Chemical space is a core concept in chemoinformatics with several practical applications in drug discovery and other areas in chemistry. Typically, chemical space is used for selecting specific sets of compounds for further computational or experimental screening, diversity, and SP(A)R analysis, and to guide the design of novel molecules. The latter application is intended such that the newly generated compounds are at the intersection of the biologically relevant chemical space. In any application, compound representation is a key variable in qualitative or quantitative chemical space analysis (including visual representation); it has to be in line with the objective of the study as it will guide the interpretation of the analysis.