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Biological Ontologies

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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...

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

BMC medical informatics and decision making
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
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...

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...

simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.

BMC genomics
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...

The text2term tool to map free-text descriptions of biomedical terms to ontologies.

Database : the journal of biological databases and curation
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types-such as disease names, cell types, or chemicals-that are used in metadata associated with biomedical data. W...

Enhancing Arden-Syntax-Based Clinical Reasoning with Ontologies.

Studies in health technology and informatics
We present a new methodological approach based on integrating Arden-Syntax-based clinical decision support (CDS) with an upstream ontology service. Incoming linguistic patient data, such as single reports about detected germs or viruses, shall be ide...