The purpose of this thesis was to design and implement a hierarchical approach to visualization of the chemical space. Such visualization is a challenging yet important topic used in diverse fields ranging from material engineering to drug design. Especially in drug design, modern methods of high- throughput screening generate large amounts of data that would benefit from hierarchical analysis. One possible approach to hierarchical classification of molecules is a structure based classification based on molecular scaffolds. The scaffolds are widely used by medicinal chemists to group molecules of similar properties. A few scaffold-based hierarchical visualization methods have been proposed. However, to our best knowledge, there exists no tool that would provide a scaffold-based hierarchical visualization of molecular data sets on the background of known chemical space. In this thesis, such tool was created. First, a scaffold tree hierarchy based on ring topologies was designed. Next, this hierarchy was used to analyze frequency of scaffolds extracted from molecules in PubChem Compound database. Subsequently, the PubChem Compound scaffold frequency data was used as a background for visualization of molecular data sets. The visualization is performed by a client-server application implemented as a part of...

This thesis studies, implements and experiments with specific application-oriented approaches for exploring and querying multi-dimensional datasets. The first part of the thesis scrutinizes indexing of the complex space of chemical compounds, and details a design of high-performance retrieval system for small molecules. The resulting system is then utilized within a wider context of federated search in heterogeneous data and metadata related to the chemical datasets. In the second part, the thesis focuses on fast visualization and exploration of many-dimensional data that originate from single- cell cytometry. Self-organizing maps are used to derive fast methods for analysis of the datasets, and used as a base for a novel data visualization algorithm. Finally, a similar approach is utilized for highly interactive exploration of multimedia datasets. The main contributions of the thesis comprise the advancement in optimization and methods for querying the chemical data implemented in the Sachem database cartridge, the federated, SPARQL-based interface to Sachem that provides the heterogeneous search support, dimensionality reduction algorithm EmbedSOM, design and implementation of the specific EmbedSOM-backed analysis tool for flow and mass cytometry, and design and implementation of the multimedia...