AIMC Topic: Biological Ontologies

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Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.

BMC systems biology
BACKGROUND: Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and widely used to identify causati...

A mode-of-action ontology model for safety evaluation of chemicals: Outcome of a series of workshops on repeated dose toxicity.

Toxicology in vitro : an international journal published in association with BIBRA
Repeated dose toxicity evaluation aims at assessing the occurrence of adverse effects following chronic or repeated exposure to chemicals. Non-animal approaches have gained importance in the last decades because of ethical considerations as well as d...

DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Cell systems
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, call...

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.

Scientific reports
Data are increasingly annotated with multiple ontologies to capture rich information about the features of the subject under investigation. Analysis may be performed over each ontology separately, but recently there has been a move to combine multipl...

Drivers for the development of an Animal Health Surveillance Ontology (AHSO).

Preventive veterinary medicine
Comprehensive reviews of syndromic surveillance in animal health have highlighted the hindrances to integration and interoperability among systems when data emerge from different sources. Discussions with syndromic surveillance experts in the fields ...

Levels and building blocks-toward a domain granularity framework for the life sciences.

Journal of biomedical semantics
BACKGROUND: With the emergence of high-throughput technologies, Big Data and eScience, the use of online data repositories and the establishment of new data standards that require data to be computer-parsable become increasingly important. As a conse...

Development of a cardiac-centered frailty ontology.

Journal of biomedical semantics
BACKGROUND: A Cardiac-centered Frailty Ontology can be an important foundation for using NLP to assess patient frailty. Frailty is an important consideration when making patient treatment decisions, particularly in older adults, those with a cardiac ...

A scoping review of ontologies related to human behaviour change.

Nature human behaviour
Ontologies are classification systems specifying entities, definitions and inter-relationships for a given domain, with the potential to advance knowledge about human behaviour change. A scoping review was conducted to: (1) identify what ontologies e...

An ontological foundation for ocular phenotypes and rare eye diseases.

Orphanet journal of rare diseases
BACKGROUND: The optical accessibility of the eye and technological advances in ophthalmic diagnostics have put ophthalmology at the forefront of data-driven medicine. The focus of this study is rare eye disorders, a group of conditions whose clinical...