AIMC Topic: Biological Ontologies
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Leveraging Transformers-based models and linked data for deep phenotyping in radiology.
Computer methods and programs in biomedicine
Jan 3, 2025
BACKGROUND AND OBJECTIVE: Despite significant investments in the normalization and the standardization of Electronic Health Records (EHRs), free text is still the rule rather than the exception in clinical notes. The use of free text has implications...
Hypothesis generation for rare and undiagnosed diseases through clustering and classifying time-versioned biological ontologies.
PloS one
Dec 26, 2024
Rare diseases affect 1-in-10 people in the United States and despite increased genetic testing, up to half never receive a diagnosis. Even when using advanced genome sequencing platforms to discover variants, if there is no connection between the var...
Core reference ontology for individualized exercise prescription.
Scientific data
Dec 18, 2024
"Exercise is medicine" emphasizes personalized prescriptions for better efficacy. Current guidelines need more support for personalized prescriptions, posing scientific challenges. Facing those challenges, we gathered data from established guidelines...
An Automatic and End-to-End System for Rare Disease Knowledge Graph Construction Based on Ontology-Enhanced Large Language Models: Development Study.
JMIR medical informatics
Dec 18, 2024
BACKGROUND: Rare diseases affect millions worldwide but sometimes face limited research focus individually due to low prevalence. Many rare diseases do not have specific International Classification of Diseases, Ninth Edition (ICD-9) and Tenth Editio...
Ontology-based integration and querying of heterogeneous rare disease data sources - POLVAS perspective.
Computers in biology and medicine
Dec 2, 2024
The integration of rare disease medical databases belonging to different countries is an important problem, as a large number of observations are required for reliable statistical inference of patient data in order to facilitate clinical research. Su...
simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.
BMC genomics
Sep 16, 2024
BACKGROUND: Bio-ontologies are keys in structuring complex biological information for effective data integration and knowledge representation. Semantic similarity analysis on bio-ontologies quantitatively assesses the degree of similarity between bio...
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...
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...
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...
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, ...
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