LORE PMKB-CV

LORE PMKB-CV Knowledge graph (LLM-ORE) 70M relations between 8k Diseases (MeSH) and 18k Genes (NCBI, human protein coding) curated by LLMs reading PubMed Data format: (D_id, G_id, PMID, relation) csv file Semantic embedding (LLM-EMB) 2.5M DG vectors created by LLMs reading the knowledge graph Data format: (D_id, G_id, vector) pkl file DG pathogenicity scores (ML-Ranker) 3.1M DG scores predicted by pretrained models Features, training annotations, pretrained models are also provided Curated key semantics taxonomy A manually curated taxonomy of 105 semantic tags about DG pathogenicity in the knowledge graph Use the github LORE Key-Semantics module to use the taxonomy as tags and add them to the knowledge graph Source project https://github.com/ailabstw/LORE Tools for running LLM-ORE relation extraction, LLM-EMB embedding, ML-Ranker prediction, Key-Semantics curation on custom datasets https://doi.org/10.1093/bib/bbaf070 Research article describing the LORE framework, analyses, experiments, and details of the PMKB-CV dataset