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Biological Ontologies

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Ontologies for Liver Diseases Representation: A Systematic Literature Review.

Journal of digital imaging
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)
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
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...

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

JCO clinical cancer informatics
PURPOSE: The purpose of OncoMX knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types.

A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.

Database : the journal of biological databases and curation
The ability to compare entities within a knowledge graph is a cornerstone technique for several applications, ranging from the integration of heterogeneous data to machine learning. It is of particular importance in the biomedical domain, where seman...

FOBI: an ontology to represent food intake data and associate it with metabolomic data.

Database : the journal of biological databases and curation
Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these t...

Using clinical reasoning ontologies to make smarter clinical decision support systems: a systematic review and data synthesis.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: The study sought to describe the literature describing clinical reasoning ontology (CRO)-based clinical decision support systems (CDSSs) and identify and classify the medical knowledge and reasoning concepts and their properties within the...

Whole-brain death and integration: realigning the ontological concept with clinical diagnostic tests.

Theoretical medicine and bioethics
For decades, physicians, philosophers, theologians, lawyers, and the public considered brain death a settled issue. However, a series of recent cases in which individuals were declared brain dead yet physiologically maintained for prolonged periods o...

Provenance for Biomedical Ontologies with RDF and Git.

Studies in health technology and informatics
The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. In order to enable consortium-wide retrospective research and prospective patient recruitment, we perform data integration into a centra...

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Current protocols in human genetics
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnost...