The research on gene-disease association based on text-mining of PubMed

BACKGROUND: The associations between genes and diseases are of critical significance in aspects of prevention, diagnosis and treatment. Although gene-disease relationships have been investigated extensively, much of the underpinnings of these associations are yet to be elucidated. METHODS: A novel method integrates MeSH database, term weight (TW), and co-occurrence methods to predict gene-disease associations based on the cosine similarity between gene vectors and disease vectors. Vectors are transformed from the texts of documents in the PubMed database according to the appearance and location of the gene or disease terms. The disease related text data has been optimized during the process of constructing vectors. RESULTS: The overall distribution of cosine similarity value was investigated. By using the gene-disease association data in OMIM database as golden standard, the performance of cosine similarity in predicting gene-disease linkage was evaluated. The effects of applying weight matrix, penalty weights for keywords (PWK), and normalization were also investigated. Finally, we demonstrated that our method outperforms heterogeneous network edge prediction (HNEP) in aspects of precision rate and recall rate. CONCLUSIONS: Our method proposed in this paper is easy to be conducted and the results can be integrated with other models to improve the overall performance of gene-disease association predictions.