AIMC Topic: Biological Ontologies

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TrhOnt: building an ontology to assist rehabilitation processes.

Journal of biomedical semantics
BACKGROUND: One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiot...

Making adjustments to event annotations for improved biological event extraction.

Journal of biomedical semantics
BACKGROUND: Current state-of-the-art approaches to biological event extraction train statistical models in a supervised manner on corpora annotated with event triggers and event-argument relations. Inspecting such corpora, we observe that there is am...

Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis.

Journal of biomedical semantics
BACKGROUND: Disease and diagnosis have been the subject of much ontological inquiry. However, the insights gained therein have not yet been well enough applied to the study, management, and improvement of data quality in electronic health records (EH...

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

Journal of biomedical semantics
BACKGROUND: Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving tho...

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

Bioinformatics (Oxford, England)
UNLABELLED: The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled term...

Knowledge Discovery from Biomedical Ontologies in Cross Domains.

PloS one
In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability s...

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

Journal of biomedical semantics
BACKGROUND: We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public heal...

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

Journal of biomedical semantics
BACKGROUND: Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most oth...

Towards natural language question generation for the validation of ontologies and mappings.

Journal of biomedical semantics
BACKGROUND: The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a d...

A method for exploring implicit concept relatedness in biomedical knowledge network.

BMC bioinformatics
BACKGROUND: Biomedical information and knowledge, structural and non-structural, stored in different repositories can be semantically connected to form a hybrid knowledge network. How to compute relatedness between concepts and discover valuable but ...