Onyx: A new Canvas‐based tool for visualizing biomedical and health ontologies

Abstract

Ontologies provide formal, machine‐readable, and human‐interpretable representations of domain knowledge. Therefore, ontologies have come into question with the development of Semantic Web technologies. People who want to use ontologies need an understanding of the ontology, but this understanding is very difficult to attain if the ontology user lacks the background knowledge necessary to comprehend the ontology or if the ontology is very large. Thus, software tools that facilitate the understanding of ontologies are needed. Ontology visualization is an important research area because visualization can help in the development, exploration, verification, and comprehension of ontologies. This paper introduces the design of a new ontology visualization tool, which differs from traditional visualization tools by providing important metrics and analytics about ontology concepts and warning the ontology developer about potential ontology design errors. The tool, called Onyx, also has advantages in terms of speed and readability. Thus, Onyx offers a suitable environment for the representation of large ontologies, especially those used in biomedical and health information systems and those that contain many terms. It is clear that these additional functionalities will increase the value of traditional ontology visualization tools during ontology exploration and evaluation.

Visualisation for ontology sense-making: A tree-map based algorithmic approach

“…Henceforth with lots of nodes and edges crossing each other, this will make the presentation canvas cognitively complex to comprehend. Refer table 1 provided in the appendix to recognise several of ontology visualisation plugins that use this method [6], [12]- [14].…”

Karyon: A scalable and easy to integrate ontology summarisation framework

“…Cytoscape.js uses Canvas technology, which provides better results in terms of performance. Therefore, in our previous work [5], we preferred Cytoscape.js library to develop a web-based ontology visualisation tool. In the study by Ozturk and Acikgoz [5], we used the key concept extraction (KCE) algorithm [12] to visualise the summaries of large ontologies.…”

“…It is getting more attention recently [2,3]. Ontology summarisation algorithms are frequently used in ontology visualisation tools (KC-Viz [4], Onyx [5]), social network analysis [6,7] and semantic abstraction [8,9].…”