Evolution of biomedical ontologies and mappings: Overview of recent approaches <s> Visualizing ontology evolution <s> BackgroundNumerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.ResultsWe present OnEX (Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, OnEX provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.ConclusionOnEX provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at http://www.izbi.de/onex. <s> BIB001 </s> Evolution of biomedical ontologies and mappings: Overview of recent approaches <s> Visualizing ontology evolution <s> Summary: Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff ). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology which users can interactively analyze in multiple ways. Availability and Implementation: CODEX is available under http: //www.izbi.de/codex and is supported by all major browsers. It is implemented in Java based on Google Web Toolkit technology. Additionally, users can access a web service interface to use the diff functionality in their applications and analyses. <s> BIB002 </s> Evolution of biomedical ontologies and mappings: Overview of recent approaches <s> Visualizing ontology evolution <s> Summary: WebProtege is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtege also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtege itself by configuring the project as an OBO project. ::: ::: Availability and implementation: WebProtege is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtege is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. ::: ::: Contact: ude.drofnats@egdirroh.wehttam ::: ::: Supplementary information: Supplementary data are available at Bioinformatics online. <s> BIB003 </s> Evolution of biomedical ontologies and mappings: Overview of recent approaches <s> Visualizing ontology evolution <s> Display Omitted Diff Abstraction Networks are introduced to summarize and visualize ontology change.The Diff Area Taxonomy (DAT) and the Diff Partial-area Taxonomy (DPAT) are introduced.DPATs are derived for three ontologies and are shown to highlight important changes.DPATs offer a compact way of viewing many changes due to various editing operations. Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such unwanted side effects often go unnoticed since biomedical ontologies are large and complex knowledge structures. Abstraction networks, which provide compact summaries of an ontology's content and structure, have been used to uncover structural irregularities, inconsistencies and errors in ontologies. In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology release. A Diff AbN can be used to support curators in identifying unintended and unwanted ontology changes. The derivation of two Diff AbNs, the Diff Area Taxonomy and the Diff Partial-area Taxonomy, is explained and Diff Partial-area Taxonomies are derived and analyzed for the Ontology of Clinical Research, Sleep Domain Ontology, and eagle-i Research Resource Ontology. Diff Taxonomy usage for identifying unintended erroneous consequences of quality assurance and ontology merging are demonstrated. <s> BIB004 </s> Evolution of biomedical ontologies and mappings: Overview of recent approaches <s> Visualizing ontology evolution <s> Ontologies can be represented as graphs, since they essentially comprise a set of interconnected concepts describing a certain field of knowledge. Consequently, ontologies are often visualized as graphs, using different visual notations and common graph drawing techniques. The visualization of static graphs has been researched a lot, but when it comes to time-varying graphs, researchers face much more challenges in order to design useful, readable, and intuitive visualizations. If we have to deal with dynamic, i.e., evolving and time-dependent ontologies, we have to adapt existing visualization techniques to this challenging problem or develop new ones. In this position paper, we take a look at the visual representation of time-varying ontologies, and provide a discussion from a dynamic graph visualization perspective. <s> BIB005
It has become more and more important to provide intuitive ways of visualizing ontology evolution (e.g.,  BIB002 BIB003 BIB004  BIB001 ). For users it is particularly important to understand the evolution of ontologies they use in order to be able to assess possible influences on their ontology-based applications. For instance, quite recently a new version of the widely used ontology lookup service 1  was introduced to inform users about ontology change histories. The CODEX 2 BIB002 tool allows users to explore complex changes computed by COnto-Diff. WebProtégé 3 BIB003 supports the tracking of ontology changes and provides precisely defined, OWL-related ontology changes and change lists. Diff Abstraction Networks BIB004 were introduced to summarize, visualize and highlight ontology changes. It further seems intuitive to provide a dynamic graph visualization perspective for time-varying ontologies BIB005 . For instance, the tool REX 4  gives an aggregated view on differently evolving ontology regions and allows users to navigate from the root into stable or strongly evolving ontology regions using a fish-eye zoom. However, still much work needs to be done to improve ontology evolution visualization techniques allowing for compact as well as detailed views e.g. on precisely defined changes of axioms in formal ontologies.