Representation of the l-lysine biosynthesis pathway in UniPathway. The l-lysine biosynthesis pathway is specialized in two chemically defined pathway variants (the DAP and AAA pathways) by an ‘IsA’ relationship. The DAP pathway is composed of seven linear subpathways (ULS) and the AAA pathway is composed of three linear subpathways (which are ‘PartOf' their respective pathway variants). Colored boxes, using the same color code as in the Supplementary figures for comparisons, indicate the subpathways. The right part of the figure presents an exploded view of the first linear subpathway (ULS) of the AAA pathway, which is composed of four Enzymatic reactions (UERs).

Example of relationships between ULS, UER and UCR. ULS00012—‘l-α-aminoadipate from 2-oxoglutarate’—is a linear subpathway composed of four UERs linked through their primary compounds. (a) The first step in ULS00012 is UER00028, associated to the chemical reaction UCR00271 (using Left-to-Right direction). This UCR involves five compounds, but only two of these, 2-oxoglutarate and (R)-homocitrate, are considered to be primary compounds in the context of UER00028. (b) The second step in ULS00012 is UER00029, associated to two chemical reactions: UCR03444 (using Left-to-Right direction) followed by UCR04371 (using Right-to-Left direction). The primary substrate of UER00029 is (R)-homocitrate and its primary product is homoisocitrate.

Overview of the UniPathway concepts. (a) Unified Modeling Language (UML)-like representation of the UniPathway classes and relationships. Legend is to the right of the main part of the figure. Multiplicity constraints read as: One UPA is composed of 0 or more ULS—One ULS is contained in exactly 1 UPA. One ULS is composed of 1 or more UER—One UER is contained in exactly 1 ULS. One UER is composed of 0 or more (alternate) UER—One UER is contained in 0 or at most 1 UER. One UER is composed of 0 or more UCR—One UCR is contained in 1 or more UER. One UCR is composed of 1 or more left UPC and 1 or more right UPC—One UPC is contained in 1 or more UCR. (b) Example of the IsA relationship defining the UniPathway controlled vocabulary hierarchy of pathway terms. A pathway instance may be a specific type of an abstract pathway entity. (c) Example of the PartOf relationship linking a pathway (UPA: light blue), its subpathways (ULS: blue) and individual enzymatic reactions that constitute the subpathway (UER: dark blue). (d) Three cases of the relationship between an UER and its chemical reaction components (UCR): (1) simple one-to-one relationship where R is catalyzed by a single enzyme; (2) R is catalyzed by an enzyme and S is a spontaneous reaction; (3) ‘OR’ relationship: the enzyme can catalyze two reactions differing by their co-substrates (e.g. NADH/NADPH).