xmen_ggponc3.yaml

name: ggponc3

cache_dir: ${oc.env:HOME}/.cache/xmen/

data_version: v2.0_agreement 

eccnp: 
    model_path: phlobo/german-ellipses-resolver-mt5-base
    batch_size: 32
    generation_max_length: 277
    tokenizer: "google/mt5-base"

dict:
    umls:
        lang: 
          - de
          - en
        meta_path: ${oc.env:UMLS_HOME}/2023AA/META
        semantic_group_file_version: v03
        semantic_groups:
          - ANAT
          - CHEM
          - CONC
          - DEVI
          - DISO
          - GEOG
          - LIVB
          - OBJC
          - PHEN
          - PHYS
          - PROC
        sabs:
          - SNOMEDCT_US 
          - MSH
          - MSHGER
          - MDR
          - MDRGER
          - NCI

linker:
    ranking:
        kb_path: ${cache_dir}/${name}/${name}.jsonl
        st_mapping_file: ggponc2tui.csv
        reranker: phlobo/xmen-de-ce-medmentions
        use_nil: False
        k_reranking: 16
    candidate_generation:
        index_base_path: ${cache_dir}/${name}/index
        k_ngram: 100
        k_sapbert: 100