We present a framework for the unification and standardization of quantum network protocols, making their realization easier and expanding their use cases to a broader range of communities interested in quantum technologies. Our framework is available as an open-source repository, the Quantum Protocol Zoo. We follow a modular approach by identifying two key components: Functionality, which connects real-world applications; and Protocol, which is a set of instructions between two or many parties, at least one of which has a quantum device. Based on the different stages of the quantum internet and use-case in the commercialization of quantum communication, our framework classifies quantum cryptographic functionalities and the various protocol designs implementing these functionalities. Towards this classification, we introduce a novel concept of resource visualization for quantum protocols, which includes two interfaces: one to identify the building blocks for implementing a given protocol and another to identify accessible protocols when certain physical resources or functionalities are available. Such classification provides a hierarchy of quantum protocols based on their use-case and resource allocation. We have identified various valuable tools to improve its representation with a range of techniques, from abstract cryptography to graphical visualizations of the resource hierarchy in quantum networks. We elucidate the structure of the zoo and its primary features in this article to a broader class of quantum information scientists, physicists, computer science theorists and end-users. Since its introduction in 2018, the quantum protocol zoo has been a cornerstone in serving the quantum networks community in its ability to establish the use cases of emerging quantum internet networks. In that spirit we also provide some of the applications of our framework from different perspectives.