Understanding the structure of knowledge domains is one of the foundational challenges in science of science. Here, we propose a neural embedding technique that leverages the information contained in the citation network to obtain continuous vector representations of scientific periodicals. We demonstrate that our periodical embeddings encode nuanced relationships between periodicals as well as the complex disciplinary and interdisciplinary structure of science, allowing us to make cross-disciplinary analogies between periodicals. Furthermore, we show that the embeddings capture meaningful "axes" that encompass knowledge domains, such as an axis from "soft" to "hard" sciences or from "social" to "biological" sciences, which allow us to quantitatively ground periodicals on a given dimension. By offering novel quantification in science of science, our framework may in turn facilitate the study of how knowledge is created and organized.