Knowledge discovery for Deep Phenotyping serious mental illness from Electronic Mental Health records

Abstract

Background: Deep Phenotyping is the precise and comprehensive analysis of phenotypic features, where the individual components of the phenotype are observed and described. In UK mental health clinical practice, most clinically relevant information is recorded as free text in the Electronic Health Record, and offers a granularity of information beyond that expressed in most medical knowledge bases. The SNOMED CT nomenclature potentially offers the means to model such information at scale, yet given a sufficiently large body of clinical text collected over many years, it’s difficult to identify the language that clinicians favour to express concepts. Methods: Vector space models of language seek to represent the relationship between words in a corpus in terms of cosine distance between a series of vectors. When utilising a large corpus of healthcare data and combined with appropriate clustering techniques and manual curation, we explore how such models can be used for discovering vocabulary relevant to the task of phenotyping Serious Mental Illness (SMI) with only a small amount of prior knowledge. Results: 20 403 n-grams were derived and curated via a two stage methodology. The list was reduced to 557 putative concepts based on eliminating redundant information content. These were then organised into 9 distinct categories pertaining to different aspects of psychiatric assessment. 235 (42%) concepts were found to be depictions of putative clinical significance. Of these, 53 (10%) were identified having novel synonymy with existing SNOMED CT concepts. 106 (19%) had no mapping to SNOMED CT. Conclusions: We demonstrate a scalable approach to discovering new depictions of SMI symptomatology based on real world clinical observation. Such approaches may offer the opportunity to consider broader manifestations of SMI symptomatology than is typically assessed via current diagnostic frameworks, and create the potential for enhancing nomenclatures such as SNOMED CT based on real world depictions.