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Paraphrased from the [http://bioinformatics.ai.sri.com/ptools/curatorsguide.pdf BioCyc guidelines]: Curator’s Guide for Pathway/Genome Databases Pathway Tools Version 12.0 by Ron Caspi, Carol Fulcher, Ingrid Keseler, Markus Krummenacker, Suzanne Paley, Alex Shearer, and Peter D. Karp, 2008. Considerations to guide the decision of where to start and end a metabolic pathway: # Pathways should be built around the production (or degradation) of stable substrates, as opposed to transient intermediates. # Biosynthetic pathways can begin with an intermediate of central metabolism (e.g., precursor metabolites) and should reference the "preceding" pathway. # Degradative pathways that produce an intermediate of central metabolism (or excreted compound) should stop at that point and may reference the pathway that processes the resulting metabolite. # Other pathways may start with the natural form of compounds being used as electron donors or acceptors, and end with the compound generated at the end of the electron transport process, which would generally be secreted by the organism. # Very large or complex pathways should usually be divided into smaller pathways at breakpoints. Breakpoints can be chosen based on various criteria such as: branch point substrates; substrates involved in regulation; a major metabolite that is further metabolized; the cellular compartment in which the reactions occur (organelle or cytosol); a transport segment or a utilization segment; or the type of reaction (oxidative or non-oxidative). Back to [[Help:Guidelines]]

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