Exploring mechanobiology network of bone and dental tissue based on Natural Language Processing

Bone and cartilage tissues are physiologically dynamic organs that are systematically regulated by mechanical inputs. At cellular level, mechanical stimulation engages an intricate network where mechano-sensors and transmitters cooperate to manipulate downstream signaling. Despite accumulating evidence, there is a notable underutilization of available information, due to limited integration and analysis. In this context, we conceived an interactive web tool named MechanoBone to introduce a new avenue of literature-based discovery. Initially, we compiled a literature database by sourcing content from Pubmed and processing it through the Natural Language Toolkit project, Pubtator, and a custom library. We identified direct co-occurrence among entities based on existing evidence, archiving in a relational database via SQLite. Latent connections were then quantified by leveraging the Link Prediction algorithm. Secondly, mechanobiological pathway maps were generated, and an entity-pathway correlation scoring system was established through weighted algorithm based on our database, String, and KEGG, predicting potential functions of specific entities. Additionally, we established a mechanical circumstance-based exploration to sort genes by their relevance based on big data, revealing the potential mechanically sensitive factors in bone research and future clinical applications. In conclusion, MechanoBone enables: 1) interpreting mechanobiological processes; 2) identifying correlations and crosstalk among molecules and pathways under specific mechanical conditions; 3) connecting clinical applications with mechanobiological processes in bone research. It offers a literature mining tool with visualization and interactivity, facilitating targeted molecule navigation and prediction within the mechanobiological framework of bone-related cells, thereby enhancing knowledge sharing and big data analysis in the biomedical realm.