1213</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48309</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001154</td>\n",
       "      <td>vermiform appendix</td>\n",
       "      <td>20</td>\n",
       "      <td>2.599498</td>\n",
       "      <td>7.693793</td>\n",
       "      <td>7.869111</td>\n",
       "      <td>5.741311e-12</td>\n",
       "      <td>1994</td>\n",
       "      <td>1278</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48611</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002240</td>\n",
       "      <td>spinal cord</td>\n",
       "      <td>48</td>\n",
       "      <td>15.127125</td>\n",
       "      <td>3.173108</td>\n",
       "      <td>3.241175</td>\n",
       "      <td>9.440405e-12</td>\n",
       "      <td>1994</td>\n",
       "      <td>7437</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48365</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001359</td>\n",
       "      <td>cerebrospinal fluid</td>\n",
       "      <td>23</td>\n",
       "      <td>4.664044</td>\n",
       "      <td>4.931342</td>\n",
       "      <td>5.017516</td>\n",
       "      <td>9.341246e-10</td>\n",
       "      <td>1994</td>\n",
       "      <td>2293</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48271</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001017</td>\n",
       "      <td>central nervous system</td>\n",
       "      <td>25</td>\n",
       "      <td>9.346395</td>\n",
       "      <td>2.674828</td>\n",
       "      <td>2.705371</td>\n",
       "      <td>1.472084e-05</td>\n",
       "      <td>1994</td>\n",
       "      <td>4595</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48624</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002298</td>\n",
       "      <td>brainstem</td>\n",
       "      <td>24</td>\n",
       "      <td>9.191808</td>\n",
       "      <td>2.611020</td>\n",
       "      <td>2.639354</td>\n",
       "      <td>3.143547e-05</td>\n",
       "      <td>1994</td>\n",
       "      <td>4519</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48569</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002106</td>\n",
       "      <td>spleen</td>\n",
       "      <td>33</td>\n",
       "      <td>19.268422</td>\n",
       "      <td>1.712647</td>\n",
       "      <td>1.727172</td>\n",
       "      <td>2.592825e-03</td>\n",
       "      <td>1994</td>\n",
       "      <td>9473</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code                  doid_name       uberon_id  \\\n",
       "36046  DOID:10652        Alzheimer's disease  UBERON:0000955   \n",
       "36047  DOID:10652        Alzheimer's disease  UBERON:0000956   \n",
       "36347  DOID:10652        Alzheimer's disease  UBERON:0001870   \n",
       "36348  DOID:10652        Alzheimer's disease  UBERON:0001871   \n",
       "36535  DOID:10652        Alzheimer's disease  UBERON:0002895   \n",
       "36439  DOID:10652        Alzheimer's disease  UBERON:0002316   \n",
       "36349  DOID:10652        Alzheimer's disease  UBERON:0001872   \n",
       "36543  DOID:10652        Alzheimer's disease  UBERON:0003017   \n",
       "36400  DOID:10652        Alzheimer's disease  UBERON:0002148   \n",
       "36358  DOID:10652        Alzheimer's disease  UBERON:0001885   \n",
       "36361  DOID:10652        Alzheimer's disease  UBERON:0001890   \n",
       "36428  DOID:10652        Alzheimer's disease  UBERON:0002264   \n",
       "36536  DOID:10652        Alzheimer's disease  UBERON:0002743   \n",
       "36541  DOID:10652        Alzheimer's disease  UBERON:0002967   \n",
       "36083  DOID:10652        Alzheimer's disease  UBERON:0001017   \n",
       "36016  DOID:10652        Alzheimer's disease  UBERON:0000011   \n",
       "36353  DOID:10652        Alzheimer's disease  UBERON:0001876   \n",
       "36525  DOID:10652        Alzheimer's disease  UBERON:0002606   \n",
       "36391  DOID:10652        Alzheimer's disease  UBERON:0002129   \n",
       "36177  DOID:10652        Alzheimer's disease  UBERON:0001359   \n",
       "36035  DOID:10652        Alzheimer's disease  UBERON:0000922   \n",
       "36359  DOID:10652        Alzheimer's disease  UBERON:0001886   \n",
       "36350  DOID:10652        Alzheimer's disease  UBERON:0001873   \n",
       "36444  DOID:10652        Alzheimer's disease  UBERON:0002336   \n",
       "36351  DOID:10652        Alzheimer's disease  UBERON:0001874   \n",
       "36414  DOID:10652        Alzheimer's disease  UBERON:0002206   \n",
       "36432  DOID:10652        Alzheimer's disease  UBERON:0002285   \n",
       "36374  DOID:10652        Alzheimer's disease  UBERON:0001908   \n",
       "36363  DOID:10652        Alzheimer's disease  UBERON:0001893   \n",
       "36082  DOID:10652        Alzheimer's disease  UBERON:0001016   \n",
       "36220  DOID:10652        Alzheimer's disease  UBERON:0001579   \n",
       "36533  DOID:10652        Alzheimer's disease  UBERON:0002704   \n",
       "36182  DOID:10652        Alzheimer's disease  UBERON:0001393   \n",
       "48234  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0000955   \n",
       "48235  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0000956   \n",
       "48646  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002363   \n",
       "48655  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002372   \n",
       "48656  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002373   \n",
       "48579  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002129   \n",
       "48730  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002981   \n",
       "48538  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001873   \n",
       "48535  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001870   \n",
       "48481  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001744   \n",
       "48539  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001874   \n",
       "48309  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001154   \n",
       "48611  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002240   \n",
       "48365  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001359   \n",
       "48271  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001017   \n",
       "48624  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002298   \n",
       "48569  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002106   \n",
       "\n",
       "                                  uberon_name  cooccurrence     expected  \\\n",
       "36046                                   brain         21745  3071.649615   \n",
       "36047                         cerebral cortex          3590   594.986283   \n",
       "36347                          frontal cortex          1212   274.191707   \n",
       "36348                           temporal lobe          1517   325.749659   \n",
       "36535              secondary olfactory cortex           492    26.029866   \n",
       "36439                            white matter           655   130.306136   \n",
       "36349                           parietal lobe           533   104.997579   \n",
       "36543                   substantia innominata           139     5.300057   \n",
       "36400                          locus ceruleus           204    19.161745   \n",
       "36358  dentate gyrus of hippocampal formation           219    31.518091   \n",
       "36361                               forebrain           140    13.297184   \n",
       "36428                          olfactory bulb           139    16.558758   \n",
       "36536                         basal forebrain            77     3.826077   \n",
       "36541                         cingulate gyrus           290    87.780234   \n",
       "36083                  central nervous system           336   144.105101   \n",
       "36016          parasympathetic nervous system           108    23.583686   \n",
       "36353                                amygdala           262   112.273397   \n",
       "36525                                neuropil            42     4.955083   \n",
       "36391                       cerebellar cortex            53    10.882366   \n",
       "36177                     cerebrospinal fluid           154    71.911425   \n",
       "36035                                  embryo            94    40.581502   \n",
       "36359                          choroid plexus            77    30.295000   \n",
       "36350                         caudate nucleus            98    46.101088   \n",
       "36444                         corpus callosum           155    86.651228   \n",
       "36351                                 putamen            84    38.041238   \n",
       "36414                         mammillary body            15     2.571625   \n",
       "36432                 telencephalic ventricle            50    21.952899   \n",
       "36374                             optic tract            66    34.152438   \n",
       "36363                           telencephalon            23     7.024928   \n",
       "36082                          nervous system            76    44.438940   \n",
       "36220                         olfactory nerve            14     4.421941   \n",
       "36533                            metathalamus            14     5.864560   \n",
       "36182                         auditory cortex            25    13.987133   \n",
       "48234                                   brain          1370   199.221615   \n",
       "48235                         cerebral cortex           288    38.589730   \n",
       "48646                              dura mater           106     4.289782   \n",
       "48655                                  tonsil            45     2.453047   \n",
       "48656                         palatine tonsil            45     2.453047   \n",
       "48579                       cerebellar cortex            29     0.705810   \n",
       "48730                        pulvinar nucleus            19     0.146451   \n",
       "48538                         caudate nucleus            27     2.990033   \n",
       "48535                          frontal cortex            60    17.783576   \n",
       "48481                         lymphoid tissue            20     2.396094   \n",
       "48539                                 putamen            20     2.467286   \n",
       "48309                      vermiform appendix            20     2.599498   \n",
       "48611                             spinal cord            48    15.127125   \n",
       "48365                     cerebrospinal fluid            23     4.664044   \n",
       "48271                  central nervous system            25     9.346395   \n",
       "48624                               brainstem            24     9.191808   \n",
       "48569                                  spleen            33    19.268422   \n",
       "\n",
       "       enrichment  odds_ratio       p_fisher  n_source  n_target  \n",
       "36046    7.079258   27.695942   0.000000e+00     30744     97944  \n",
       "36047    6.033753    8.029408   0.000000e+00     30744     18972  \n",
       "36347    4.420265    5.133663   0.000000e+00     30744      8743  \n",
       "36348    4.656950    5.504657   0.000000e+00     30744     10387  \n",
       "36535   18.901365   45.673895   0.000000e+00     30744       830  \n",
       "36439    5.026624    5.884237  1.900170e-251     30744      4155  \n",
       "36349    5.076308    5.933660  9.777043e-207     30744      3348  \n",
       "36543   26.226133  143.752630  4.794031e-177     30744       169  \n",
       "36400   10.646212   15.577900  8.877886e-146     30744       611  \n",
       "36358    6.948390    8.660334  8.555847e-114     30744      1005  \n",
       "36361   10.528545   15.290791  7.857538e-100     30744       424  \n",
       "36428    8.394349   11.082130   2.111415e-84     30744       528  \n",
       "36536   20.125054   52.980334   2.108781e-83     30744       122  \n",
       "36541    3.303705    3.594449   1.545982e-68     30744      2799  \n",
       "36083    2.331632    2.452561   1.969408e-44     30744      4595  \n",
       "36016    4.579437    5.194450   5.497682e-39     30744       752  \n",
       "36353    2.333589    2.451261   4.465622e-35     30744      3580  \n",
       "36525    8.476145   11.196955   7.290708e-27     30744       158  \n",
       "36391    4.870265    5.575854   3.156373e-21     30744       347  \n",
       "36177    2.141523    2.229869   6.029588e-18     30744      2293  \n",
       "36035    2.316326    2.423792   1.747443e-13     30744      1294  \n",
       "36359    2.541674    2.679410   2.704534e-13     30744       966  \n",
       "36350    2.125763    2.210032   7.639637e-12     30744      1470  \n",
       "36444    1.788780    1.839894   9.401869e-12     30744      2763  \n",
       "36351    2.208130    2.301574   3.514023e-11     30744      1213  \n",
       "36414    5.832887    6.917764   3.791430e-08     30744        82  \n",
       "36432    2.277604    2.378122   1.094974e-07     30744       700  \n",
       "36374    1.932512    1.994810   5.286643e-07     30744      1089  \n",
       "36363    3.274055    3.536168   8.017514e-07     30744       224  \n",
       "36082    1.710212    1.752322   7.118732e-06     30744      1417  \n",
       "36220    3.166030    3.405901   1.533381e-04     30744       141  \n",
       "36533    2.387221    2.500165   2.500189e-03     30744       187  \n",
       "36182    1.787357    1.834791   4.306279e-03     30744       446  \n",
       "48234    6.876764   20.045677   0.000000e+00      1994     97944  \n",
       "48235    7.463126    8.670647  2.660713e-153      1994     18972  \n",
       "48646   24.709882   27.366239  8.296144e-108      1994      2109  \n",
       "48655   18.344530   19.432784   7.933935e-41      1994      1206  \n",
       "48656   18.344530   19.432784   7.933935e-41      1994      1206  \n",
       "48579   41.087518   45.388873   6.113355e-37      1994       347  \n",
       "48730  129.736592  177.569907   7.053657e-35      1994        72  \n",
       "48538    9.030001    9.292537   2.588297e-17      1994      1470  \n",
       "48535    3.373900    3.464460   1.851998e-15      1994      8743  \n",
       "48481    8.346917    8.549529   1.345051e-12      1994      1178  \n",
       "48539    8.106074    8.298407   2.270103e-12      1994      1213  \n",
       "48309    7.693793    7.869111   5.741311e-12      1994      1278  \n",
       "48611    3.173108    3.241175   9.440405e-12      1994      7437  \n",
       "48365    4.931342    5.017516   9.341246e-10      1994      2293  \n",
       "48271    2.674828    2.705371   1.472084e-05      1994      4595  \n",
       "48624    2.611020    2.639354   3.143547e-05      1994      4519  \n",
       "48569    1.712647    1.727172   2.592825e-03      1994      9473  "
      ]
     },
     "execution_count": 63,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alzkb_dla"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['both', 'left_only', 'right_only']\n",
       "Categories (3, object): ['left_only', 'right_only', 'both']"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "check4 = dla_hetionet.merge(alzkb_dla, on=['doid_code','uberon_id'], how='outer', indicator=True)\n",
    "check4['_merge'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "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>doid_code</th>\n",
       "      <th>doid_name_x</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name_x</th>\n",
       "      <th>cooccurrence_x</th>\n",
       "      <th>expected_x</th>\n",
       "      <th>enrichment_x</th>\n",
       "      <th>odds_ratio_x</th>\n",
       "      <th>p_fisher_x</th>\n",
       "      <th>doid_name_y</th>\n",
       "      <th>uberon_name_y</th>\n",
       "      <th>cooccurrence_y</th>\n",
       "      <th>expected_y</th>\n",
       "      <th>enrichment_y</th>\n",
       "      <th>odds_ratio_y</th>\n",
       "      <th>p_fisher_y</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "      <th>_merge</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002037</td>\n",
       "      <td>cerebellum</td>\n",
       "      <td>303.0</td>\n",
       "      <td>86.548368</td>\n",
       "      <td>3.500933</td>\n",
       "      <td>3.740149</td>\n",
       "      <td>3.504584e-76</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002707</td>\n",
       "      <td>corticospinal tract</td>\n",
       "      <td>47.0</td>\n",
       "      <td>14.146789</td>\n",
       "      <td>3.322309</td>\n",
       "      <td>3.485427</td>\n",
       "      <td>2.195121e-12</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002741</td>\n",
       "      <td>diagonal band of Broca</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.149900</td>\n",
       "      <td>33.355626</td>\n",
       "      <td>87.314751</td>\n",
       "      <td>1.232902e-07</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001981</td>\n",
       "      <td>blood vessel</td>\n",
       "      <td>120.0</td>\n",
       "      <td>72.944965</td>\n",
       "      <td>1.645076</td>\n",
       "      <td>1.671772</td>\n",
       "      <td>1.916178e-07</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001771</td>\n",
       "      <td>pupil</td>\n",
       "      <td>41.0</td>\n",
       "      <td>23.721635</td>\n",
       "      <td>1.728380</td>\n",
       "      <td>1.755132</td>\n",
       "      <td>6.975371e-04</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002130</td>\n",
       "      <td>cerebellar nuclear complex</td>\n",
       "      <td>9.0</td>\n",
       "      <td>3.035470</td>\n",
       "      <td>2.964945</td>\n",
       "      <td>3.081966</td>\n",
       "      <td>3.702878e-03</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0002037</td>\n",
       "      <td>cerebellum</td>\n",
       "      <td>101.0</td>\n",
       "      <td>9.042268</td>\n",
       "      <td>11.169764</td>\n",
       "      <td>12.229208</td>\n",
       "      <td>8.895081e-70</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>DOID:11949</td>\n",
       "      <td>Creutzfeldt-Jakob disease</td>\n",
       "      <td>UBERON:0001969</td>\n",
       "      <td>blood plasma</td>\n",
       "      <td>16.0</td>\n",
       "      <td>2.266929</td>\n",
       "      <td>7.058006</td>\n",
       "      <td>7.215848</td>\n",
       "      <td>2.408667e-09</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code                doid_name_x       uberon_id  \\\n",
       "2   DOID:10652        Alzheimer's disease  UBERON:0002037   \n",
       "9   DOID:10652        Alzheimer's disease  UBERON:0002707   \n",
       "14  DOID:10652        Alzheimer's disease  UBERON:0002741   \n",
       "15  DOID:10652        Alzheimer's disease  UBERON:0001981   \n",
       "18  DOID:10652        Alzheimer's disease  UBERON:0001771   \n",
       "19  DOID:10652        Alzheimer's disease  UBERON:0002130   \n",
       "22  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0002037   \n",
       "26  DOID:11949  Creutzfeldt-Jakob disease  UBERON:0001969   \n",
       "\n",
       "                 uberon_name_x  cooccurrence_x  expected_x  enrichment_x  \\\n",
       "2                   cerebellum           303.0   86.548368      3.500933   \n",
       "9          corticospinal tract            47.0   14.146789      3.322309   \n",
       "14      diagonal band of Broca             5.0    0.149900     33.355626   \n",
       "15                blood vessel           120.0   72.944965      1.645076   \n",
       "18                       pupil            41.0   23.721635      1.728380   \n",
       "19  cerebellar nuclear complex             9.0    3.035470      2.964945   \n",
       "22                  cerebellum           101.0    9.042268     11.169764   \n",
       "26                blood plasma            16.0    2.266929      7.058006   \n",
       "\n",
       "    odds_ratio_x    p_fisher_x doid_name_y uberon_name_y  cooccurrence_y  \\\n",
       "2       3.740149  3.504584e-76         NaN           NaN             NaN   \n",
       "9       3.485427  2.195121e-12         NaN           NaN             NaN   \n",
       "14     87.314751  1.232902e-07         NaN           NaN             NaN   \n",
       "15      1.671772  1.916178e-07         NaN           NaN             NaN   \n",
       "18      1.755132  6.975371e-04         NaN           NaN             NaN   \n",
       "19      3.081966  3.702878e-03         NaN           NaN             NaN   \n",
       "22     12.229208  8.895081e-70         NaN           NaN             NaN   \n",
       "26      7.215848  2.408667e-09         NaN           NaN             NaN   \n",
       "\n",
       "    expected_y  enrichment_y  odds_ratio_y  p_fisher_y  n_source  n_target  \\\n",
       "2          NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "9          NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "14         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "15         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "18         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "19         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "22         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "26         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "\n",
       "       _merge  \n",
       "2   left_only  \n",
       "9   left_only  \n",
       "14  left_only  \n",
       "15  left_only  \n",
       "18  left_only  \n",
       "19  left_only  \n",
       "22  left_only  \n",
       "26  left_only  "
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "check4[(check4['_merge']=='left_only')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "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>doid_code</th>\n",
       "      <th>doid_name_x</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name_x</th>\n",
       "      <th>cooccurrence_x</th>\n",
       "      <th>expected_x</th>\n",
       "      <th>enrichment_x</th>\n",
       "      <th>odds_ratio_x</th>\n",
       "      <th>p_fisher_x</th>\n",
       "      <th>doid_name_y</th>\n",
       "      <th>uberon_name_y</th>\n",
       "      <th>cooccurrence_y</th>\n",
       "      <th>expected_y</th>\n",
       "      <th>enrichment_y</th>\n",
       "      <th>odds_ratio_y</th>\n",
       "      <th>p_fisher_y</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "      <th>_merge</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001771</td>\n",
       "      <td>pupil</td>\n",
       "      <td>41.0</td>\n",
       "      <td>23.721635</td>\n",
       "      <td>1.728380</td>\n",
       "      <td>1.755132</td>\n",
       "      <td>0.000698</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002130</td>\n",
       "      <td>cerebellar nuclear complex</td>\n",
       "      <td>9.0</td>\n",
       "      <td>3.035470</td>\n",
       "      <td>2.964945</td>\n",
       "      <td>3.081966</td>\n",
       "      <td>0.003703</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>left_only</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     doid_code          doid_name_x       uberon_id  \\\n",
       "18  DOID:10652  Alzheimer's disease  UBERON:0001771   \n",
       "19  DOID:10652  Alzheimer's disease  UBERON:0002130   \n",
       "\n",
       "                 uberon_name_x  cooccurrence_x  expected_x  enrichment_x  \\\n",
       "18                       pupil            41.0   23.721635      1.728380   \n",
       "19  cerebellar nuclear complex             9.0    3.035470      2.964945   \n",
       "\n",
       "    odds_ratio_x  p_fisher_x doid_name_y uberon_name_y  cooccurrence_y  \\\n",
       "18      1.755132    0.000698         NaN           NaN             NaN   \n",
       "19      3.081966    0.003703         NaN           NaN             NaN   \n",
       "\n",
       "    expected_y  enrichment_y  odds_ratio_y  p_fisher_y  n_source  n_target  \\\n",
       "18         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "19         NaN           NaN           NaN         NaN       NaN       NaN   \n",
       "\n",
       "       _merge  \n",
       "18  left_only  \n",
       "19  left_only  "
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# urberon id does not exists in new version\n",
    "check4[(check4['_merge']=='left_only')&(check4['uberon_id'].isin(uberon_df['uberon_id']))]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "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>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "      <th>n_source</th>\n",
       "      <th>n_target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36392</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002130</td>\n",
       "      <td>cerebellar nuclear complex</td>\n",
       "      <td>11</td>\n",
       "      <td>6.836760</td>\n",
       "      <td>1.608949</td>\n",
       "      <td>1.641538</td>\n",
       "      <td>0.083991</td>\n",
       "      <td>30744</td>\n",
       "      <td>218</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36306</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001771</td>\n",
       "      <td>pupil</td>\n",
       "      <td>50</td>\n",
       "      <td>51.463867</td>\n",
       "      <td>0.971555</td>\n",
       "      <td>0.970614</td>\n",
       "      <td>0.601737</td>\n",
       "      <td>30744</td>\n",
       "      <td>1641</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code            doid_name       uberon_id  \\\n",
       "36392  DOID:10652  Alzheimer's disease  UBERON:0002130   \n",
       "36306  DOID:10652  Alzheimer's disease  UBERON:0001771   \n",
       "\n",
       "                      uberon_name  cooccurrence   expected  enrichment  \\\n",
       "36392  cerebellar nuclear complex            11   6.836760    1.608949   \n",
       "36306                       pupil            50  51.463867    0.971555   \n",
       "\n",
       "       odds_ratio  p_fisher  n_source  n_target  \n",
       "36392    1.641538  0.083991     30744       218  \n",
       "36306    0.970614  0.601737     30744      1641  "
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# p value larger than 0.005\n",
    "cooc_df[((cooc_df['doid_code']=='DOID:10652')&cooc_df['uberon_id'].isin(['UBERON:0001771','UBERON:0002130']))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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