Tadata annotations making use of RDF (Resource Description Format; Lassila and Swick, 999). It
Tadata annotations using RDF (Resource Description Format; Lassila and Swick, 999). It has a data style of XML ID (the XML identifier kind; see Section 3..six), which indicates every metaid value has to be globally distinctive inside an SBML file. The metaid worth serves to determine a model component for purposes for example referencing that component from metadata placed within annotation components (see Section three.2.4). Such metadata can use RDF description elements, in which an RDF attribute called ” rdf:about” points for the metaid identifier of an BMS-582949 (hydrochloride) object defined inside the SBML model. This topic is discussed in higher detail in Section 6. three.2.2 The sboTerm attributeThe attribute referred to as sboTerm is supplied on SBase to assistance the use of the Systems Biology Ontology (SBO; see Section five). When a worth is given to this attribute, it ought to conform for the data form SBOTerm (Sections 3..9). SBO terms are a sort of optional annotation, and each and every distinctive class of SBML object derived from SBase imposes its personal requirements regarding the values permitted for sboTerm. Particular information on the permitted values are offered together with the definitions of SBML classes throughout this specification document, as well as a broader is provided in Section five. three.two.three The notes elementThe element notes in SBase is often a container for XHTML .0 (Pemberton et al 2002) content. It’s intended to serve as a location for storing optional information intended to become seen by humans. An instance use on the notes element will be to include formatted user comments about the model element in which the notes element is enclosed. Each and every object derived directly or indirectly from form SBase can possess a separateAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; offered in PMC 207 June 02.Hucka et al.Pagevalue for notes, enabling customers considerable freedom when adding comments to their models. XHTML .0 is just a formulation of HTML four in XML .0. This means the complete energy of HTML formatting is obtainable for use in notes content. The intention behind requiring XHTML (as an alternative to, for example, plain HTML or plain text) for notes content will be to balance numerous conflicting targets: picking a format for notes which is compatible together with the XML kind of SBML (plain HTML wouldn’t be); (two) supporting an international formatting typical in order that users have additional control over the appearance of notes and can predict to PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23637907 some degree how their notes is going to be displayed in unique tools and environments (which argues against utilizing plaintext notes); and (3) reaching these targets employing an approach which is hopefully uncomplicated enough for computer software developers to assistance utilizing offtheshelf programming libraries. It can be worth noting in passing that the requirement for XHTML will not prevent customers from entering plaintext content material with basic spacetabnewline formatting: it merely calls for making use of the common pre… pre element of (X)HTML. Contemporary libraries for displaying and editing (X)HTML content material are usually available in modern software program programming environments, and computer software developers may possibly wish to avail themselves of those facilities in lieu of implementing their own XHTML help systems. XML namespace needs for notes: The XML content of notes elements ought to declare the use of the XHTML XML namespace. This could be completed in multiple techniques. 1 way is to location a namespace declaration for the acceptable namespace URI (which can be http: w3.org999xhtml) around the toplevel Sbml object (see Section 4.).