SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations

• Main Authors: Nícia Rosário-Ferreira, Victor Guimarães, Vítor S. Costa, Irina S. Moreira
• Format: Article
• Language: English
• Published: BMC 2021-10-01
• Series: BMC Bioinformatics
• Subjects: Disease-disease associations; Natural language processing; Biomedical text-mining; Deep learning; Blood cancers
• Online Access: https://doi.org/10.1186/s12859-021-04397-w

Abstract Background Blood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources establishing Disease-Disease Associations (DDAs), the knowledge is scattered and not accessible in a straightforward way to the scientific community. Here, we propose SicknessMiner, a biomedical Text-Mining (TM) approach towards the centralization of DDAs. Our methodology encompasses Named Entity Recognition (NER) and Named Entity Normalization (NEN) steps, and the DDAs retrieved were compared to the DisGeNET resource for qualitative and quantitative comparison. Results We obtained the DDAs via co-mention using our SicknessMiner or gene- or variant-disease similarity on DisGeNET. SicknessMiner was able to retrieve around 92% of the DisGeNET results and nearly 15% of the SicknessMiner results were specific to our pipeline. Conclusions SicknessMiner is a valuable tool to extract disease-disease relationship from RAW input corpus.