AIMC Topic: Biological Ontologies
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Jackalope Plus tool for post-coordination, ontology development, and precise mapping in observational health studies.
Scientific reports
Jul 2, 2025
Accurate mapping of complex health data to the OMOP CDM while preserving clinical nuance remains a challenge. We introduce Jackalope Plus, a novel tool leveraging SNOMED CT post-coordination and a GPT-4o mini LLM, to significantly enhance the precisi...
Enhancing the Accuracy of Human Phenotype Ontology Identification: Comparative Evaluation of Multimodal Large Language Models.
Journal of medical Internet research
Jun 2, 2025
BACKGROUND: Identifying Human Phenotype Ontology (HPO) terms is crucial for diagnosing and managing rare diseases. However, clinicians, especially junior physicians, often face challenges due to the complexity of describing patient phenotypes accurat...
Development and evaluation of the COntextualised and Personalised Physical activity and Exercise Recommendations (COPPER) Ontology.
The international journal of behavioral nutrition and physical activity
May 5, 2025
BACKGROUND: Personalised recommendations for action and coping plans for physical activity (PA) may reduce user burden and increase plan quality. Ontologies are a promising alternative to existing black-box approaches for creating such personalised r...
Knowledge Representation and Management: 2023 Highlights and the Rise of Knowledge Graph Embeddings.
Yearbook of medical informatics
Apr 8, 2025
OBJECTIVES: We aim to identify, select, and summarize the best papers published in 2023 for the Knowledge Representation and Management (KRM) section of the International Medical Informatics Association (IMIA) Yearbook.
MIO: An ontology for annotating and integrating medical knowledge in myocardial infarction to enhance clinical decision making.
Computers in biology and medicine
Apr 1, 2025
As biotechnology and computer science continue to advance, there's a growing amount of biomedical data worldwide. However, standardizing and consolidating these data remains challenging, making analysis and comprehension more difficult. To enhance re...
Digital evolution: Novo Nordisk's shift to ontology-based data management.
Journal of biomedical semantics
Mar 22, 2025
The amount of biomedical data is growing, and managing it is increasingly challenging. While Findable, Accessible, Interoperable and Reusable (FAIR) data principles provide guidance, their adoption has proven difficult, especially in larger enterpris...
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping.
Journal of biomedical informatics
Mar 21, 2025
OBJECTIVE: To illustrate the use of an ontology in evaluating data quality in the medical field, focusing on phenotyping lung cancers.
GNOme, an ontology for glycan naming and subsumption.
Analytical and bioanalytical chemistry
Feb 8, 2025
While GlyTouCan provides stable identifiers for referencing glycan structures, they are not organized semantically. GNOme, a glycan naming and subsumption ontology and a member of the OBOFoundry, organizes GlyTouCan accessions for automated reasoning...
An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets.
Scientific data
Feb 8, 2025
Although rare diseases (RDs) affect over 260 million individuals worldwide, low data quality and scarcity challenge effective care and research. This work aims to harmonise the Common Data Set by European Rare Disease Registry Infrastructure, Health ...
An Ontology for Digital Medicine Outcomes: Development of the Digital Medicine Outcomes Value Set (DOVeS).
JMIR medical informatics
Feb 6, 2025
BACKGROUND: Over the last 10-15 years, US health care and the practice of medicine itself have been transformed by a proliferation of digital medicine and digital therapeutic products (collectively, digital health tools [DHTs]). While a number of DHT...
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