AIMC Topic: Biological Ontologies
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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...
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...
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