Conceptualisation and Annotation of Drug Nonadherence Information for Knowledge Extraction from Patient-Generated Texts

Approaches to knowledge extraction (KE) in the health domain often start by annotating text to indicate the knowledge to be extracted, and then use the annotated text to train systems to perform the KE. This may work for annotat- ing named entities or other contiguous noun phrases (drugs, some drug effects), but be- comes increasingly difficult when items tend to be expressed across multiple, possibly non- contiguous, syntactic constituents (e.g. most descriptions of drug effects in user-generated text). Other issues include that it is not al- ways clear how annotations map to actionable insights, or how they scale up to, or can form part of, more complex KE tasks. This paper reports our efforts in developing an approach to extracting knowledge about drug nonadher- ence from health forums which led us to con- clude that development cannot proceed in sep- arate steps but that all aspects—from concep- tualisation to annotation scheme development, annotation, KE system training and knowl- edge graph instantiation—are interdependent and need to be co-developed. Our aim in this paper is two-fold: we describe a generally ap- plicable framework for developing a KE ap- proach, and present a specific KE approach, developed with the framework, for the task of gathering information about antidepressant drug nonadherence. We report the conceptual- isation, the annotation scheme, the annotated corpus, and an analysis of annotated texts.