Cross-lingual Medical Entity Linking Recommenders for INCEpTION

Simple integration of pre-configured xMEN pipelines as recommenders for (biomedical) entity linking in INCEpTION.

German SNOMED CT Linking

Install dependencies

• pip install -r requirements.txt (see here for known issues during installation of xmen)

Prepare xMEN KB and index

Option 1 (faster):

• Download pre-computed xMEN index and extract contents into xmen_index:
  • HPI Nextcloud Link (password: name of this repository)

Option 2 (more flexible):

• Create xMEN files from scratch (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

Run the recommender

• Start the Ariadne Server (on http://localhost:5000/xmen_snomed):
  • python run_snomed_german_recommender.py ./xmen_index/index