This repository contains a docker image for the MedSecId project, which contains annotations for sections of clinical notes, such as electronic health care (EHR) medical documents. It also comes with a model to automatically section notes.
If all you want is the mednlp tooling or predicting sections using mednlp, you can clone this repository and comment out the mimicdb section. However, if you want to access MIMIC-III data, follow the instructions on how to obtain or build the database from the mimicdb repository.
The makefile controls building of the image and its life cycle. To build the image from scratch:
- Build or obtain the mimicdb image as explained in the MedSecId docs.
- Remove any previous Docker image:
make dockerrm - Clean any previous derived objects:
make cleanall - Build the image:
make build - Start the image(s):
make up
The Docker image can be installed with:
docker pull plandes/mimicsid:latest