AGPL v3.0 NOTICE
PLEASE INCLUDE AT START OF ALL SOURCE CODE FILES PERTAINING TO THIS PROGRAM
PROGRAM TITLE: PathReporter
Copyright (C) 2022
Hansen Lam, M.D., Freddy Nguyen, M.D., Ph.D., Aryeh Stock, M.D., Xintong Wang, M.D., Volha Lenskaya, M.D.
Alexandros Polydorides, M.D., Qiusheng Si, M.D., John Kim, M.D., Karl Eichorn, Dan Wild
Disclaimer: This software is intended for research purposes only. This software is not
for clinical use. The authors and contributors shall not be liable for any damages or
losses resulting from the use of this software. The authors and contributors shall not
be liable for any actions or decisions resulting rom the use of this software.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published
by the Free Software Foundation, either version 3 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
OBJECTIVE: This program processes semi-structured pathology reports in XML format to create tabulated data and facilitate data collection from free-text reports.
CONTRIBUTORS: @kaeichorn https://github.com/kaeichorn @hansenlam
METHODS: This program implements an object oriented approach, using Python v3.x. Dependencies include but are not limited to: pandas, numpy, openpyxl, re, string, math, lxml, ujson, collections
USE NOTES: Example uses are documented in "scenarios_script.py" In summary, XML documents containing collections of subspecialty reports should be grouped in to folders by subspecialty. Sample code is provided which acesses each XML file in a folder. Key functions include the "report_extract" and "report_extract_feats" functions. A slightly modified function, "report_extract_prostate" is also provided to demonstrate how different modules can be added to alter feature extraction. Key classes include the XMLDocument class which parses individual reports into accessioning information, demographics, diagnostic text, and gross specimen descriptions, and saves to a new instance.
ROADMAP:
- Adding comments for code clarification
- Re-visiting class and method organization to improve readability
- Open to suggestions from wider community