Pathway models are an effective way to capture and share our current understanding of biological processes. A pathway model is defined here as a set of interactions among biological entities (e.g., proteins and metabolites) relevant to a particular context, curated and organized to illustrate a particular process. Properly modeled pathways can be used in the analysis and visualization of diverse types of omics and other biomedical data [1,2]. The modeling process involves taking our knowledge about biological pathways—however messy and incomplete— and encoding it in standardized data formats that can be shared, reused, and synthesized with other knowledge in accordance with the Findable, Accessible, Interoperable, and Reusable (FAIR) principles [3]. The rules presented here serve as an introduction and guide to the pathway modeling process, leveraging freely available tools and resources.
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