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model.tex
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model.tex
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\subsection{Model}
\label{sec:Model}
\begin{figure}[ht]
\begin{center}
\includegraphics[scale=0.6]{uml/model}
\caption[]{Diagram of the \sbol{Model} class and its associated properties.}
\label{uml:model}
\end{center}
\end{figure}
The purpose of the \sbol{Model} class is to serve as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model.
In this way, there is minimal duplication of standardization efforts and users of SBOL can elaborate descriptions of \sbol{Component} function in the language of their choice.
The meta-data provided by the \sbol{Model} class include the following properties: the \sbolmult{source:M}{source} or location of the actual content of the model, the \sbol{language} in which the model is implemented, and the model's \sbol{framework}.
\subparagraph{The \sbolheading{source} property}\label{sec:source:M}
The \sbolmult{source:M}{source} property is REQUIRED and MUST contain a \sbol{IRI} reference to the source file for a model.
\subparagraph{The \sbolheading{language} property}\label{sec:language}
The \sbol{language} property is REQUIRED and MUST contain a \sbol{IRI} that specifies the language in which the model is implemented.
It is RECOMMENDED that this \sbol{IRI} refer to a term from the EMBRACE Data and Methods (EDAM) ontology. \ref{tbl:model_types} provides a list of a few suggested languages from this ontology and their \sbol{IRI}s.
If the \sbol{language} property of a \sbol{Model} is well-described by one these terms, then it MUST contain the \sbol{IRI} for this term as its value.
\begin{table}[ht]
\begin{edtable}{tabular}{ll}
\toprule
\textbf{Model Language} & \textbf{URL for EDAM Term} \\
\midrule
SBML & \url{http://identifiers.org/EDAM:format_2585}\\
CellML & \url{http://identifiers.org/EDAM:format_3240}\\
BioPAX & \url{http://identifiers.org/EDAM:format_3156}\\
\bottomrule
\end{edtable}
\caption{Terms from the EDAM ontology to specify the \sbol{language} property of a \sbol{Model}.}
\label{tbl:model_types}
\end{table}
\subparagraph{The \sbolheading{framework} property}\label{sec:framework}
The \sbol{framework} property is REQUIRED and MUST contain a \sbol{IRI} that specifies the framework in which the model is implemented.
It is RECOMMENDED this \sbol{IRI} refer to a term from the modeling framework branch of the SBO when possible. A few suggested modeling frameworks and their corresponding \sbol{IRI}s are shown in \ref{tbl:model_frameworks}. If the \sbol{framework} property of a \sbol{Model} is well-described by one these terms, then it MUST contain the \sbol{IRI} for this term as its value.
\begin{table}[ht]
\begin{edtable}{tabular}{ll}
\toprule
\textbf{Framework} & \textbf{URL for SBO Term} \\
\midrule
Continuous & \url{http://identifiers.org/SBO:0000062}\\
Discrete & \url{http://identifiers.org/SBO:0000063}\\
\bottomrule
\end{edtable}
\caption{SBO terms to specify the \sbol{framework} property of a \sbol{Model}.}
\label{tbl:model_frameworks}
\end{table}