Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients.

BACKGROUND: Two years into the COVID-19 pandemic and with more than five million deaths worldwide, the healthcare establishment continues to struggle with every new wave of the pandemic resulting from a new coronavirus variant. Research has demonstrated that there are variations in the symptoms, and even in the order of symptom presentations, in COVID-19 patients infected by different SARS-CoV-2 variants (e.g., Alpha and Omicron). Textual data in the form of admission notes and physician notes in the Electronic Health Records (EHRs) is rich in information regarding the symptoms and their orders of presentation. Unstructured EHR data is often underutilized in research due to the lack of annotations that enable automatic extraction of useful information from the available extensive volumes of textual data. METHODS: We present the design of a COVID Interface Terminology (CIT), not just a generic COVID-19 terminology, but one serving a specific purpose of enabling automatic annotation of EHRs of COVID-19 patients. CIT was constructed by integrating existing COVID-related ontologies and mining additional fine granularity concepts from clinical notes. The iterative mining approach utilized the techniques of 'anchoring' and 'concatenation' to identify potential fine granularity concepts to be added to the CIT. We also tested the generalizability of our approach on a hold-out dataset and compared the annotation coverage to the coverage obtained for the dataset used to build the CIT. RESULTS: Our experiments demonstrate that this approach results in higher annotation coverage compared to existing ontologies such as SNOMED CT and Coronavirus Infectious Disease Ontology (CIDO). The final version of CIT achieved about 20% more coverage than SNOMED CT and 50% more coverage than CIDO. In the future, the concepts mined and added into CIT could be used as training data for machine learning models for mining even more concepts into CIT and further increasing the annotation coverage. CONCLUSION: In this paper, we demonstrated the construction of a COVID interface terminology that can be utilized for automatically annotating EHRs of COVID-19 patients. The techniques presented can identify frequently documented fine granularity concepts that are missing in other ontologies thereby increasing the annotation coverage.

Barriers and facilitators involved in standardised care plan individualisation process in acute hospitalisation wards: A grounded theory approach.

OBJECTIVE: To identify and classify the barriers and facilitators of the individualisation process of the standardised care plan in hospitalisation wards. BACKGROUND: The administration of individualised care is one of the features of the nursing process. Care plans are the structured record of the diagnosis, planning and evaluation stages of the nursing process. Although the creation of standardised care plan has made recording easier, it is still necessary to record the individualisation of the care. It is important to study the elements that influence the individualisation process from the nurses' perspective. DESIGN: Qualitative study with the grounded theory approach developed by Strauss and Corbin. METHODS: Thirty-nine nurses from three hospitals participated by way of theoretical sampling. In-depth interviews were conducted, as well as participant observation, document analysis and focus group discussion. The analysis consisted of open, axial and selective coding until data saturation was reached. EQUATOR guidelines for qualitative research (COREQ) were applied. RESULTS: For both barriers and facilitators, three thematic categories emerged related to organisational, professional and individual aspects. The identified barriers included routines acquired in the wards, the tradition of narrative records, lack of knowledge and limited interest in individualisation. The identified facilitators included holding clinical care sessions, use of standardised care plan and an interface terminology, the nurse's expertise and willingness to individualise. CONCLUSION: The individualisation process of the standardised care plan involves multiple barriers and facilitators, which influence its degree of accuracy. RELEVANCE TO CLINICAL PRACTICE: Implementing strategies at an organisational level, professional level and individual level to improve the way the process is carried out would encourage individualising the standardised care plan in a manner that is consistent with the needs of the patient and family; it would improve the quality of care and patient satisfaction.

Standardization of immunotherapy adverse events in patient information leaflets and development of an interface terminology for outpatients' monitoring.

INTRODUCTION: Immunotherapy is effective for treating cancer, but it is also associated with a wide spectrum of adverse events. In order to detect them early, the patients need to be monitored at home, between the therapy administrations, e.g., by asking them to report outcomes, usually including symptoms and quality of life measures. For the collected data to be reusable, the symptoms need to be in a standardized form. The aim of this study is to explore the standardization of the information contained in the patient information leaflets (PILs) of immunotherapy drugs, by creating an interface terminology of immunotherapy-related adverse events, which should support a consistent collection of symptoms from the patients. METHODS: PILs contain a significant amount of information in free text, but they mix patient-reportable and clinically assessable events. We extracted a list of patient-reportable adverse events, mapped them to reference terminologies and compared the mapping results to choose the best-performing reference terminology. RESULTS: The PILs standardization led to the extraction of 151 symptoms and 424 terms, including both preferred terms and synonyms in English and Italian. Among the reference terminologies we considered, SNOMED CT allowed us to map all concepts and became, hence, the main reference terminology for the resulting interface terminology. A preliminary validation on the PIL of a new immunotherapy drug showed that our interface terminology already contained all the mentioned symptoms. CONCLUSION: PILs provide a valuable source for determining adverse events. The resulting interface terminology includes Italian and English terms for patient-reportable adverse events for five immunotherapy drugs representative of their category. Further work will be undertaken to evaluate the usability of the interface terminology and the patients' experience and satisfaction with the proposed terms, made available for example through an app, as well as its effectiveness on data quality and quality of care.

Personalising Symptoms Reporting in Telemonitoring Applications for Cancer Patients.

Patient reported outcomes have been shown to be predictive of cancer patients' prognosis, and their monitoring through electronic applications have been shown to positively impact survival. On the other hand, patient apps in general show a number of criticalities that often lead patients to abandon their use. One of them is usability. A scarce attention to usability during app development leads to unsatisfactory user experience. In this work, we present an algorithm to facilitate patient symptoms reporting, by personalising the list of symptoms according to their probability of occurrence in the specific patient. This avoids searching long lists of items, thus decreasing the patients' burden in symptom reporting.

Aligning an interface terminology to the Logical Observation Identifiers Names and Codes (LOINC®).

OBJECTIVE: Our study consists in aligning the interface terminology of the Bordeaux university hospital (TLAB) to the Logical Observation Identifiers Names and Codes (LOINC). The objective was to facilitate the shared and integrated use of biological results with other health information systems. MATERIALS AND METHODS: We used an innovative approach based on a decomposition and re-composition of LOINC concepts according to the transversal relations that may be described between LOINC concepts and their definitional attributes. TLAB entities were first anchored to LOINC attributes and then aligned to LOINC concepts through the appropriate combination of definitional attributes. Finally, using laboratory results of the Bordeaux data-warehouse, an instance-based filtering process has been applied. RESULTS: We found a small overlap between the tokens constituting the labels of TLAB and LOINC. However, the TLAB entities have been easily aligned to LOINC attributes. Thus, 99.8% of TLAB entities have been related to a LOINC analyte and 61.0% to a LOINC system. A total of 55.4% of used TLAB entities in the hospital data-warehouse have been mapped to LOINC concepts. We performed a manual evaluation of all 1-1 mappings between TLAB entities and LOINC concepts and obtained a precision of 0.59. CONCLUSION: We aligned TLAB and LOINC with reasonable performances, given the poor quality of TLAB labels. In terms of interoperability, the alignment of interface terminologies with LOINC could be improved through a more formal LOINC structure. This would allow queries on LOINC attributes rather than on LOINC concepts only.

What patients' problems do nurses e-chart? Longitudinal study to evaluate the usability of an interface terminology.

BACKGROUND: The nurses' ability to document patient's status, problems and progress is an important issue in patients' safety. Nursing terminologies are intended to support nursing practice but as any other clinical tool, they should be evaluated to assure quality and warrant effective written communication among clinicians. OBJECTIVES: This study was aimed to evaluate the usability of the diagnosis axis of an interface terminology by assessing its completeness and the frequency of use of its concepts. DESIGN: Observational, longitudinal, multicentre study. SETTING: A total of 8 hospitals representing 162 acute medical-surgical, obstetric and mental health nursing wards, step-down units and home in-patient units were included. PARTICIPANTS: Overall, 246,400 electronic care plans were studied; 53.5% from male patients; 14.6% paediatrics and 33.7% from patients elder than 70 years old. Most were admitted due to cardiocirculatory, respiratory, digestive or musculoskeletal conditions (50.5%), other acute medical or surgical disorders (29.8%) and obstetrics (19.3%). METHODS: The main outcome measures were: the use of nursing diagnoses from the interface terminology evaluated and their accumulated frequency, analysed over a 3-year retrospective review of the electronic nursing care plans. The analysis of data included descriptive statistics with a confidence level of 95% for confidence intervals. RESULTS: Most of the diagnostic concepts from the interface terminology were used (92.3%) by nurses to illustrate patients' problems in the electronic care plans. Their frequency of use widely varied, from some very frequent diagnoses like Risk for haemorrhage (51.4%; CI 95%: 51.25-51.65) or Acute pain (49.6%; CI: 49.49-49.88) to others used only in exceptional cases like Faecal impaction or Extravasation. The first nursing diagnosis related to family or caregiver emerges in the 32nd place of the ranking. CONCLUSIONS: Results for outcome measures oriented that the diagnosis axis of this interface terminology meets the usability criterion of completeness when assessing for the use of its concepts in the acute care setting.

Analysis of free text with omaha system targets in community-based care to inform practice and terminology development.

The Omaha system is one of the most widely used interface terminologies for documentation of community-based care. It is influential in disseminating evidence-based practice and generating data for health care quality research. Thus, it is imperative to ensure that the Omaha system reflects current health care knowledge and practice. The purpose of this study was to evaluate free text associated with Omaha system terms to inform issues with electronic health record system use and future Omaha system standard development. Two years of client records from two diverse sites (a skilled homecare, hospice, and palliative care program and a maternal child health home visiting program) were analyzed for the use of free text as a component of the intervention when structured targets for interventions were not identified. Intervention text entries very commonly contained duplicate "carry forward entries", multiple concepts, mismatched problem focus, or failure to identify an existing appropriate target. Our findings support the need to better address education gaps for clinicians. We identified additional suggested targets for Omaha system problems, and propose new targets for consideration in future Omaha system revisions.