What are 10 other phenotypes that are annotated?
Adv. Heart Disease, Adv. Lung Disease, Alcohol Abuse, Chronic Neurologic Dystrophies, Dementia, Depression, Developmental Delay, Obesity, Psychiatric disorders and Substance Abuse
A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.
With the widespread adoption of electronic health records (EHRs), medical data are being generated and stored digitally in vast quantities BIBREF0. While much EHR data are structured and amenable to analysis, there appears to be limited homogeneity in data completeness and quality BIBREF1, and it is estimated that the majority of healthcare data are being generated in unstructured, text-based format BIBREF2. The generation and storage of these unstructured data come concurrently with policy initiatives that seek to utilize preventative measures to reduce hospital admission and readmission BIBREF3. Chronic illnesses, behavioral factors, and social determinants of health are known to be associated with higher risks of hospital readmission, BIBREF4 and though behavioral factors and social determinants of health are often determined at the point of care, their identification may not always be curated in structured format within the EHR in the same manner that other factors associated with routine patient history taking and physical examination are BIBREF5. Identifying these patient attributes within EHRs in a reliable manner has the potential to reveal actionable associations which otherwise may remain poorly defined. As EHRs act to streamline the healthcare administration process, much of the data collected and stored in structured format may be those data most relevant to reimbursement and billing, and may not necessarily be those data which were most relevant during the clinical encounter. For example, a diabetic patient who does not adhere to an insulin treatment regimen and who thereafter presents to the hospital with symptoms indicating diabetic ketoacidosis (DKA) will be treated and considered administratively as an individual presenting with DKA, though that medical emergency may have been secondary to non-adherence to the initial treatment regimen in the setting of diabetes. In this instance, any retrospective study analyzing only the structured data from many similarly selected clinical encounters will necessarily then underestimate the effect of treatment non-adherence with respect to hospital admissions. While this form of high context information may not be found in the structured EHR data, it may be accessible in patient notes, including nursing progress notes and discharge summaries, particularly through the utilization of natural language processing (NLP) technologies. BIBREF6, BIBREF7 Given progress in NLP methods, we sought to address the issue of unstructured clinical text by defining and annotating clinical phenotypes in text which may otherwise be prohibitively difficult to discern in the structured data associated with the text entry. For this task, we chose the notes present in the publicly available MIMIC database BIBREF8. Given the MIMIC database as substrate and the aforementioned policy initiatives to reduce unnecessary hospital readmissions, as well as the goal of providing structure to text, we elected to focus on patients who were frequently readmitted to the ICU BIBREF9. In particular, a patient who is admitted to the ICU more than three times in a single year. By defining our cohort in this way we sought to ensure we were able to capture those characteristics unique to the cohort in a manner which may yield actionable intelligence on interventions to assist this patient population.