Ontology based annotation of contextualized vital signs

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters

Proceedings of the 15th Conference on Knowledge Organization WissOrg'17 of theGerman Chapter of the International Society for Knowledge Organization (ISKO),30th November - 1st December 2017, Freie Universität Berlin

Wissensorganisation is the name of a series of biennial conferences / workshops with a long tradition, organized by the German chapter of the International Society of Knowledge Organization (ISKO). The 15th conference in this series, held at Freie Universität Berlin, focused on knowledge organization for the digital humanities. Structuring, and interacting with, large data collections has become a major issue in the digital humanities. In these proceedings, various aspects of knowledge organization in the digital humanities are discussed, and the authors of the papers show how projects in the digital humanities deal with knowledge organization.Wissensorganisation ist der Name einer Konferenzreihe mit einer langjährigen Tradition, die von der Deutschen Sektion der International Society of Knowledge Organization (ISKO) organisiert wird. Die 15. Konferenz dieser Reihe, die an der Freien Universität Berlin stattfand, hatte ihren Schwerpunkt im Bereich Wissensorganisation und Digital Humanities. Die Strukturierung von und die Interaktion mit großen Datenmengen ist ein zentrales Thema in den Digital Humanities. In diesem Konferenzband werden verschiedene Aspekte der Wissensorganisation in den Digital Humanities diskutiert, und die Autoren der einzelnen Beiträge zeigen, wie die Digital Humanities mit Wissensorganisation umgehen

SemEHR:A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research

OBJECTIVE: Unlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs. METHODS: SemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces. RESULTS: SemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe's largest providers of mental health services. In 2 Clinical Record Interactive Search-based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King's College Hospital in London, as part of the CogStack program (github.com/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100 000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy. CONCLUSION: Results from the multiple case studies demonstrate SemEHR's efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https://github.com/CogStack/SemEHR

Improving Access and Mental Health for Youth Through Virtual Models of Care

The overall objective of this research is to evaluate the use of a mobile health smartphone application (app) to improve the mental health of youth between the ages of 14–25 years, with symptoms of anxiety/depression. This project includes 115 youth who are accessing outpatient mental health services at one of three hospitals and two community agencies. The youth and care providers are using eHealth technology to enhance care. The technology uses mobile questionnaires to help promote self-assessment and track changes to support the plan of care. The technology also allows secure virtual treatment visits that youth can participate in through mobile devices. This longitudinal study uses participatory action research with mixed methods. The majority of participants identified themselves as Caucasian (66.9%). Expectedly, the demographics revealed that Anxiety Disorders and Mood Disorders were highly prevalent within the sample (71.9% and 67.5% respectively). Findings from the qualitative summary established that both staff and youth found the software and platform beneficial

The Impact of Digital Technologies on Public Health in Developed and Developing Countries

This open access book constitutes the refereed proceedings of the 18th International Conference on String Processing and Information Retrieval, ICOST 2020, held in Hammamet, Tunisia, in June 2020.* The 17 full papers and 23 short papers presented in this volume were carefully reviewed and selected from 49 submissions. They cover topics such as: IoT and AI solutions for e-health; biomedical and health informatics; behavior and activity monitoring; behavior and activity monitoring; and wellbeing technology. *This conference was held virtually due to the COVID-19 pandemic

The Impact of Digital Technologies on Public Health in Developed and Developing Countries

This open access book constitutes the refereed proceedings of the 18th International Conference on String Processing and Information Retrieval, ICOST 2020, held in Hammamet, Tunisia, in June 2020.* The 17 full papers and 23 short papers presented in this volume were carefully reviewed and selected from 49 submissions. They cover topics such as: IoT and AI solutions for e-health; biomedical and health informatics; behavior and activity monitoring; behavior and activity monitoring; and wellbeing technology. *This conference was held virtually due to the COVID-19 pandemic

Does Enrichment of Clinical Texts by Ontology Concepts Increases Classification Accuracy?

In the medical domain, multiple ontologies and terminology systems are available. However, existing classification and prediction algorithms in the clinical domain often ignore or insufficiently utilize semantic information as it is provided in those ontologies. To address this issue, we introduce a concept for augmenting embeddings, the input to deep neural networks, with semantic information retrieved from ontologies. To do this, words and phrases of sentences are mapped to concepts of a medical ontology aggregating synonyms in the same concept. A semantically enriched vector is generated and used for sentence classification. We study our approach on a sentence classification task using a real world dataset which comprises 640 sentences belonging to 22 categories. A deep neural network model is defined with an embedding layer followed by two LSTM layers and two dense layers. Our experiments show, classification accuracy without content enriched embeddings is for some categories higher than without enrichment. We conclude that semantic information from ontologies has potential to provide a useful enrichment of text. Future research will assess to what extent semantic relationships from the ontology can be used for enrichment

Proceedings of the 15th Conference on Knowledge Organization WissOrg'17 of the German Chapter of the International Society for Knowledge Organization (ISKO), 30th November - 1st December 2017, Freie Universität Berlin

Wissensorganisation is the name of a series of biennial conferences / workshops with a long tradition, organized by the German chapter of the International Society of Knowledge Organization (ISKO). The 15th conference in this series, held at Freie Universität Berlin, focused on knowledge organization for the digital humanities. Structuring, and interacting with, large data collections has become a major issue in the digital humanities. In these proceedings, various aspects of knowledge organization in the digital humanities are discussed, and the authors of the papers show how projects in the digital humanities deal with knowledge organization.Wissensorganisation ist der Name einer Konferenzreihe mit einer langjährigen Tradition, die von der Deutschen Sektion der International Society of Knowledge Organization (ISKO) organisiert wird. Die 15. Konferenz dieser Reihe, die an der Freien Universität Berlin stattfand, hatte ihren Schwerpunkt im Bereich Wissensorganisation und Digital Humanities. Die Strukturierung von und die Interaktion mit großen Datenmengen ist ein zentrales Thema in den Digital Humanities. In diesem Konferenzband werden verschiedene Aspekte der Wissensorganisation in den Digital Humanities diskutiert, und die Autoren der einzelnen Beiträge zeigen, wie die Digital Humanities mit Wissensorganisation umgehen