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.