{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!-- \n",
    "    #  Copyright (C) 2023-2024 Y Hsu <yh202109@gmail.com>\n",
    "    #\n",
    "    #  This program is free software: you can redistribute it and/or modify\n",
    "    #  it under the terms of the GNU General Public license as published by\n",
    "    #  the Free software Foundation, either version 3 of the License, or\n",
    "    #  any later version.\n",
    "    #\n",
    "    #  This program is distributed in the hope that it will be useful,\n",
    "    #  but WITHOUT ANY WARRANTY; without even the implied warranty of\n",
    "    #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n",
    "    #  GNU General Public License for more details\n",
    "    #\n",
    "    #  You should have received a copy of the GNU General Public license\n",
    "    #  along with this program. If not, see <https://www.gnu.org/license/> \n",
    "-->"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# H/ICH/eCTD/US/4.0/Heading\n",
    "\n",
    "The Electronic Common Technical Document (eCTD) standard format is used by regulatory agencies for data and file submitted electronically [^1]. \n",
    "The standard format provides a structure to organize, tag, and link submitted datasets and documents.\n",
    "The module `ectd` includes functions for working with the eCTD format. \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The Comprehensive Table of Contents Headings and Hierarchy (CTOC) by FDA \n",
    "\n",
    "The current FDA supporting version of eCTD standard is 3.2.2 and the newest testing version is 4.0 with base implementation package v1.5 [^2].\n",
    "FDA has released guidance on heading hierarchy of eCTD [^3]<sup>,</sup>[^4].\n",
    "The `ectd` module provides functions for listing and searching within the heading hierarchy.\n",
    "\n",
    "**Disclaimer**: this module is shared for quick searching and preview headings with the intention to be helpful. The author can not guarantee the correctness of the heading. Please notify the author if any typos were found.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Module 1\n",
    "\n",
    "To view CTOC of Module 1:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "from mtbp3.health import ectd\n",
    "ctoc = ectd.ctoc_by_fda(ectd_version='4.0', ctoc_version='1.0')\n",
    "print('\\n'.join(ctoc.show_ctoc_tree(1)))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "source": [
    "## Module 2\n",
    "\n",
    "To view CTOC of Module 2:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print('\\n'.join(ctoc.show_ctoc_tree(2)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Module 3\n",
    "\n",
    "To view CTOC of Module 3:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print('\\n'.join(ctoc.show_ctoc_tree(3)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Module 4\n",
    "\n",
    "To view CTOC of Module 4:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print('\\n'.join(ctoc.show_ctoc_tree(4)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Module 5\n",
    "\n",
    "To view CTOC of Module 5:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print('\\n'.join(ctoc.show_ctoc_tree(5)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Find Sections Using Keywords\n",
    "\n",
    "Please note that keywords are not case sensitive, but titles are case sensitive. \n",
    "\n",
    "To search for a word within the hierarchy:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print('\\n'.join(ctoc.find_section_given_words('REMS')))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To include the upper CTOC sections that include search results:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print(\"\\n\".join(ctoc.find_section_given_words(\"REMS\", outfmt='tree')))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To search for multiple keywords:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print(\"\\n\".join(ctoc.find_section_given_words(words=[\"REMS\",\"dsur\"], outfmt='tree', colored=['magenta','blue','red','whatever'])))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To use another color:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "print(\"\\n\".join(ctoc.find_section_given_words(words=\"dsur\", outfmt='tree', colored='green')))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Reference\n",
    "\n",
    "[^1]: FDA. (2023). Electronic Common Technical Document (eCTD). ([web page](https://www.fda.gov/drugs/electronic-regulatory-submission-and-review/electronic-common-technical-document-ectd))\n",
    "[^2]: FDA. (2023). Electronic Common Technical Document (eCTD) v4.0. ([web page](https://www.fda.gov/drugs/electronic-regulatory-submission-and-review/electronic-common-technical-document-ectd-v40))\n",
    "[^3]: FDA. (2020). The Comprehensive Table of Contents Headings and Hierarchy Version 2.3.3. ([pdf](https://www.fda.gov/media/76444/download))\n",
    "[^4]: FDA. (2021). The Comprehensive Table of Contents Headings and Hierarchy Version 4.0. ([pdf](https://www.fda.gov/media/150309/download))"
   ]
  }
 ],
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   "name": "python"
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}