diff --git a/README.md b/README.md index 5dc733b..86e4bc3 100644 --- a/README.md +++ b/README.md @@ -2,33 +2,28 @@ Simple integration of pre-configured [xMEN](https://github.com/hpi-dhc/xmen) pipelines as recommenders for (biomedical) entity linking in [INCEpTION](https://github.com/inception-project/inception). -## German SNOMED CT Linking - ![External Recommender](assets/recommender.png) -### With Docker - -- `docker build -t inception-xmen-snomed .` -- `docker run -m=12g -p 5002:5000 -v "$(pwd)"/xmen_index/index:/index/ inception-xmen-snomed` - -### Without Docker +## German SNOMED CT Quickstart (with Docker) -#### Install dependencies - -- `pip install -r requirements.txt` (see [here](https://github.com/hpi-dhc/xmen/issues/37) for known issues during installation of `xmen`) +- Download pre-computed xMEN index for SNOMED CT and extract contents into `xmen_index`: + - [HPI Nextcloud Link](https://nextcloud.hpi.de/s/LQM7s5oWGnoHRJ6) (password: name of this repository) -#### Prepare xMEN KB and index +- `docker run -m=12g -p 5000:5000 -v "$(pwd)"/xmen_index/index:/index/ ghcr.io/hpi-dhc/xmen-inception-recommender:main` -**Option 1 (faster)**: -- Download pre-computed xMEN index and extract contents into `xmen_index`: - - [HPI Nextcloud Link](https://nextcloud.hpi.de/s/LQM7s5oWGnoHRJ6) (password: name of this repository) +## Create xMEN KB and Index from Scratch -**Option 2 (more flexible)**: -- Create xMEN files from scratch (takes about 1 hour with a GPU) +- Adapt `snomed_german.yaml` as needed +- Create KB and indices (takes about 1 hour with a GPU) - `git clone https://github.com/hpi-dhc/xmen` - `xmen dict snomed_german.yaml --code xmen/examples/dicts/umls_source.py` - `xmen index snomed_german.yaml --all --overwrite` +## Running the Recommender without Docker + +### Install dependencies + +- `pip install -r requirements.txt` (see [here](https://github.com/hpi-dhc/xmen/issues/37) for known issues during installation of `xmen`) ### Run the recommender