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Biological Ontologies

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Large-Scale Coarse-to-Fine Object Retrieval Ontology and Deep Local Multitask Learning.

Computational intelligence and neuroscience
Object retrieval plays an increasingly important role in video surveillance, digital marketing, e-commerce, etc. It is facing challenges such as large-scale datasets, imbalanced data, viewpoint, cluster background, and fine-grained details (attribute...

PhenPath: a tool for characterizing biological functions underlying different phenotypes.

BMC genomics
BACKGROUND: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For...

Phenotype annotation with the ontology of microbial phenotypes (OMP).

Journal of biomedical semantics
BACKGROUND: Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond m...

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

Journal of biomedical informatics
BACKGROUND: In precision medicine, deep phenotyping is defined as the precise and comprehensive analysis of phenotypic abnormalities, aiming to acquire a better understanding of the natural history of a disease and its genotype-phenotype associations...

Predicting instances of pathway ontology classes for pathway integration.

Journal of biomedical semantics
BACKGROUND: To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology as a unifying ontology for or...

Consensus Development of a Modern Ontology of Emergency Department Presenting Problems-The Hierarchical Presenting Problem Ontology (HaPPy).

Applied clinical informatics
OBJECTIVE: Numerous attempts have been made to create a standardized "presenting problem" or "chief complaint" list to characterize the nature of an emergency department visit. Previous attempts have failed to gain widespread adoption as they were no...

Ontology-based metabolomics data integration with quality control.

Bioanalysis
 The complications that arise when performing meta-analysis of datasets from multiple metabolomics studies are addressed with computational methods that ensure data quality, completeness of metadata and accurate interpretation across studies. This p...

An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.

Nutrients
BACKGROUND: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research out...

Sentiment Analysis of Social Media on Childhood Vaccination: Development of an Ontology.

Journal of medical Internet research
BACKGROUND: Although vaccination rates are above the threshold for herd immunity in South Korea, a growing number of parents have expressed concerns about the safety of vaccines. It is important to understand these concerns so that we can maintain hi...

Ontology-Based Interactive Visualization of Patient-Generated Research Questions.

Applied clinical informatics
BACKGROUND: Crohn's disease and colitis are chronic conditions that affect every facet of patients' lives (e.g., social interaction, family, work, diet, and sleep). Thus, treatment consists largely of disease management. The University of North Carol...