AIMC Topic: Biological Ontologies
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The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
A requirement of realism-based ontology design is that classes denote exclusively entities that exist objectively in reality and that their definitions adhere to strict criteria to ensure that the classes are re-usable in other ontologies while prese...
Evaluation of Semantic Web Technologies for Storing Computable Definitions of Electronic Health Records Phenotyping Algorithms.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelera...
Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
While biomedical ontologies have traditionally been used to guide the identification of concepts or relations in biomedical data, recent advances in deep learning are able to capture high-quality knowledge from textual data and represent it in graphi...
Improving the 'Fitness for Purpose' of Common Data Models through Realism Based Ontology.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Apr 16, 2018
Common data models are designed and built based on requirements that are aimed towards fitness for purpose. But when common data models are used as lenses through which reality is observed from the perspective according to which they are built, then ...
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.
Journal of biomedical semantics
Apr 12, 2018
BACKGROUND: Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CV...
An ontological approach to identifying cases of chronic kidney disease from routine primary care data: a cross-sectional study.
BMC nephrology
Apr 10, 2018
BACKGROUND: Accurately identifying cases of chronic kidney disease (CKD) from primary care data facilitates the management of patients, and is vital for surveillance and research purposes. Ontologies provide a systematic and transparent basis for cli...
SSDOnt: An Ontology for Representing Single-Subject Design Studies.
Methods of information in medicine
Apr 5, 2018
BACKGROUND: Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate ...
Matching biomedical ontologies based on formal concept analysis.
Journal of biomedical semantics
Mar 19, 2018
BACKGROUND: The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analy...
Design and validation of an ontology-driven animal-free testing strategy for developmental neurotoxicity testing.
Toxicology and applied pharmacology
Mar 13, 2018
Developmental neurotoxicity entails one of the most complex areas in toxicology. Animal studies provide only limited information as to human relevance. A multitude of alternative models have been developed over the years, providing insights into mech...
An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies.
Journal of biomedical informatics
Mar 13, 2018
One of the basic challenges in developing structural methods for systematic audition on the quality of biomedical ontologies is the computational cost usually involved in exhaustive sub-graph analysis. We introduce ANT-LCA, a new algorithm for comput...
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