AIMC Topic: Biological Ontologies
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The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.
Mammalian genome : official journal of the International Mammalian Genome Society
Apr 19, 2023
Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for ...
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.
Journal of biomedical informatics
Mar 17, 2023
BACKGROUND: Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical or other natural products are co-consumed with pharmaceutical drugs. With the growing use of natural products, the risk for potential NPDIs and consequent adve...
Content and quality of physical activity ontologies: a systematic review.
The international journal of behavioral nutrition and physical activity
Mar 13, 2023
INTRODUCTION: Ontologies are a formal way to represent knowledge in a particular field and have the potential to transform the field of health promotion and digital interventions. However, few researchers in physical activity (PA) are familiar with o...
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.
Journal of biomedical semantics
Feb 24, 2023
BACKGROUND: Evaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically important in an age of greater pollution and chemicals in our environment. Environmental health utilizes many differ...
Defining the distance between diseases using SNOMED CT embeddings.
Journal of biomedical informatics
Feb 3, 2023
Characterizing disease relationships is essential to biomedical research to understand disease etiology and improve clinical decision-making. Measurements of distance between disease pairs enable valuable research tasks, such as subgrouping patients ...
Brain Data Standards - A method for building data-driven cell-type ontologies.
Scientific data
Jan 24, 2023
Large-scale single-cell 'omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due to the diversity and complexity of the brain. But this poses a problem: How do we organise...
Knowledge Graph Embeddings for ICU readmission prediction.
BMC medical informatics and decision making
Jan 19, 2023
BACKGROUND: Intensive Care Unit (ICU) readmissions represent both a health risk for patients,with increased mortality rates and overall health deterioration, and a financial burden for healthcare facilities. As healthcare became more data-driven with...
Klarigi: Characteristic explanations for semantic biomedical data.
Computers in biology and medicine
Dec 22, 2022
Annotation of biomedical entities with ontology classes provides for formal semantic analysis and mobilisation of background knowledge in determining their relationships. To date, enrichment analysis has been routinely employed to identify classes th...
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs.
Journal of biomedical semantics
Aug 13, 2022
BACKGROUND: The Vaccine Ontology (VO) is a biomedical ontology that standardizes vaccine annotation. Errors in VO will affect a multitude of applications that it is being used in. Quality assurance of VO is imperative to ensure that it provides accur...
DCSO: towards an ontology for machine-actionable data management plans.
Journal of biomedical semantics
Jul 26, 2022
The concept of Data Management Plan (DMP) has emerged as a fundamental tool to help researchers through the systematical management of data. The Research Data Alliance DMP Common Standard (DCS) working group developed a set of universal concepts char...
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