-
Notifications
You must be signed in to change notification settings - Fork 9
/
sbol3.tex
176 lines (133 loc) · 5.35 KB
/
sbol3.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
\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:editors@sbolstandard.org}{\sffamily editors@sbolstandard.org}}\\
\\
\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}