Lessen the potential for collisions among annotations written by distinctive applications
Minimize the prospective for collisions between annotations written by different applications, SBML Level 2 Version 5 stipulates that tools need to use XML namespaces (Bray et al 999) to specify the intended vocabulary of every annotation. The application’s developers need to decide on a URI (Universal Resource Identifier; Harold and Implies 200; W3C 2000a) reference that uniquely identifies the vocabulary the application will use, plus a prefix string for the annotations. Right here is an example. Suppose an application utilizes the URI http: mysim.orgns along with the prefix mysim when writing annotations related to screen layout. The content material of an annotation may possibly appear like the following:Author Manuscript Author Manuscript Author Manuscript Author ManuscriptIn this particularly uncomplicated instance, the content material consists of a single XML element ( nodecolors) with two attributes ( bgcolor, fgcolor), all of which are prefixed by the string mysim. (Presumably this particular content would have meaning to the hypothetical application in query.) The content in this certain example is small, however it should be clear that there could effortlessly have been an arbitrarily massive amount of information placed inside the mysim:nodecolors element. The crucial point from the example above is that applicationspecific annotation data is entirely contained inside a single toplevel element within the SBML annotation container. SBML Level two Version 5 places the following restrictions on annotations: Inside a provided SBML annotation element, there can only be a single toplevel element working with a provided namespace. An annotation element can contain various toplevel elements but every single must be inside a various namespace.J Integr Bioinform. Author manuscript; accessible in PMC 207 June 02.Hucka et al.PageNo toplevel element in an annotation may use an SBML XML namespace, either explicitly by referencing one of many SBML XML namespace URIs or implicitly by failing to specify any namespace on the annotation. As of SBML Level two Version five, the defined SBML namespaces will be the following URIs: http:sbml.orgsbmllevel http:sbml.orgsbmllevel2 http:sbml.orgsbmllevel2version2 http:sbml.orgsbmllevel2version3 http:sbml.orgsbmllevel2version4 http:sbml.orgsbmllevel2version5 http:sbml.orgsbmllevel3versioncore http:sbml.orgsbmllevel3version2coreAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptThe ordering of toplevel components inside a provided annotation element isn’t substantial. An application shouldn’t count on that its annotation content material appears first within the annotation element, nor in any other unique place. In addition, the ordering of toplevel annotation elements might be changed by distinctive applications as they study and write the identical SBML file.The use of XML namespaces within this manner is intended to improve the ability of numerous applications to spot annotations on SBML model elements with reduced risks of interference or name collisions. Annotations stored by distinct simulation packages can for that reason coexist within the similar model definition. Cyclic somatostatin PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 The rules governing the content material of annotation components are created to enable applications to quickly add, modify, and eliminate their annotations from SBML components though simultaneously preserving annotations inserted by other applications when mapping SBML from input to output. As a additional simplification for developers of computer software and to improve software interoperability, applications are only necessary to preserve other annotations (i.e annotations they usually do not recognize) when th.