[sbml-svn] SF.net SVN: sbml:[21771] trunk/specifications/sbml-level-3/version-1/fbc/ spec

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Revision: 21771
          http://sourceforge.net/p/sbml/code/21771
Author:   bgoli
Date:     2014-11-27 20:44:43 +0000 (Thu, 27 Nov 2014)
Log Message:
-----------
fbc package, updated pkgspec to 1.6.0 and drafted RC 1 of FBC version 2

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/fbc/spec/acknowledgments.tex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/background.tex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/main.pdf
    trunk/specifications/sbml-level-3/version-1/fbc/spec/main.synctex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/main.tex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/syntax.tex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/syntax_gene_association.tex

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-new.tex
    trunk/specifications/sbml-level-3/version-1/fbc/spec/sbml-fbc-version-2-rc-20141127.pdf

Removed Paths:
-------------
    trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-gene_association.tex

Modified: trunk/specifications/sbml-level-3/version-1/fbc/spec/acknowledgments.tex
===================================================================

--- trunk/specifications/sbml-level-3/version-1/fbc/spec/acknowledgments.tex	2014-11-27 14:32:24 UTC (rev 21770)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/acknowledgments.tex	2014-11-27 20:44:43 UTC (rev 21771)
@@ -8,5 +8,7 @@
 
 A special word of thanks goes to Sarah Keating for her invaluable work with the \textsf{libSBML} and \textsf{SBML Toolbox} implementations and critical reading of this document.
 
-We also would like to thank (in alphabetical order) Ben Heavner, Daniel Hyduke, Nicolas Le Nov\`{e}re, Keiran Smallbone, Lucian Smith, Neil Swainston, members of the \textsf{FBC Package Working Group} and all others who contributed to discussions on various occasions.
+We also would like to thank (in alphabetical order) \newtxt{Andreas Dr\"{a}ger}, Ben Heavner, Daniel Hyduke, Nicolas Le Nov\`{e}re, Keiran Smallbone, Lucian Smith, Neil Swainston, \newtxt{Alex Thomas}, members of the \textsf{FBC Package Working Group} and all others who contributed to discussions on various occasions.
 
+\newtxt{If you feel you should be mentioned in this section please contact the authors and ask to be included.}
+

Deleted: trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-gene_association.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-gene_association.tex	2014-11-27 14:32:24 UTC (rev 21770)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-gene_association.tex	2014-11-27 20:44:43 UTC (rev 21771)
@@ -1,147 +0,0 @@
-% -*- TeX-master: "main"; fill-column: 72 -*-
-
-%\subsection{Encoding Gene Protein Associations in SBML}
-
-%This specification drafted by \emph{Brett G. Olivier} and \emph{Frank T. Bergmann} (2013) with contributions by members of the \emph{FBC working group} as well as \emph{FBC} and \emph{SBML} communities. It builds on and supersedes the proposal included in \ref{future} of the \FBCPackage version 1 specification and as such implemented as an annotation in \textsf{libSBML}.
-
-%\subsection{ Introduction and motivation }
-%\label{intro-ga}
-
-%\subsection{The extended \class{Model} class}
-%\label{listofgeneassociations-class}
-%
-%\subsubsection{The \FBC \class{listOfGeneAssociations}}
-%
-%The \ListOfGeneAssociations extends \sbmlthreecore, is derived from \SBase and inherits the attributes \token{metaid} and \token{sboTerm} as well as the subcomponents for \Annotation and \Notes (as shown in \ref{fig:fbc_uml_ga_all}). If defined \ListOfGeneAssociations must contain at least one \GeneAssociation (as defined below in \ref{geneassociation-class}).
-%
-%\subsection{The extended \class{Species} class}
-%\label{species-class-ga}
-%
-%The \FBCPackage \textsf{Gene Association Proposal} (this document) extends the \sbmlthreecore \Species class (in addition to \token{charge} and \token{chemicalFormula}) with the addition of an attribute \token{isGene}.
-%%
-%\begin{figure}[h!]
-%  \centering
-%  % Requires \usepackage{graphicx}
-%  \includegraphics[width=6cm]{images/fbc_uml_species-v2.pdf}\\
-%  \caption{A UML representation of the extended \SBML \Species class used in
-%  the \FBCPackage. See \ref{conventions} for conventions related to this
-%  figure.}
-%  \label{fig:fbc_uml_species_ga}
-%\end{figure}
-%
-%\paragraph{The \token{isGene} attribute}
-%The optional attribute \token{isGene} contains a \primtype{boolean} referring to the fact that the \Species is not a metabolite that should be included in the reaction network but rather represents a \Gene product that participates in an \Association. In addition for a \Species where \verb+isGene="true"+ there should be at least one \Gene that refers to it via its \token{species} attribute (for more details see \ref{gene-class}).
-%%
-%\exampleFile{examples/ex_spec_l3_v2.txt}
-
-%
-%\subsubsection{The \FBC \class{listOfGeneAssociations}}
-%
-%The \ListOfGeneAssociations extends \sbmlthreecore, is derived from \SBase and inherits the attributes \token{metaid} and \token{sboTerm} as well as the subcomponents for \Annotation and \Notes (as shown in \ref{fig:fbc_uml_ga_all}). If defined \ListOfGeneAssociations must contain at
-
-\begin{figure}[h!]
-  \centering
-  % Requires \usepackage{graphicx}
-  \includegraphics[width=\textwidth]{images/fbc_uml_ga_all2.pdf}\\
-  \caption{A UML representation of the \FBCPackage. Derived from \SBase, the \FBC classes inherit support for constructs such as SBML \Notes and \Annotation's. See \ref{conventions} for conventions related to this figure. The individual classes are further discussed in the text.}
-  \label{fig:fbc_uml_ga_all}
-\end{figure}
-
-\subsection{The extended \class{Reaction} class}
-\label{reaction-class-ga}
-
-The \FBCPackage extends the \sbmlthreecore \Reaction class with the addition
-of a new optional element \GeneAssociation.
-
-\subsection{The \FBC \class{GeneAssociation} class}
-\label{geneassociation-class}
-
-The \FBCPackage defines a \GeneAssociation class that derives from \SBase and inherits the attributes \token{metaid} and \token{sboTerm}, as well as the subcomponents for \Annotation and \Notes. As shown in Fig.~ \ref{fig:fbc_uml_ga_all} the \GeneAssociation class connects a \Reaction (flux) with one or more gene (or gene products) in some form of association.
-
-\paragraph{The \token{id} attribute}
-The \GeneAssociation class defines an optional attribute: \token{id} of type \primtype{SId}
-
-%\paragraph{The \token{reaction} attribute}
-%The required \token{reaction} attribute of type \primtype{SIdRef}. This attribute must refer to a \Reaction element defined within the enclosing model.
-
-\paragraph{The \token{association} element}
-Each \GeneAssociation must contain a single \Association, however, as described in \ref{association-class} an \Association is an abstract class such that \token{association} should contain an instance of one of its sub-classes \GeneAnd, \GeneOr or \Gene.
-
-\begin{figure}[h!]
-  \centering
-  % Requires \usepackage{graphicx}
-  \includegraphics[width=5cm]{images/fbc_uml_ga.pdf}\\
-  \caption{A UML representation of the \FBCPackage \GeneAssociation class. See  \ref{conventions} for conventions related to this figure.}
-  \label{fig:fbc_uml_ga}
-\end{figure}
-
-\paragraph{Encoding the \GeneAssociation}
-As described in \ref{geneassociation-class} the \GeneAssociation is simply a container that relates a \Reaction to one of three types of \Association, either holding a single \Gene or two or more genes in an \GeneAnd or \GeneOr relationship. For example the following typical gene--protein association
-%
-\begin{verbatim}
- ((B3670 and B3671) or (B0077 and B0078) or (B3768 and B3769 and B3767))
-\end{verbatim}
-%
-from the BiGG database \emph{E.~coli} reconstruction (iJR904) \cite{ijr904, bigg} is now encoded in XML as:
-%
-\exampleFile{examples/spec-example1-ga.txt}
-%\pagebreak
-
-\subsection{The \FBC \class{Association} class}
-\label{association-class}
-
-The \FBCPackage defines an abstract \Association class that is derived from \SBase and inherits the attributes \token{metaid} and \token{sboTerm}, as well as the subcomponents for \Annotation and \Notes. It represents either a single gene or a collection of genes and should only ever be instantiated as one of its subclasses: \Gene (\ref{gene-class}), \GeneAnd (\ref{and-class}) and \GeneOr (\ref{or-class}).
-
-\begin{figure}[h!]
-  \centering
-  % Requires \usepackage{graphicx}
-  \includegraphics[width=10cm]{images/fbc_uml_ass.pdf}\\
-  \caption{A UML representation of the \FBCPackage \Association and derived classes. See \ref{conventions} for conventions related to this figure.}
-  \label{fig:fbc_uml_ass}
-\end{figure}
-
-\subsection{The \FBC \class{Gene} class}
-\label{gene-class}
-
-The \FBCPackage defines a \Gene class that represents a gene (or gene product) is derived from an \Association and thereby inherits the \SBase attributes \token{metaid} and \token{sboTerm}, as well as the subcomponents for \Annotation and \Notes as described in \ref{fig:fbc_uml_ass}.
-
-It is highly recommended that for future interoperability genes should be annotated using the inherited MIRIAM compliant SBML \Annotation mechanism thus reducing the ambiguity of using an overloaded, semantically meaningful \token{reference}.
-
-\paragraph{The \token{id} attribute}
-The \GeneAssociation class defines an optional attribute \token{id} of type \primtype{SId}.
-
-%\paragraph{The \token{species} attribute}
-%The optional attribute \token{species} attribute of type \primtype{SIdRef} can  refer to a \Species element defined within the enclosing model. The intention here is to allow gene--protein associations to be linked to \Species which may represent them in the model thus bridging two conceptually different (yet equally valid) ways of representing such relations. This attribute should be used in conjunction with the extended \Species attribute \token{isGene} (see \ref{species-class-ga} for details).
-
-\paragraph{The \token{reference} attribute}
-The \token{reference} attribute holds a string referring to the nameof a gene (or gene product). However, as seen in the example shown in \ref{intro-ga} there is no set format for this identifier e.g.~\verb+Rv0649+, \verb+3074.1+ or \verb+CRv4_Au5.s2.g9153.t1+. While ideally some form of restriction should be placed on the value of \token{reference} at this point it is left as a best practice suggestion that this attribute's value conform to the definition of an \primtype{SId}. As an example take an existing GPR annotation:
-\begin{verbatim}
- <p>GENE_ASSOCIATION: (Rv0649)</p>
-\end{verbatim}
-%
-this can now be formally (and unambiguously) encoded as:
-%
-\exampleFile{examples/spec-example1-gene.txt}
-
-\subsection{The \FBC \class{And} class}
-\label{and-class}
-
-The \FBCPackage defines an \GeneAnd class that represents a gene (or gene product) and is derived from and \Association and thereby inherits the \SBase attributes \token{metaid} and \token{sboTerm}, as well as the subcomponents for \Annotation and \Notes as described in \ref{fig:fbc_uml_ass}. This class represents a set of two or more associations that are related in an order independent \emph{`and'} relationship.
-
-\paragraph{The \token{elements} element}
-Each \GeneAnd must contain two or more instances (not necessarily of the same type) of any \Association subclass (\GeneAnd, \GeneOr, \Gene).
-
-\exampleFile{examples/spec-example1-geneand.txt}
-
-\subsection{The \FBC \class{Or} class}
-\label{or-class}
-
-The \FBCPackage defines an \GeneOr class that represents a gene (or gene product) and is derived from and \Association and thereby inherits the \SBase attributes \token{metaid} and \token{sboTerm}, as well as the subcomponents for \Annotation and \Notes as described in \ref{fig:fbc_uml_ass}. This class represents a set of two or more associations that are related in an order independent \emph{`or'} relationship.
-
-\paragraph{The \token{elements} element}
-Each \GeneOr must contain two or more instances (not necessarily of the same type) of any \Association subclass (\GeneAnd, \GeneOr, \Gene).
-%
-\exampleFile{examples/spec-example1-geneor.txt}
-
-
-

Added: trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-new.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-new.tex	                        (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-new.tex	2014-11-27 20:44:43 UTC (rev 21771)
@@ -0,0 +1,9 @@
+% -*- TeX-master: "main"; fill-column: 72 -*-
+\section{Summary of changes between versions} 
+\label{apdx-new}
+
+\subsection{Version 1 to version 2} 
+\label{apdx-new-one-to-two}
+
+\newtxt{Awaiting confirmation.}
+

Modified: trunk/specifications/sbml-level-3/version-1/fbc/spec/background.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/background.tex	2014-11-27 14:32:24 UTC (rev 21770)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/background.tex	2014-11-27 20:44:43 UTC (rev 21771)
@@ -17,7 +17,7 @@
 parameter ID's. Furthermore, reaction annotations are generally stored as
 tool specific HTML key-value pairs in a \Notes element which has routinely
 led to different research groups and software using in-house and/or tool
-specific ways to describe the same information. 
+specific ways to describe the same information.
 %
 \newtxt{An common example of such an annotation is the so called `gene association' used to assess the effect of gene deletions on a reaction network.}
 %
@@ -33,10 +33,9 @@
 %fluxes at steady state where, by definition, the variable \Species are
 %constant.
 %
-In addition, certain attributes that were widely used by the constraint based
-modelling community such as the \Species attribute \token{charge} were
+In addition, certain attributes that were widely used by the constraint based modelling community such as the \Species attribute \token{charge} were
 removed from SBML. This has had the effect that a significant number of
-tools and models are still limited to using SBML Level~2 Version~1.\cite{oberhardt_2009}
+tools and models are still limited to using SBML Level~2 Version~1 \cite{oberhardt_2009}.
 
 \subsection{Past work on this problem or similar topics}
 The problem of describing and annotating FBA models in SBML has been raised

Modified: trunk/specifications/sbml-level-3/version-1/fbc/spec/main.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/main.pdf	2014-11-27 14:32:24 UTC (rev 21770)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/main.pdf	2014-11-27 20:44:43 UTC (rev 21771)
@@ -211,95 +211,72 @@
 (5.1 Examples contrasting the current SBML L2 encoding with L3 and FBC)
 endobj
 141 0 obj
-<< /S /GoTo /D (section.6) >>
+<< /S /GoTo /D (appendix.A) >>
 endobj
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-(6 Future development)
+(A Validation of SBML documents)
 endobj
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-<< /S /GoTo /D (subsection.6.1) >>
+<< /S /GoTo /D (subsection.A.1) >>
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+<< /S /GoTo /D (appendix.B) >>
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+(B Summary of changes between versions)
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+(Acknowledgments)
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[sbml-svn] SF.net SVN: sbml:[21771] trunk/specifications/sbml-level-3/version-1/fbc/ spec

A file format for exchanging computational models in systems biology

[sbml-svn] SF.net SVN: sbml:[21771] trunk/specifications/sbml-level-3/version-1/fbc/ spec