We will present the research design of annotation practices of scientists working with printed scientific documents. The research is focused on the usefulness and usability of the types of annotations generated by interactions of the scientist with the text. The aim of the accomplished empirical research was to identify the limitations of cognitive work during annotating and to deduce consequences for the ecological interface design of web-based format of eBook. The poster presents the current state of complex research, which is still in the implementation phase and some of the first results of the study. To date, 20 scientists, representatives of humanities, social and natural sciences (linguistics, psychology, geography respectively), as well as scientists active in interdisciplinary research, have participated in the research. The study is based on the formative paradigm of HCI design and the socio-cognitive paradigm of information behavior. Ecological interface design (EID) and cognitive work analysis (CWA) were used as the theoretical framework guiding the research. In carrying out the task scientists read scientific papers, books and diploma theses. They talk aloud about their work and identified cognitive functions activated in the process of interacting with text by categories. The audio and video recordings acquired were processed using verbal protocol analysis and abstract hierarchy analysis. The results obtained indicate a topological tension between cognitive functions and note-taking tools. Underestimating the importance of space, haptics and perception in electronic texts, which are typical for human-printed text interaction, leads to the disembodied design of the reading software interface. Disembodied design emphasizes deep cognitive control instead of perceptive and activity surface control, which has a negative impact on the effectiveness of cognitive work and the usefulness of eBooks.