Figure 1

Different layers of sequences. We illustrate the layers in the ontology of sequences. At the bottom level, sequences can refer to chains of molecules. These chains correspond to the primary structures of DNA and RNA molecules as well as proteins. The middle level illustrates sequences as representations of molecules. These can be in different formats such as the FASTA file format, plain text, graph-based representations or similar. Sequence representations exhibit a syntactic structure that resembles the structures of molecule chains. However, not every instance of Syntactic sequence represents a chain of molecules; sequence representations can represent no, one or many molecules. The upper level shows abstract sequences, symbolized as equivalence classes of sequence representations.