Synonym Augmentation for Rare Disease Identification in Unstructured Data

The significant challenges associated with rare diseases in the medical and research domains include the scarcity of information, which is often confined to unstructured formats. Although existing approaches provide valuable insights, there is a need to develop effective methods to identify information pertinent to rare diseases for advancing rare disease research. We identified mentions of rare diseases in relevant texts and assessed their relevance using derived scores, the confidence score and semantic similarity from a fine-tuned BioMedBERT encoder. This encoder was fine-tuned using rare disease related text from Online Mendelian Inheritance in Man (OMIM), Orphanet, a manually validated dataset, and STS benchmark datasets. The process of identifying meaningful rare disease mentioned was presented through two case studies that retrieved relevant NIH-funded projects, utilizing a generated knowledge graph in Neo4j to host data on 2,067 GARD diseases with over 320,000 NIH funded projects. Through various case studies with NIH-funded projects related to rare diseases, we demonstrated the effectiveness of our approach in systematically providing rare disease related data to enhance our understanding of rare diseases for future investigations.