SBGN proses diyagramlarının yönetimi ve gösterimi için geliştirilen metotlar ve araçlar

Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In vi- sualization of graphs, automatic layout, interactive editing and complexity man- agement of crowded graphs are essential for effective utilization of underlying information. Advances in graphical user interfaces have given rise and value to interactive editing and diagramming techniques in graph visualization. As the size of the information to be visualized vastly increased, it became harder to analyze such networks, making use of relational information needed to be acquired. To over- come this problem, sophisticated and domain-specific complexity management techniques should be provided. The Systems Biology Graphical Notation (SBGN) has been developed over a number of years by biochemists and computer scientists to standardize visual representation of biochemical and cellular processes. SBGN introduces a concrete, detailed set of symbols for scientists to represent network of interactions, in a way that is not open to more than one interpretation. It also describes the manner, in which such graphical information should be interpreted. The SBGN Process Description (PD) language shows how entities are influ- enced by processes, which are represented by several reaction types in a biological pathway. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. We developed methods and tools to effectively visualize and manage SBGN- PD diagrams. Specifically, we introduced new algorithms for proper manage- ment of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes places. In ad- dition, we provided software components and web-based tools that implement these methods. These tools use state-of-the-art web technologies and libraries.