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sbol3.tex
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sbol3.tex
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\errorcontextlines=200
\documentclass[finalspec]{sbmlpkgspec}
%% \documentclass[draftspec]{sbmlpkgspec}
\usepackage{microtype}
\usepackage{color}
\usepackage{todonotes}
\usepackage[color]{changebar}
\usepackage{xcolor}
\usepackage{soul}
\usepackage{subcaption}
\usepackage{longtable}
% Make changebars switchable to allow faster compilation:
%\def\fullchangebars{} % comment this out to simplify changebars and speed up compilation
% Macros just for this document:
\newcommand{\sbmlpkg}{\texorpdfstring{%
\textls[-25]{\textsc{SBMLPkgSpec}}}{%
\textsc{SBMLPkgSpec}}\xspace}
\newcommand{\sbmlpkghead}{\texorpdfstring{%
\textls[-50]{\textsc{SBMLPkgSpec}}}{%
\textsc{SBMLPkgSpec}}\xspace}
\newcommand{\sbmlpkgfile}{\literalFont{sbmlpkgspec.cls}\xspace}
\newcommand{\latex}{\LaTeX{}\xspace}
\newcommand{\tex}{\TeX{}\xspace}
\newcommand{\distURL}{http://sourceforge.net/projects/sbml/files/specifications/tex}
\newcommand{\srcURL}{https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/project/tex/sbmlpkgspec}
\newcommand{\webURL}{http://sbml.org/Documents/Specifications/The_SBMLPkgSpec_LaTeX_class}
\newcommand{\cmd}[1]{\literalFont{\textbackslash #1}}
% Custom latex listing style, for use with the listings package. The default
% highlights far too many things, IMHO. This keeps it simple and only adjusts
% the appearance of comments within listings.
\lstdefinelanguage{mylatex}{%
morekeywords={},%
sensitive,%
alsoother={0123456789$_},%$
morecomment=[l]\%%
}[keywords,tex,comments]
\lstdefinestyle{latex}{language=mylatex}
%Command to format the listings containing SBOL RDF/XML serialization examples
\newcommand{\lstsetsbol}{
\lstset{language=sbol,
tabsize=2
}
}
%Commands to format SBOL terms in the document
% Use sbolheading when you are referencing an SBOL data model class/field in a
% section heading.
\newcommand{\sbolheading}[1]{\texttt{#1}}
% Use sbol when you are referencing an SBOL data model class/field in text.
\newcommand{\sbol}[1]{\texttt{\hyperref[sec:#1]{#1}}}
% Use prov when you are using a class borrowed from Prov-O, this will prepend the "prov:" prefix as well
\newcommand{\prov}[1]{\texttt{\hyperref[sec:prov:#1]{prov:#1}}}
% Use provmult for Prov-O fields that appear in multiple classes, for example
% \sbolmult{hadRole:U}{hadRole}. This ensures the reference links to the correct
% section.
\newcommand{\provmult}[2]{\texttt{\hyperref[sec:prov:#1]{prov:#2}}}
% Use om when you are using a class borrowed from Ontology of Units & Measures, this will prepend the "om:" prefix as well
\newcommand{\om}[1]{\texttt{\hyperref[sec:om:#1]{om:#1}}}
% Use provmult for OM fields that appear in multiple classes, for example
% \sbolmult{hadUnit:M}{hadUnit}. This ensures the reference links to the correct
% section.
\newcommand{\ommult}[2]{\texttt{\hyperref[sec:om:#1]{om:#2}}}
% Use sbolmult for SBOL fields that appear in multiple classes, for example
% \sbolmult{types:CD}{types}. This ensures the reference links to the correct
% section.
\newcommand{\sbolmult}[2]{\texttt{\hyperref[sec:#1]{#2}}}
% Rarely used. Use refObj you want to put the field in angle brackets.
\newcommand{\refObj}[1]{$\langle$#1$\rangle$}
%Command to format external terms in the document
\newcommand{\external}[1]{\texttt{#1}}
%Commands to highlight SBOL versions
%\newcommand{\threeonezero}[1]{%
% \cbcolor{red}
% \cbstart%
% {\color{red}%
% \version{3.1.0}%
% #1
% }
% \cbend
%}
% -----------------------------------------------------------------------------
% Start of document
% -----------------------------------------------------------------------------
\begin{document}
\packageTitle{\latex Class for SBML Package Specifications}
\packageVersion{Version 3.1.0}
\packageVersionDate{October 26, 2022}
\title{
Synthetic Biology Open Language \texorpdfstring{\\[3pt]}{}\mbox{(SBOL) Version~3.1.0}}
\author{{\bf Editors:}\hfil\\
\begin{tabular}{l>{\hspace*{15pt}}r}
Lukas Buecherl & \emph{University of Colorado Boulder, USA}\\
Thomas Mitchell & \emph{Raytheon BBN Technologies, USA} \\
James Scott-Brown & \emph{University of Edinburgh, UK} \\
Prashant Vaidyanathan & \emph{Oxford Biomedica, UK}\\
Gonzalo Vidal Pe\~{n}a & \emph{Newcastle University, UK}\\
\multicolumn{2}{c}{\href{mailto:[email protected]}{\sffamily [email protected]}}\\
\\
\multicolumn{2}{c}{ {\bf Chair:} } \\
Chris Myers & \emph{University of Colorado Boulder, USA}\\
\\
\multicolumn{2}{c}{{\bf Additional authors:}} \\
Hasan Baig & \emph{University of Connecticut, USA}\\
Bryan Bartley & \emph{Raytheon BBN Technologies, USA} \\
Jacob Beal & \emph{Raytheon BBN Technologies, USA}\\
Matthew Crowther & \emph{Newcastle University, UK} \\
Pedro Fontanarrosa & \emph{University of Colorado Boulder, USA}\\
Thomas Gorochowski & \emph{University of Bristol, UK}\\
Raik Gr\"unberg & \emph{KAUST, SA}\\
Vishwesh Kulkarni & \emph{University of Warwick, UK}\\
James McLaughlin & \emph{Newcastle University, UK}\\
Goksel Misirli & \emph{Keele University, UK}\\
Ernst Oberortner & \emph{DOE Joint Genome Institute, USA}\\
Anil Wipat & \emph{Newcastle University, UK}\\
\end{tabular}\\
}
\maketitlepage
\maketableofcontents
\input{purpose}
\input{history}
\input{overview}
\input{vocabulary}
\input{dataModel}
\input{practices}
% \input{examples_model}
\input{serialization}
\input{compliance}
\input{mapping}
\newpage
\bibliography{sbol}
\appendix
\input{complementary_standards}
\input{apdx-validation}
\end{document}