AIMC Topic: Biological Ontologies
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Similarity Calculation, Enrichment Analysis, and Ontology Visualization of Biomedical Ontologies using UFO.
Current protocols
Apr 1, 2021
The rapid growth of biomedical ontologies observed in recent years has been reported to be useful in various applications. In this article, we propose two main-function protocols-term-related and entity-related-with the three most common ontology ana...
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease.
Database : the journal of biological databases and curation
Feb 16, 2021
Omics technologies offer great promises for improving our understanding of diseases. The integration and interpretation of such data pose major challenges, calling for adequate knowledge models. Disease maps provide curated knowledge about disorders'...
The Human Phenotype Ontology in 2021.
Nucleic acids research
Jan 8, 2021
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for ...
Using Neural Networks for Relation Extraction from Biomedical Literature.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedic...
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.
Journal of the American Medical Informatics Association : JAMIA
Jul 1, 2020
OBJECTIVE: The goal of this study is to develop a robust Time Event Ontology (TEO), which can formally represent and reason both structured and unstructured temporal information.
Development of the Gender, Sex, and Sexual Orientation ontology: Evaluation and workflow.
Journal of the American Medical Informatics Association : JAMIA
Jul 1, 2020
OBJECTIVE: The study sought to create an integrated vocabulary system that addresses the lack of standardized health terminology in gender and sexual orientation.
A Semantic Similarity Evaluation for Healthcare Ontologies Matching to HL7 FHIR Resources.
Studies in health technology and informatics
Jun 16, 2020
Healthcare 4.0 demands healthcare data to be shaped into a common standardized and interoperable format for achieving more efficient data exchange. Most of the techniques addressing this domain are dealing only with specific cases of data transformat...
Ontologies for Liver Diseases Representation: A Systematic Literature Review.
Journal of digital imaging
Jun 1, 2020
Ontology, as a useful knowledge engineering technique, has been widely used for reducing ambiguity and helping with information sharing. It is considered originally to be clear, comprehensive, and with well-defined format. It characterizes several do...
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Bioinformatics (Oxford, England)
Apr 1, 2020
MOTIVATION: Over the past years, significant resources have been invested into formalizing biomedical ontologies. Formal axioms in ontologies have been developed and used to detect and ensure ontology consistency, find unsatisfiable classes, improve ...
Evaluation of ontology structural metrics based on public repository data.
Briefings in bioinformatics
Mar 23, 2020
The development and application of biological ontologies have increased significantly in recent years. These ontologies can be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In th...
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