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Biological Ontologies

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Bayesian-knowledge driven ontologies: A framework for fusion of semantic knowledge under uncertainty and incompleteness.

PloS one
The modeling of uncertain information is an open problem in ontology research and is a theoretical obstacle to creating a truly semantic web. Currently, ontologies often do not model uncertainty, so stochastic subject matter must either be normalized...

Developing an ontology of non-pharmacological treatment for emotional and mood disturbances in dementia.

Scientific reports
Emotional and mood disturbances are common in people with dementia. Non-pharmacological interventions are beneficial for managing these disturbances. However, effectively applying these interventions, particularly in the person-centred approach, is a...

PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data.

Briefings in bioinformatics
Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for...

Ontological representation, modeling, and analysis of parasite vaccines.

Journal of biomedical semantics
BACKGROUND: Pathogenic parasites are responsible for multiple diseases, such as malaria and Chagas disease, in humans and livestock. Traditionally, pathogenic parasites have been largely an evasive topic for vaccine design, with most successful vacci...

On the relationship between scientific theory and ontology in everything flows.

History and philosophy of the life sciences
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, ...

Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.

BMC medical informatics and decision making
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...

MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology.

Neuroinformatics
Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges inherent in...

Predicting Future Disorders via Temporal Knowledge Graphs and Medical Ontologies.

IEEE journal of biomedical and health informatics
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...

CoRTEx: contrastive learning for representing terms via explanations with applications on constructing biomedical knowledge graphs.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVES: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of ...