Tadata annotations employing RDF (Resource Description Format; Lassila and Swick, 999). It
Tadata annotations utilizing RDF (Resource Description Format; Lassila and Swick, 999). It includes a data style of XML ID (the XML identifier form; see Section 3..6), which means every single metaid worth has to be globally exceptional inside an SBML file. The metaid value serves to determine a model component for purposes such as referencing that element from metadata placed within annotation components (see Section three.two.four). Such metadata can use RDF description elements, in which an RDF PK14105 attribute referred to as ” rdf:about” points to the metaid identifier of an object defined inside the SBML model. This subject is discussed in higher detail in Section six. three.two.two The sboTerm attributeThe attribute called sboTerm is offered on SBase to help the usage of the Systems Biology Ontology (SBO; see Section 5). When a worth is given to this attribute, it need to conform for the data variety SBOTerm (Sections 3..9). SBO terms are a form of optional annotation, and each unique class of SBML object derived from SBase imposes its personal specifications in regards to the values permitted for sboTerm. Precise particulars around the permitted values are provided using the definitions of SBML classes throughout this specification document, plus a broader is supplied in Section five. 3.2.3 The notes elementThe element notes in SBase can be a container for XHTML .0 (Pemberton et al 2002) content material. It is intended to serve as a location for storing optional facts intended to be noticed by humans. An example use from the notes element will be to contain formatted user comments about the model element in which the notes element is enclosed. Just about every object derived directly or indirectly from form SBase can possess a separateAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; readily available in PMC 207 June 02.Hucka et al.Pagevalue for notes, permitting customers considerable freedom when adding comments to their models. XHTML .0 is just a formulation of HTML four in XML .0. This means the full energy of HTML formatting is obtainable for use in notes content material. The intention behind requiring XHTML (as opposed to, for instance, plain HTML or plain text) for notes content material should be to balance a number of conflicting ambitions: picking out a format for notes that’s compatible using the XML kind of SBML (plain HTML would not be); (two) supporting an international formatting normal so that customers have far more control more than the appearance of notes and may predict to PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23637907 some degree how their notes might be displayed in various tools and environments (which argues against working with plaintext notes); and (3) attaining these objectives utilizing an method that is hopefully effortless sufficient for software program developers to assistance applying offtheshelf programming libraries. It is worth noting in passing that the requirement for XHTML doesn’t stop customers from getting into plaintext content material with straightforward spacetabnewline formatting: it merely demands using the normal pre… pre element of (X)HTML. Contemporary libraries for displaying and editing (X)HTML content material are frequently available in contemporary software program programming environments, and software program developers could want to avail themselves of those facilities rather than implementing their very own XHTML help systems. XML namespace needs for notes: The XML content of notes elements need to declare the use of the XHTML XML namespace. This could be performed in various techniques. One way would be to location a namespace declaration for the appropriate namespace URI (which is http: w3.org999xhtml) around the toplevel Sbml object (see Section 4.).
