Visualizing BioPortal ontology mappings¶

Introduction¶

Ontologies in biomedicine are used for several tasks including the standardization of terminology, the verification of data consistency, and the integration of heterogeneous biomedical databases. One can picture a set of biomedical ontologies as a web of biomedical concepts (an analogy to the World Wide Web, where we talk about a web of documents). A single ontology can be described as a group of closely related biomedical concepts.

When ontologists build new ontologies they often collect existing ontologies to avoid redundancy of concepts. Therefore, it is important to understand relations between existing ontologies. These relations are expressed through so called ontology mappings. Mappings among ontologies identify concepts with similar meanings.Two ontologies are mapped when they contain at least one pair of concepts with similar meaning (i.e., the concept c1 from the ontology O1 has similar meaning as the concept c2 from the ontology O2). Identifying ontology mappings is also a critical step in integrating data and applications that use different ontologies. As the number of biomedical ontologies grows, also the number of mappings between these ontologies increases. Presenting this information to users can be a challenging task and visualization technique offer one of the solutions.

Our group is developing OntoFinder, i.e., a tool for searching relevant BioPortal (https://bioportal.bioontology.org/) ontologies and building new ontologies based on existing ones. The pre-alpha version of OntoFinder can be found on http://ontofinder.dbcls.jp. As a part of OntoFinder we are also developing a tool for visual representation of mappings between ontologies. The following are some of the features that we wish to visualize within our tool: 1) Number of mappings between ontologies, 2) Communities of densely connected ontologies, 3) Bridging ontologies, i.e., ontologies that connect many other ontologies/communities, 4) Ontology overlap, 6) Ontology Authorship, and 5) Types of mappings. On this webpage we present our current progress.

Progress¶

Check our Wiki page for current progress.

List of contributors¶

• Kim Jin-Dong, Database Center for Life Sciences
• Kocbek Simon, Database Center for Life Sciences
• Perret Jean-Luc, Novartis Animal Health
• Whetzel L. Patricia, Stanford University

Publications¶

• Kocbek S, Kim JD, Perret JL, Whetzel PL, Visualizing ontology mappings to help ontology engineers identify relevant ontologies for their reuse, ICBO 2013, Montreal, Canada, (http://www.unbsj.ca/sase/csas/data/ws/icbo2013/)
• Kocbek S, Perret JL, Kim JD, Applying Visualization Techniques to Biomedical Ontology Mappings, PacificVis 2013, Sydney, Australia, http://rp-www.cs.usyd.edu.au/~visual/pvis2013/welcome/index.php. (Poster)
• Kocbek S, Perret JL, Kim JD, Visual presentation of mappings between biomedical ontologies, SWAT4LS 2012, http://ceur-ws.org/Vol-952/paper_22.pdf. (Poster)

 

This work is licensed under a Creative Commons Attribution 3.0 Unported License (http://creativecommons.org/licenses/by/3.0/).
Last updated: June, 2013