Background: The choice of a bioinformatics tool that is used to design and analyse bioinformatics models is usually influenced by the choice of format used to store the models on the hard drive and vice versa and may seem irrelevant to researchers who design and analyse biological models using high-level computer software. However, the method for saving created models, which is usually opaque to users, can have an important impact on their work and have several important consequences.
Objective: Review various computer representations of bioinformatics models based on the structure of the files used to store them.
Results: We defined three classes of formats—formats with the internal structure hidden from the user, specialized programming languages, and controlled natural languages—and provide examples as well as list advantages and disadvantages of each class. Finally, we present recommendations on the groups of tools researchers should use.
Conclusion: Indeed, the choice of the format used to store the bioinformatics models can have important consequences for the entire investigation. A correctly chosen format provides all functionalities required by the modeller and offers high flexibility in analysing the model, making collaboration with other researchers easier and helping to develop the model further in the future. In our opinion, both users and developers tend to underestimate slightly the specialized programming languages and controlled natural languages which should be studied more in-depth.