Methods in biomedical ontology

Methods in biomedical ontology

Research on ontologies is becoming widespread in the biomedical informatics community. At the same time, it has become apparent that the challenges of properly constructing and maintaining ontologies have proven more difficult than many workers in the field initially expected. Discovering general, feasible methods has thus become a central activity for many of those hoping to reap the benefits ...

Mechanisms in biomedical ontology

The concept of a mechanism has become a standard proposal for explanations in biology. It has been claimed that mechanistic explanations are appropriate for systems biology, because they occupy a middle ground between strict reductionism and holism. Because of their importance in the field a formal ontological description of mechanisms is desirable. The standard philosophical accounts of mechan...

Exploring biomedical ontology mappings with graph theory methods

BACKGROUND In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patte...

Natural Language Processing methods and systems for biomedical ontology learning

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they must achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-...

Advancing Ontology Alignment: New Methods for Biomedical Ontology Alignment using Non Equivalence Relations