Biological pathway abstractions: from two-dimensional drawings to multidimensional linked data

This thesis focuses on biological pathways, with the citric acid cycle as a prominent example commonly taught in high schools. It emphasizes the evolving role of these pathways beyond mere illustrative tools to now being integral in analyzing vast amounts of scientific data. The thesis underscores the importance of keeping these pathways up-to-date with current scientific literature, a task that necessitates various instruments not only for monitoring literature but also for representing this knowledge in a format conducive to automated processing. It explores various methods and techniques that aid in the maintenance or biocuration of these pathways. A central theme is the role of the semantic web, an extension of the World Wide Web, which allows for the swift reuse of data. Moreover, the thesis examines techniques that enable the research community to contribute collectively, highlighting the collaborative nature of scientific research in the modern era.