A lightweight API-based approach for building flexible clinical NLP systems

Abstract

Natural language processing (NLP) has become essential for secondary use of clinical data. Over the last two decades, many clinical NLP systems were developed in both academia and industry. However, nearly all existing systems are restricted to specific clinical settings mainly because they were developed for and tested with specific datasets, and they often fail to scale up. Therefore, using existing NLP systems for one’s own clinical purposes requires substantial resources and long-term time commitments for customization and testing. Moreover, the maintenance is also troublesome and time-consuming. This research presents a lightweight approach for building clinical NLP systems with limited resources. Following the design science research approach, we propose a lightweight architecture which is designed to be composable, extensible, and configurable. It takes NLP as an external component which can be accessed independently and orchestrated in a pipeline via web APIs. To validate its feasibility, we developed a web-based prototype for clinical concept extraction with six well-known NLP APIs and evaluated it on three clinical datasets. In comparison with available benchmarks for the datasets, three high F1 scores (0.861, 0.724, and 0.805) were obtained from the evaluation. It also gained a low F1 score (0.373) on one of the tests, which probably is due to the small size of the test dataset. The development and evaluation of the prototype demonstrates that our approach has a great potential for building effective clinical NLP systems with limited resources.