Preliminary Processing and Analysis of an Adverse Event Dataset for Detecting Sepsis-Related Events

Abstract

Adverse event (AE) reports contain notes detailing procedural and guideline deviations, and unwanted incidents that can bring harm to patients. Available datasets mainly focus on vigilance or post-market surveillance of adverse drug reactions or medical device failures. The lack of clinical-related AE datasets makes it challenging to study healthcare-related AEs. AEs affect 10% of hospitalized patients, and almost half are preventable. Having an AE dataset can assist in identifying possible patient safety interventions and performing quality surveillance to lower AE rates. The free-text notes can provide insight into the cause of incidents and lead to better patient care. The objective of this study is to introduce a Norwegian AE dataset and present preliminary processing and analysis for sepsis-related events, specifically peripheral intravenous catheter-related bloodstream infections. Therefore, the methods focus on performing a domain analysis to prepare and better understand the data through screening, generating synthetic free-text notes, and annotating notes.

Terminology and ontology development for semantic annotation: A use case on sepsis and adverse events

“…This paper significantly extends the papers [66] and [67], by adding an ontology with instances and including evaluation of the correctness and ability to answer competency questions. In addition, instances from the annotated corpus in [67] were added into the terminology, the terminology was evaluated using competency questions, and an ontology was developed to answer competency questions with clinical knowledge.…”

“…Documents for annotation are from an AE synthetic dataset. The documents are based on unstructured free-text AE notes within the extracted AE reports from the electronic incident reporting system at St. Olavs hospital, Trondheim University Hospital in Trondheim, Norway, between September 2015 to December 2019 [67]. The synthetic dataset contains 100 AE notes or documents manually created and verified by a nurse to ensure clinical data is anonymized.…”

“…The synthetic documents were annotated by 8 annotators with clinical backgrounds over 4 annotation sessions [67]. Each annotator annotated 10 documents in session 1 and 20 documents in the remaining 3 sessions (i.e., 70 documents annotated over 4 annotation session).…”

“…Furthermore, to capture relationships between categories for downstream analysis (e.g., infection sign at a specific location), the following four relationships to link categories were included: A preliminary annotation guideline was created using the seven categories and four relationships. Annotation guidelines from each of the 4 annotation sessions are available online 1 [67].…”

Method for Designing Semantic Annotation of Sepsis Signs in Clinical Text

“…We had access to 18 555 Norwegian adverse event (AE) reports extracted from a hospital's electronic incident reporting system (Yan et al, 2021). Extracted AE reports described procedural deviations, misunderstandings, resource needs, and risky patient behavior.…”