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Biological Ontologies

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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 ...

Merging Biomedical Ontologies with BioSTransformers.

Studies in health technology and informatics
Ontologies play a key role in representing and structuring domain knowledge. In the biomedical domain, the need for this type of representation is crucial for structuring, coding, and retrieving data. However, available ontologies do not encompass al...

Dementia Ontology Development to Facilitate Collection of High-Quality Dementia Data.

Studies in health technology and informatics
The population of dementia patients is on the rise, as society undergoes rapid aging. This led to an expansion of dementia-related data. This study aims to develop a comprehensive dementia ontology to facilitate the collection and analysis of high-qu...

OntoBridge Versus Traditional ETL: Enhancing Data Standardization into CDM Formats Using Ontologies Within the DATOS-CAT Project.

Studies in health technology and informatics
Common Data Models (CDMs) enhance data exchange and integration across diverse sources, preserving semantics and context. Transforming local data into CDMs is typically cumbersome and resource-intensive, with limited reusability. This article compare...

Active Learning Pipeline to Identify Candidate Terms for a CDSS Ontology.

Studies in health technology and informatics
Ontology is essential for achieving health information and information technology application interoperability in the biomedical fields and beyond. Traditionally, ontology construction is carried out manually by human domain experts (HDE). Here, we e...

Modelling Events in Biomedical Decision Support Systems Using Ontologies.

Studies in health technology and informatics
Biomedical decision support systems play a crucial role in modern healthcare by assisting clinicians in making informed decisions. Events, such as physiological changes or drug reactions, are integral components of these systems, influencing patient ...

Ontologies related to livestock for the Global Burden of Animal Diseases programme: a review.

Revue scientifique et technique (International Office of Epizootics)
The Global Burden of Animal Diseases (GBADs) programme aims to assess the impact of animal health on agricultural animals, livestock production systems and associated communities worldwide. As part of the objectives of GBADs'Animal Health Ontology th...

Interpretive Description in Computerized Ontology Development: Rigour.

Studies in health technology and informatics
This poster presents the use of Interpretive Description in ontology development. The methods selected attended to the need for quality and rigour.

Towards the development of a FAIR-compliant biomedical ontology for colorectal cancer.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Despite the widespread development of ontologies in many domains of healthcare, the field of colorectal cancer (CRC) presents a notable gap considering the lack of standardized data models tailored to the CRC domain. To address this gap, we developed...

FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology.

Bioinformatics (Oxford, England)
MOTIVATION: Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing...