Biological data such as protein structure and function, DNA sequences, and metabolic pathways require conceptual modeling characteristics that are not available in the widely used ER (Entity-Relationship) model and its variant the EER (enhanced-ER) model. In this paper, we suggest a solution to this problem, requiring only minimal changes to the EER model by introducing specialized formal relationships for ordering, input/output processes and spatial structure. These changes facilitate more accurate modeling of biological ontologies, their structures, and mediator systems. We propose new EER schema constructs to represent the ordering of DNA sequences, the structure of proteins, and the processes of metabolic pathways.