Identifying the Presence, Activity, and Status of Extraintestinal Manifestations of Inflammatory Bowel Disease Using Natural Language Processing of Clinical Notes.

BACKGROUND: Extraintestinal manifestations (EIMs) occur commonly in inflammatory bowel disease (IBD), but population-level understanding of EIM behavior is difficult. We present a natural language processing (NLP) system designed to identify both the presence and status of EIMs using clinical notes from patients with IBD. METHODS: In a single-center retrospective study, clinical outpatient electronic documents were collected in patients with IBD. An NLP EIM detection pipeline was designed to determine general and specific symptomatic EIM activity status descriptions using Python 3.6. Accuracy, sensitivity, and specificity, and agreement using Cohen's kappa coefficient were used to compare NLP-inferred EIM status to human documentation labels. RESULTS: The 1240 individuals identified as having at least 1 EIM consisted of 54.4% arthritis, 17.2% ocular, and 17.0% psoriasiform EIMs. Agreement between reviewers on EIM status was very good across all EIMs (κ = 0.74; 95% confidence interval [CI], 0.70-0.78). The automated NLP pipeline determining general EIM activity status had an accuracy, sensitivity, specificity, and agreement of 94.1%, 0.92, 0.95, and κ = 0.76 (95% CI, 0.74-0.79), respectively. Comparatively, prediction of EIM status using administrative codes had a poor sensitivity, specificity, and agreement with human reviewers of 0.32, 0.83, and κ = 0.26 (95% CI, 0.20-0.32), respectively. CONCLUSIONS: NLP methods can both detect and infer the activity status of EIMs using the medical document an information source. Though source document variation and ambiguity present challenges, NLP offers exciting possibilities for population-based research and decision support in IBD.

Extraintestinal manifestations of inflammatory bowel disease impact on patient experience, but are poorly captured by electronic health records. Natural language processing systems are capable of not only detecting extraintestinal manifestations, but also inferring activity information by automated analysis of clinical notes.

Equitable Research PRAXIS: A Framework for Health Informatics Methods.

OBJECTIVES: There is growing attention to health equity in health informatics research. However, the literature lacks a comprehensive framework outlining critical considerations for health informatics research with marginalized groups. METHODS: Literature review and experiences from nine equity-focused health informatics conducted in the United States and Canada. Studies focus on disparities related to age, disability or chronic illness, gender/sex, place of residence (rural/urban), race/ethnicity, sexual orientation, and socioeconomic status. RESULTS: We found four key equity-related methodological considerations. To assist informaticists in addressing equity, we contribute a novel framework to synthesize these four considerations: PRAXIS (Participation and Representation, Appropriate methods and interventions, conteXtualization and structural competence, Investigation of Systematic differences). Participation and representation refers to the necessity for meaningful participation of marginalized groups in research, to elevate the voices of marginalized people, and to represent marginalized people as they are comfortable (e.g., asset-based versus deficit-based). Appropriate methods and interventions mean targeting methods, instruments, and interventions to reach and engage marginalized people. Contextualization and structural competence mean avoiding individualization of systematic disparities and targeting social conditions that (re-)produce inequities. Investigation of systematic differences highlights that experiences of people marginalized according to specific traits differ from those not so marginalized, and thus encourages studying the specificity of these differences and investigating and preventing intervention-generated inequality. We outline guidance for operationalizing these considerations at four research stages. CONCLUSIONS: This framework can assist informaticists in systematically addressing these considerations in their research in four research stages: project initiation; sampling and recruitment; data collection; and data analysis. We encourage others to use these insights from multiple studies to advance health equity in informatics.