  Understanding how genes interact and relate to each other is a fundamental
question in biology. However, current practices for describing these
relationships, such as drawing diagrams or graphs in a somewhat arbitrary
manner, limit our ability to integrate various aspects of the gene functions
and view the genome holistically. To overcome these limitations, we need a more
appropriate way to describe the intricate relationships between genes.
Interestingly, category theory, an abstract field of mathematics seemingly
unrelated to biology, has emerged as a powerful language for describing
relations in general. We propose that category theory could provide a framework
for unifying our knowledge of genes and their relationships.
  As a starting point, we construct a category of genes, with its morphisms
abstracting various aspects of the relationships betweens genes. These
relationships include, but not limited to, the order of genes on the
chromosomes, the physical or genetic interactions, the signalling pathways, the
gene ontology causal activity models (GO-CAM) and gene groups. Previously, they
were encoded by miscellaneous networks or graphs, while our work unifies them
in a consistent manner as a category. By doing so, we hope to view the
relationships between genes systematically. In the long run, this paves a
promising way for us to understand the fundamental principles that govern gene
regulation and function.
