Mcalmodulindependent protein kinase kind II alpha chain” is often a part of
Mcalmodulindependent protein kinase form II alpha chain” is often a part of the above pointed out “calcium and calmodulindependent protein kinase complex”.Author ManuscriptIt is attainable describe a element with many alternative sets of qualified annotations. For instance, the following species represents a pool of GMP, GDP and GTP. We annotate it together with the three corresponding KEGG compound identifiers but also using the 3 corresponding ChEBI identifiers. The two option annotations are encoded in separate hasVersion qualifier elements.Author Manuscript Author ManuscriptThe following instance presents a reaction being actually the mixture of three distinct elementary molecular reactions. We annotate it together with the three corresponding KEGG reactions, but additionally with all the 3 corresponding enzymatic activities. Again the twoJ Integr Bioinform. Author manuscript; offered 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 approach TCS-OX2-29 biological activity represented by theAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptReaction structure is composed of three parts, and not six components.It’s attainable to mix various URIs inside a provided set. The following example presents two option annotations in the human hemoglobin, the initial with ChEBI heme along with the second with KEGG heme.As formally defined above it’s attainable to use distinctive qualifiers inside the same annotation element. The following phosphorylation is annotated by its exact KEGG counterpart and by the generic GO term “phosphorylation”.The following instance demonstrates the use of nested terms to describe not simply that a species is in a certain compartment, but why this really is believed to become correct: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 be true as a result of the proof ” 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 specific protein:Author Manuscript Author Manuscript Author Manuscript7 Instance models expressed in XML utilizing SBMLIn this section, we present numerous examples of total models encoded in XML working with SBML Level two. 7. A very simple instance application of SBML Think about the following representation of an enzymatic reaction:The following may be the minimal SBML document encoding the model shown above:J Integr Bioinform. Author manuscript; obtainable in PMC 207 June 02.Hucka et al.PageAuthor Manuscript Author Manuscript Author ManuscriptIn this example, the model has the identifier ” EnzymaticReaction”. The model includes a single compartment (with identifier ” cytosol”), four species (with identifiers ” ES”, ” P”, ” S”, and ” E”), and two reactions (” veq” and ” vcat”). The components inside the listOfReactants and listOfProducts in each reaction refer for the names of components listed inside the listOfSpecies. The correspondences in between the different components is explicitly stated by the speciesReference elements. The model also attributes regional parameter definitions in each reaction. Within this case, the three parameters (” kon”, ” koff”, ” kcat”) all have exclusive identifiers and they could also have just as easily been declared international parameters inside the model. Regional parameters frequently develop into much more us.
