parse_ICD10_xml_file.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Parse ICD10 codes from CMS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>name</th>\n",
       "      <th>load_ts</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A00</td>\n",
       "      <td>Cholera</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>A000</td>\n",
       "      <td>Cholera due to Vibrio cholerae 01, biovar chol...</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>A001</td>\n",
       "      <td>Cholera due to Vibrio cholerae 01, biovar eltor</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A009</td>\n",
       "      <td>Cholera, unspecified</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>A01</td>\n",
       "      <td>Typhoid and paratyphoid fevers</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>A010</td>\n",
       "      <td>Typhoid fever</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>A0100</td>\n",
       "      <td>Typhoid fever, unspecified</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>A0101</td>\n",
       "      <td>Typhoid meningitis</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>A0102</td>\n",
       "      <td>Typhoid fever with heart involvement</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>A0103</td>\n",
       "      <td>Typhoid pneumonia</td>\n",
       "      <td>2024-02-05 18:04:48.377417+00:00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "     code                                               name  \\\n",
       "0     A00                                            Cholera   \n",
       "1    A000  Cholera due to Vibrio cholerae 01, biovar chol...   \n",
       "2    A001    Cholera due to Vibrio cholerae 01, biovar eltor   \n",
       "3    A009                               Cholera, unspecified   \n",
       "7     A01                     Typhoid and paratyphoid fevers   \n",
       "8    A010                                      Typhoid fever   \n",
       "9   A0100                         Typhoid fever, unspecified   \n",
       "10  A0101                                 Typhoid meningitis   \n",
       "11  A0102               Typhoid fever with heart involvement   \n",
       "12  A0103                                  Typhoid pneumonia   \n",
       "\n",
       "                            load_ts  \n",
       "0  2024-02-05 18:04:48.377417+00:00  \n",
       "1  2024-02-05 18:04:48.377417+00:00  \n",
       "2  2024-02-05 18:04:48.377417+00:00  \n",
       "3  2024-02-05 18:04:48.377417+00:00  \n",
       "7  2024-02-05 18:04:48.377417+00:00  \n",
       "8  2024-02-05 18:04:48.377417+00:00  \n",
       "9  2024-02-05 18:04:48.377417+00:00  \n",
       "10 2024-02-05 18:04:48.377417+00:00  \n",
       "11 2024-02-05 18:04:48.377417+00:00  \n",
       "12 2024-02-05 18:04:48.377417+00:00  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# download ICD codes from CMS as an .xml file\n",
    "# https://www.cms.gov/medicare/coding-billing/icd-10-codes/2024-icd-10-cm\n",
    "import pandas as pd\n",
    "import xml.dom.minidom\n",
    "df = [] # results container\n",
    "doc = xml.dom.minidom.parse('icd10cm_tabular_2024.xml')\n",
    "# the .xml file has nested structure (chapter, section, diag, subdiag)\n",
    "chapters = doc.documentElement.getElementsByTagName(\"chapter\")\n",
    "for chapter in chapters:\n",
    "    sections = chapter.getElementsByTagName(\"section\")\n",
    "    for section in sections:\n",
    "        diags = section.getElementsByTagName(\"diag\")\n",
    "        for diag in diags:\n",
    "            diagNameElement = diag.getElementsByTagName(\"name\")[0]\n",
    "            diagDescElement = diag.getElementsByTagName(\"desc\")[0]\n",
    "            df.append([diagNameElement.childNodes[0].data, diagDescElement.childNodes[0].data])\n",
    "            subdiags = diag.getElementsByTagName(\"diag\")\n",
    "            for subdiag in subdiags:\n",
    "                subdiagNameElement = subdiag.getElementsByTagName(\"name\")[0]\n",
    "                subdiagDescElement = subdiag.getElementsByTagName(\"desc\")[0]\n",
    "                df.append([subdiagNameElement.childNodes[0].data, subdiagDescElement.childNodes[0].data])\n",
    "df = pd.DataFrame(df, columns = ['code', 'name']) # convert to pandas df\n",
    "df = df.drop_duplicates() # drop any duplicate rows\n",
    "df['load_ts'] = pd.Timestamp.utcnow() # add timestamp\n",
    "df.head(10) # quick check result\n",
    "df.to_csv('icd10_codes_2024.csv', index = False) # save to .csv"
   ]
  }
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