Identifying "bridging ontologies" and communities of densely connected ontologies

In this part of our work we wish to visualize mappings between all BioPortal ontologies and its main purpose is to answer the following two questions:
  1. Which BioPortal ontologies form communities of densely connected ontologies?, and
  2. Which BioPortal ontologies connect many other ontologies/communities?

We use Gephi ( to visualize our data. Gephi provides layout algorithms to draw large graphs as well as node and edge filtering capabilities. In addition, a number of graph and node properties can be calculated with Gephi. We use the following two main features of Gephi: Modularity Analysis (or Community Detection) and Betweenness centrality. The former was used to answer the first question above, while the latter was used to answer the second question.

Since mapping information on BioPortal changes through time, different versions of our visualizations are available.

Version: Examples of graph interpretation:


This work is licensed under a Creative Commons Attribution 3.0 Unported License (
Last updated: June, 2013

88x31.png (4.63 KB) Simon Kocbek, 02/18/2013 02:07 PM