AIMC Topic: Biological Ontologies

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Special supplement issue on quality assurance and enrichment of biological and biomedical ontologies and terminologies.

BMC medical informatics and decision making Aug 30, 2024
Ontologies and terminologies serve as the backbone of knowledge representation in biomedical domains, facilitating data integration, interoperability, and semantic understanding across diverse applications. However, the quality assurance and enrichme...
Humans COVID-19 Electronic Health Records Biological Ontologies Vocabulary, Controlled
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An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology.

Journal of biomedical semantics Aug 30, 2024
Automatic disease progression prediction models require large amounts of training data, which are seldom available, especially when it comes to rare diseases. A possible solution is to integrate data from different medical centres. Nevertheless, vari...
Humans Retrospective Studies Amyotrophic Lateral Sclerosis Multiple Sclerosis Semantics Biological Ontologies
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Concretizing plan specifications as realizables within the OBO foundry.

Journal of biomedical semantics Aug 20, 2024
BACKGROUND: Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a "realizable concretizat...
Biological Ontologies
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Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models.

Journal of biomedical semantics Aug 10, 2024
BACKGROUND: Vaccines have revolutionized public health by providing protection against infectious diseases. They stimulate the immune system and generate memory cells to defend against targeted diseases. Clinical trials evaluate vaccine performance, ...
Humans Natural Language Processing Vaccines Biological Ontologies Clinical Trials as Topic Unified Medical Language System
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An ontology-based tool for modeling and documenting events in neurosurgery.

BMC medical informatics and decision making Jul 31, 2024
BACKGROUND: Intraoperative neurophysiological monitoring (IOM) plays a pivotal role in enhancing patient safety during neurosurgical procedures. This vital technique involves the continuous measurement of evoked potentials to provide early warnings a...
Humans Software Neurosurgical Procedures Documentation Biological Ontologies
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Predicting Future Disorders via Temporal Knowledge Graphs and Medical Ontologies.

IEEE journal of biomedical and health informatics Jul 2, 2024
Despite the vast potential for insights and value present in Electronic Health Records (EHRs), it is challenging to fully leverage all the available information, particularly that contained in the free-text data written by clinicians describing the h...
Humans Algorithms Electronic Health Records Biological Ontologies
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Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis.

Journal of biomedical semantics Jun 19, 2024
BACKGROUND: The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. The heterogeneity of cancer vaccine data significantly impedes effective integration and analysis. While CanVaxKB ser...
Humans Data Analysis Cancer Vaccines Biological Ontologies Reference Standards
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Report of the HIMSS-SIIM Enterprise Imaging Community Data Standards Evaluation Workgroup: Anatomic Ontology Assessment.

Journal of imaging informatics in medicine Jun 10, 2024
Previously, the lack of a standard body part ontology has been identified as a critical deficiency needed to enable enterprise imaging. This whitepaper aims to provide a comprehensive assessment of anatomical ontologies with the aim of facilitating e...
Humans Diagnostic Imaging Medical Informatics Systematized Nomenclature of Medicine Biological Ontologies Terminology as Topic Anatomy
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On the relationship between scientific theory and ontology in everything flows.

History and philosophy of the life sciences May 30, 2024
In their anthology Everything Flows: Towards a Processual Philosophy of Biology, Daniel J. Nicholson and John Dupré argue that modern theories of biology imply that the fundamental structure of reality is processual at its core. In the present work, ...
Biology Biological Ontologies Philosophy Metaphysics
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Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.

BMC medical informatics and decision making May 22, 2024
BACKGROUND: One significant challenge in addressing the coronavirus disease 2019 (COVID-19) pandemic is to grasp a comprehensive picture of its infectious mechanisms. We urgently need a consistent framework to capture the intricacies of its complicat...
Humans COVID-19 SARS-CoV-2 Biological Ontologies Homeostasis
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