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labop.tex
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labop.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=labop,
tabsize=2
}
}
%Commands to format SBOL terms in the document
% Use sbolheading when you are referencing a data model class/field in a
% section heading.
\newcommand{\labopheading}[1]{\texttt{#1}}
% Use sbol when you are referencing a LabOP data model class/field in text.
\newcommand{\labop}[1]{\texttt{\hyperref[sec:labop:#1]{#1}}}
% 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{\labopmult}[2]{\texttt{\hyperref[sec:labop:#1]{#2}}}
% Use sbolheading when you are referencing an SBOL data model class/field in a
% section heading.
\newcommand{\umlheading}[1]{\texttt{uml:#1}}
% Use sbol when you are referencing an SBOL data model class/field in text.
\newcommand{\uml}[1]{\texttt{\hyperref[sec:uml:#1]{uml:#1}}}
% 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{\umlmult}[2]{\texttt{\hyperref[sec:uml:#1]{uml:#2}}}
% Use sbol when you are using a class borrowed from SBOL, this will prepend the "sbol:" prefix as well
\newcommand{\sbol}[1]{\texttt{\hyperref[sec:sbol:#1]{sbol:#1}}}
% 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:sbol:#1]{sbol:#2}}}
% 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}}}
%Command to format external terms in the document
\newcommand{\external}[1]{\texttt{#1}}
% Rarely used. Use refObj you want to put the field in angle brackets.
\newcommand{\refObj}[1]{$\langle$#1$\rangle$}
\setcounter{tocdepth}{5}
\setcounter{secnumdepth}{5}
% -----------------------------------------------------------------------------
% Start of document
% -----------------------------------------------------------------------------
\begin{document}
\packageTitle{\latex LabOP Specifications}
\packageVersion{Version 1.0-alpha}
\packageVersionDate{TBD, 2021}
\title{Laboratory Open Protocol language \texorpdfstring{\\[3pt]}{}\mbox{(LabOP) Version~1.0.0-alpha}}
\author{
\begin{tabular}{l>{\hspace*{15pt}}r}
Bryan Bartley & \emph{Raytheon BBN Technologies, USA} \\
Jacob Beal & \emph{Raytheon BBN Technologies, USA}\\
Daniel Bryce & \emph{SIFT, USA}\\
Robert P. Goldman & \emph{SIFT, USA}\\
Benjamin Keller & \emph{University of Washington, USA}\\
Peter Lee & \emph{Strateos, USA}\\
Joshua Nowak & \emph{Strateos, USA}\\
Miles Rogers & \emph{Raytheon BBN Technologies, USA}\\
Mark Weston & \emph{Netrias, USA}\\
Additional authors & from contributing organizations\\
\end{tabular}\\
}
\maketitlepage
\maketableofcontents
\input{purpose}
%\input{overview}
\input{vocabulary}
\input{sbolImports}
\section{Imported UML Classes}
\label{sec:uml}
LabOP builds on the Unified Modeling Language (UML) version 2.5.1~\citep{uml251} to describe the organization of actions in a protocol.
In order to make this document more self-contained, this section describes the classes from UML that have been imported for use with LabOP.
In particular, each such class has been adapted to be an SBOL subclass, assigned to either \sbol{Identified} or \sbol{TopLevel}, in order to be able to be used with SBOL closure assumptions in an RDF environment.
\input{umlDataModel}
\section{LabOP Data Model}
\label{sec:labop}
\input{labopDataModel}
\input{serialization}
\newpage
\bibliography{labop}
\appendix
%\input{examples}
\end{document}