From 2cbfe57f82d4b5c9e136d2c678faaf048c017094 Mon Sep 17 00:00:00 2001 From: Adam Yala Date: Wed, 24 Jan 2018 17:28:36 -0500 Subject: [PATCH] Update README.md --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 5e977c3..ea1604a 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,13 @@ OncoText is an information extraction service designed to parse structured data All pretrained models are available on a [docker image](dockerhub.com/yala/oncotext:0.1.0), and were trained/developed in a collaboration with Dr. Kevin Hughes from Mass General, and Regina Barzilay's Lab at MIT CSAIL. All models were trained on Partners Healthcare Pathology reports, and results may transfer poorly to pathology reports from other venues, if the phrasing there is significantly diferent. OncoText is currently deployed at Mass General and is designed to support adding new categories, new training data, and new sets of documents to parse. In principle, this can be used on any free text reports given you provide training data via the API. It's setup as a webservice and can be accessed through HTTP requests. +You can run the docker as follows: +``` + + sudo docker run -it -p 5000:5000 -e LOGFILE=/OncoText/LOGS -e PICKLEDIR=/OncoText/oncotext_files -e CONFIG_XLSX=/OncoText/config.xlsx -v PATH_TO_YOUR_LOGFILE:/OncoText/LOGS -v PATH_TO_DB_DIR:/OncoText/oncotext_files -v PATH_TO_CONFIG_EXCEL:/OncoText/config.xlsx yala/oncotext:0.1.0 + +``` +
## System Requirements