A2H_Linking_Data_MONDO_UMLS

The `data` folder contains the ontology resources used for entity linking. For each terminology (`mondo` and `umls`), it provides: - `embeddings/` — precomputed ontology term embeddings- `*_term_id_pairs.json` or `*_term_id_pairs_combined.json` — mappings between surface forms / synonyms and ontology IDs- `*_id_to_term_map.json` — mappings from ontology IDs to canonical normalized terms These resources are used during SapBERT-based normalization of extracted drug and disease mentions. Expected structure: data/├── mondo/│ ├── embeddings/│ ├── mondo_term_id_pairs.json│ └── mondo_id_to_term_map.json└── umls/ ├── embeddings/ ├── umls_term_id_pairs_combined.json └── umls_id_to_term_map.json The ontology resources were generated in the upstream **Preclinical_Pipeline** project and are not created within this repository itself. Generation code and documentation are available here: - https://github.com/Ineichen-Group/Preclinical_Pipeline Specifically, these files are produced in /04_normalization, see docu in the main README under Named entity normalization (NEN).