Metabolite AUXUILIARY UNITS ENTITY POOL NODES Simple chemical Protein Macromolecule mRNA ct:mrna Nucleic acid feature: mRNA State variable: unchanged/default Protein Protein @Thr14 State variable: phosphorylated Protein P State variable: phosphorylated at threonine 14 Protein P@Thr14 State variable: unchanged/default at threonine 14 Protein N:2 Multimer Gene ct:gene Nucleic acid feature: gene LABEL Protein Protein Complex Gene ct:gene mRNA ct:mrna Unit of information: conceptual type - messenger RNA Unit of information: conceptual type - gene State variable: acetylated Protein Ac State variable: ubiquitinated Protein Ub Perterbing agent LABEL Empty set (previously - source/sink) Process (State transition) Protein Protein Omitted process Protein Protein Unkown process Protein Protein ? Degradation Protein Homodimer formation Protein Association Protein Catalysis Protein Inhibition Protein Protein Protein Stimulation Protein Protein Protein PROCESS NODES PROCESS REGULATION Protein Protein Protein \\ Protein N:2 Metabolite Metabolite Metabolite Process (Metabolic reaction) Metabolite Metabolite Process (Metabolic reaction) Metabolite Metabolite Metabolite Protein LABEL Protein Protein Protein Protein Protein Protein Protein LABEL Protein Protein Dissociation mRNA ct:mrna Gene ct:gene mRNA ct:mrna Modulation Necessary stimulation (transctiption) Necessary stimulation (translation) Protein Protein LOGIC OPERATORS OR Protein Protein Protein Protein AND Protein Protein Protein NOT Protein Protein Protein ≡ NOT operator Equivalence operator OR operator AND operator LABEL Phenotype LABEL LABEL Compartment LABEL Unspecified entitty LABEL Submap ENCAPSULATION NODE State variable: glycosylated Protein G State variable: hydroxylated Protein OH State variable: methylated Protein Me State variable: myristoylated Protein My State variable: palmytoylated Protein Pa State variable: prenylated Protein Pr State variable: protonated Protein H State variable: sulfatied Protein S CONTAINER NODE Gene region ct:grr Start site ct:tss Unit of information: conceptual type - transcription start site Unit of information: conceptual type - gene regulatory region Gene region ct:coding Unit of information: conceptual type - gene coding region Protein N:3 Unit of information: multimer cardinality P P P P P P P P P 2