AIMC Topic: Biological Ontologies
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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...
Patient safety classifications, taxonomies and ontologies: A systematic review on development and evaluation methodologies.
Journal of biomedical informatics
Jul 22, 2022
INTRODUCTION: Patient safety classifications/ontologies enable patient safety information systems to receive and analyze patient safety data to improve patient safety. Patient safety classifications/ontologies have been developed and evaluated using ...
Performance assessment of ontology matching systems for FAIR data.
Journal of biomedical semantics
Jul 15, 2022
BACKGROUND: Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data and, thus, creating the need...
Toward a standard formal semantic representation of the model card report.
BMC bioinformatics
Jul 14, 2022
BACKGROUND: Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health's Bridge2AI initiative to address the FAIR chal...
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.
Journal of biomedical semantics
Jun 27, 2022
BACKGROUND: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and met...
A vector-based semantic relatedness measure using multiple relations within SNOMED CT and UMLS.
Journal of biomedical informatics
Jun 9, 2022
OBJECTIVE: To propose a new vector-based relatedness metric that derives word vectors from the intrinsic structure of biomedical ontologies, without consulting external resources such as large-scale biomedical corpora.
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