Installation of NegBio¶

This part of the documentation covers the installation of NegBio. The first step to using any software package is getting it properly installed.

Prerequisites¶

Note: since v1.0, MetaMap is not required. You can use the vocabularies (e.g., patterns/cxr14_phrases_v2.yml) instead.

If you want to use MetaMap to extract findings!!!

Download MetaMap full version and extract inot the directory called public_mm.
Install MetaMap locally. Installation instructions can be found at https://metamap.nlm.nih.gov/Installation.shtml.
```
cd public_mm
./bin/install.sh
```

Start the server.

./bin/skrmedpostctl start
./bin/wsdserverctl start

NegBio is actively developed on GitHub, where the code is always available.

You can clone the public repository

$ git clone https://github.com/ncbi-nlp/NegBio.git
$ cd negbio

Once you have a copy of the source, you can prepare a virtual environment

$ conda create --name negbio python=3.6
$ source activate negbio
$ pip install --upgrade pip setuptools

or

$ virtualenv --python=/usr/bin/python3.6 negbio_env
$ source negbio_env/bin/activate

Finally, you can install the required packages:

$ pip install -r requirements3.txt