Though David's answer is technically correct, I offer an alternative for those who struggle with the term in broader contexts.
Definition
Canonical simply means relating to a historically established paradigm, or relating to a common or standard model (which simplifies things!). For example, a biochemical pathway or a mechanism, for example, may be understood to include certain typical players or long-understood elements or interactions. These are canonical elements. They relate to the scientific canon. They depend on the history of discovery and organization of our theories, rather than any biological phenomenon.
Example
For instance, a synapse is canonically composed of a pre-synaptic neuron and a post-synaptic neuron. This has been long known and to this day scientists broadly speak in terms of the two, as a simplification of the system. However, most synapses are tripartite, including a glial cell cradling and modulating the environment between the communicating neurons. The glial cell can be considered to be the non-canonical element, even though it may be essential, or very important in the system. But it hasn't been studied as long, and introduces more considerations and complexities to think about which go beyond a simple way of thinking about it.
The use of the word
Some pathways or mechanisms have been strictly defined and outlined, where one can clearly draw the line between the canonical and non-canonical elements. There is no flexibility in how you use the word. On the other hand, other times the word is used in cases of systems where there is no strict definition dividing the two, it's just a judgment call, of what most scientists consider central, primary and emblematic (as opposed to peripheral, or secondary, or not validated enough 'to have entered the canon') to the system. There the use of the term canonical is colloquial!