Towards Discovery: An End-to-End System for Uncovering Novel Biomedical Relations

This contains the embeddings as specified in the work: "Towards Discovery: An End-to-End System for Uncovering Novel Biomedical Relations". The embeddings are created from 4 seperate knowledge bases: Cellosaurus: Concepts CTD-Disease: Concepts, Definitions, Synonyms MeSH: Concepts, Definitions, Synonyms. This includes embeddings for both the main and supplementary files, for Concepts and Definitions. NCBI-Gene: Concepts. Due ot the large size of the NCBI-cGene corpus we only provide the embeddings for the following top 7 organisms most prevalent in the corpus: 10090: house mouse 10116: Norway Rat 11676: human immunodeficiency virus (HIV) 12814: Respiratory syncytial virus 3702: thale cress 7955: zebrafish 9606: and human NCBI-Taxonomy: Names The embeddings supplied were created using the SapBERT model, for the knowledge bases as of March 2024. The exact files used to generate the embeddings are provided as jsonl files.