Studies in health technology and informatics
May 25, 2022
Representing temporal information is a recurrent problem for biomedical ontologies. We propose a foundational ontology that combines the so-called three-dimensional and four-dimensional approaches in order to be able to track changes in an individual...
Mathematical biosciences and engineering : MBE
May 19, 2022
Computing the minimal axiom sets (MinAs) for an unsatisfiable class is an important task in incoherent ontology debugging. Ddebugging ontologies based on patterns (DOBP) is a pattern-based debugging method that uses a set of heuristic strategies base...
Nucleic acids research
Jan 7, 2022
The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on availa...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
The data FAIR Guiding Principles state that all data should be Findable, Accessible, Interoperable, and Reusable. Ontology is critical to data integration, sharing, and analysis. Given thousands of ontologies have been developed in the era of artific...
Health informatics journal
Jan 1, 2022
Pneumonia is difficult to differentiate from other pulmonary diseases because it shares many symptoms with these diseases. Diagnosing pneumonia in clinical practice would benefit from having access to a codified representation of clinical knowledge....
Studies in health technology and informatics
Nov 18, 2021
Ontologies listed in the OBO Foundry are often regarded as reliable choices to be reused but ontology interoperability of them remains unknown. This study evaluated the resolvability of URIs and consistency of axioms in the OBO Foundry library, BFO o...
Studies in health technology and informatics
Oct 27, 2021
The wide-spread use of Common Data Models and information models in biomedical informatics encourages assumptions that those models could provide the entirety of what is needed for knowledge representation purposes. Based on the lack of computable se...
Database : the journal of biological databases and curation
Oct 26, 2021
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are deve...
Briefings in bioinformatics
Jul 20, 2021
Ontologies have long been employed in the life sciences to formally represent and reason over domain knowledge and they are employed in almost every major biological database. Recently, ontologies are increasingly being used to provide background kno...
Database : the journal of biological databases and curation
Jul 9, 2021
The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions...