Indented Tree or Graph? A Usability Study of Ontology Visualization Techniques in the Context of Class Mapping Evaluation

IrGO: Iranian traditional medicine General Ontology and knowledge base

Background

Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been proposed for the concepts of this medicine up to the present time. Considering the extensive terminology in the numerous textbooks written by the scholars over centuries, comprehending the totality of concepts is obviously a very challenging task. To resolve this issue, overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity.

Construction and content

Makhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of the concepts used to describe medicinal substances. The steps followed to accomplish this task included (1) compiling the list of classes via examination of textbooks, and text mining the resource followed by manual review to ensure comprehensiveness of extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms, and definitions (English and Persian); (5) ontology evaluation. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry.

Utility and discussion

The ontology was finalized with inclusion of 3521 classes, 15 properties, and 20,903 axioms in the Iranian traditional medicine General Ontology (IrGO) database, freely available at http://ir-go.net/. An indented list and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in UNaProd database to create a knowledge base of ITM materia medica.

Conclusion

We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. This ontology will aid Persian medicine practitioners in clinical decision-making to select drugs. Extending IrGO will bridge the gap between traditional and conventional schools of medicine, helping guide future research in the process of drug discovery.

KGDDS: A System for Drug-Drug Similarity Measure in Therapeutic Substitution based on Knowledge Graph Curation

Measuring drug-drug similarity is important but challenging. Significant progresses have been made in drugs whose labeled training data is sufficient and available. However, handling data skewness and incompleteness with domain-specific knowledge graph, is still a relatively new territory and an under-explored prospect. In this paper, we present a system KGDDS for node-link-based bio-medical Knowledge Graph curation and visualization, aiding Drug-Drug Similarity measure. Specifically, we reuse existing knowledge bases to alleviate the difficulties in building a high-quality knowledge graph, ranging in size up to 7 million edges. Then we design a prediction model to explore the pharmacology features and knowledge graph features. Finally, we propose a user interaction model to allow the user to better understand the drug properties from a drug similarity perspective and gain insights that are not easily observable in individual drugs. Visual result demonstration and experimental results indicate that KGDDS can bridge the user/caregiver gap by facilitating antibiotics prescription knowledge, and has remarkable applicability, outperforming existing state-of-the-art drug similarity measures.

Visualizations of bibliographic information: A user experience study

Bibliographic information was presented using five different prototype systems, including four different visualizations of FRBR-based bibliographic information and one more traditional bibliographic information system. This study reports user performance and perceptions using the same tasks across the different visualizations. Users include undergraduate students of a large university in the USA. The study’s methodology is based on a continuation of a study testing the same prototype interfaces in Slovenia, with a number of modifications. The findings show visualization displays performing better on a number of measures than the traditional library catalog interface. A comparison of results highlights some of the differences in findings between the two groups of users. The paper concludes with a discussion on the implications for the design of future bibliographic information interfaces.

Ontology visualization methods and tools: a survey of the state of the art

Various ontology visualization tools using different visualization methods exist and new ones are being developed every year. The goal of this paper is to follow up on previous surveys with an updated classification of ontology visualization methods and a comprehensive survey of available tools. The tools are analyzed for the used visualization methods, interaction techniques and supported ontology constructs. It shows that most of the tools apply two-dimensional node-link visualizations with a focus on class hierarchies. Color and shape are used with little variation, support for constructs introduced with version 2 of the OWL Web Ontology Language is limited, and it often remains vague what tasks and use cases are supported by the visualizations. Major challenges are the limited maturity and usability of many of the tools as well as providing an overview of large ontologies while also showing details on demand. We see a high demand for a universal ontology visualization framework implementing a core set of visual and interactive features that can be extended and customized to respective use cases.

Methods and applications for visualization of SNOMED CT concept sets

Inconsistent use of SNOMED CT concepts may reduce comparability of information in health information systems. Terminology implementation should be approached by common strategies for navigating and selecting proper concepts. This study aims to explore ways of illustrating common pathways and ancestors of particular sets of concepts, to support consistent use of SNOMED CT and also assess potential applications for such visualizations. The open source prototype presented is an interactive web-based re-implementation of the terminology visualization tool TermViz that provides an overview of concepts and their hierarchical relations. It provides terminological features such as interactively rearranging graphs, fetching more concept nodes, highlighting least common parents and shared pathways in merged graphs etc. Four teams of three to four people used the prototype to complete a terminology mapping task and then, in focus group interviews, discussed the user experience and potential future tool usage. Potential purposes discussed included SNOMED CT search and training, consistent selection of concepts and content management. The evaluation indicated that the tool may be useful in many contexts especially if integrated with existing systems, and that the graph layout needs further tuning and development.