Mcalmodulindependent protein kinase kind II alpha chain” is a a part of
Mcalmodulindependent protein kinase variety II alpha chain” can be a a part of the above pointed out “calcium and calmodulindependent protein kinase complex”.Author ManuscriptIt is achievable describe a element with various alternative sets of certified annotations. As an example, the following species represents a pool of GMP, GDP and GTP. We annotate it together with the 3 corresponding KEGG compound identifiers but in addition with all the three corresponding ChEBI identifiers. The two option annotations are encoded in separate hasVersion qualifier elements.Author Manuscript Author ManuscriptThe following example presents a reaction getting in fact the mixture of 3 diverse elementary molecular reactions. We annotate it together with the three corresponding KEGG reactions, but in addition with all the three corresponding enzymatic activities. Once more the twoJ Integr Bioinform. Author manuscript; out there in PMC 207 June 02.Hucka et al.PagehasPart elements represent two alternative annotations. The PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23153055 course of action represented by theAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptReaction structure is composed of three components, and not six parts.It can be probable to mix unique URIs within a offered set. The following instance presents two option annotations from the human hemoglobin, the initial with ChEBI heme and the second with KEGG heme.As formally defined above it’s feasible to make use of unique qualifiers inside the exact same annotation element. The following phosphorylation is annotated by its exact KEGG counterpart and by the generic GO term “phosphorylation”.The following example demonstrates the usage of nested terms to describe not merely that a species is in a specific compartment, but why this is believed to be accurate:J Integr Bioinform. Author manuscript; offered in PMC 207 June 02.Hucka et al.PageAuthor ManuscriptIn descriptive terms, the SBML species ” S” (with metaid ” _000004″) occurs in ” goGO: 0005764″ (the lysosome). This is described by the publication ” pubmed”, and is believed to become correct as a result of the evidence ” ecoECO:0000004″ (cell fractionation proof). The following instance demonstrates the usage of nested terms to describe that the annotated species represents a phosphorylated type of a certain protein:Author Manuscript Author Manuscript Author Manuscript7 Instance models expressed in XML applying SBMLIn this section, we present quite a few examples of complete models encoded in XML applying SBML Level 2. 7. A very simple example application of SBML Think about the following representation of an enzymatic reaction:The following is the minimal SBML document encoding the model shown above:J Integr Bioinform. Author manuscript; out there in PMC 207 June 02.Hucka et al.PageAuthor Manuscript Author Manuscript Author ManuscriptIn this example, the model has the identifier ” EnzymaticReaction”. The model contains one particular compartment (with identifier ” cytosol”), four species (with identifiers ” ES”, ” P”, ” S”, and ” E”), and two reactions (” veq” and ” vcat”). The elements in the listOfReactants and listOfProducts in each reaction refer for the names of components listed in the listOfSpecies. The correspondences among the several components is explicitly stated by the speciesReference components. The model also options neighborhood parameter Tubacin definitions in every single reaction. In this case, the three parameters (” kon”, ” koff”, ” kcat”) all have unique identifiers and they could also have just as conveniently been declared global parameters in the model. Neighborhood parameters frequently turn into far more us.