Documents to submit to Bioinformatics as answer to the major revision…

…. Includes latest publication and everything.

doc/publication/draft/document.tex

@@ -23,7 +23,9 @@
 \application
 \firstpage{1}
 
-\title[KEGGtranslator]{KEGGtranslator: visualizing and translating the KEGG PATHWAY database} %% TODO: Irgendwas mit modelling oder simulation oder so klingt besser.
+%\title[KEGGtranslator]{KEGGtranslator: visualizing and translating the KEGG PATHWAY database}
+\title[KEGGtranslator]{KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats}
+
 \author[Wrzodek \textit{et~al}]{Clemens Wrzodek\,$^{1,*}$, Andreas Dr\"ager\,$^{1,*}$ and Andreas Zell\,$^{1,}$\footnote{to whom correspondence should be addressed}}
 \address{$^{1}$Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 T\"ubingen, Germany}
 
@@ -77,7 +79,7 @@ \section{Introduction}
 %The reason for this is that KEGG releases those XML-files primarily for graphical visualizations of the pathway. For creating fully functional models of the pathway, the content of the XML-file is not sufficient.
 By improving the annotation and translating the KGML-files to other file formats, researchers could use the KEGG database for many applications: Individual pathway pictures could be created; pathway simulation and modeling applications could be executed; graph-operations on the pathways or stoichiometric analyses (e.g., linear relationships) could be performed; or the KEGG pathway database could be used for gene set enrichment analyses.
 %
-For these purposes, only a few converters are available: KEGGconverter \citep{KEGGconverter} or KEGG2SBML \citep{KEGG2SBML} offer command-line or web-based conversion of KGML-files to SBML-files. KEGGgraph \citep{KEGGgraph} is able to convert KGML-files to R-based graph structures. None of these tools has a graphical user interface, is capable to validate and autocomplete KEGG reactions, adds standard identifiers (such as MIRIAM URNs) to pathway elements, or is able to write KGML files in multiple ouput formats.
+For these purposes, only a few converters are available: KEGGconverter \citep{KEGGconverter}, SuBliMinaL \citep{Swainston2011}, or KEGG2SBML \citep{KEGG2SBML} offer command-line or web-based conversion of KGML-files to SBML-files. KEGGgraph \citep{KEGGgraph} is able to convert KGML-files to R-based graph structures. None of these tools has a graphical user interface, is capable to validate and autocomplete KEGG reactions, adds standard identifiers (such as MIRIAM URNs) to pathway elements, or is able to write KGML files in multiple ouput formats.
 
 We here present KEGGtranslator, which reads and completes the content of an XML-file by retrieving online-annotation of all genes and reactions using the KEGG API \citep{KEGGapi}. KGML-files can be converted to many output formats. Minor deficiencies are corrected (e.g., the name of a gene), new information is added (e.g., multiple MIRIAM identifiers for each gene and reaction \citep{Novere2005}, or SBO terms describing the function) and some crucial deficiencies (like missing reactants) are addressed.
 
@@ -175,8 +177,10 @@ \section{Discussion}
 
 \section*{Acknowledgement}
 We gratefully acknowledge very fruitful discussions with Jochen Supper, Akira Funahashi, and Toshiaki Katayama.
+
 %\emph{Funding\textcolon}
 \paragraph{Funding\textcolon} The Federal Ministry of Education and Research (BMBF, Germany) funded this work in the projects Spher4Sys (grant number 0315384C) and NGFNplus (grant number 01GS08134).
+%The Federal Ministry of Education and Research (BMBF, Germany) funded this work in the projects Spher4Sys and NGFNplus (grant numbers 0315384C and 01GS08134).
 
 %\paragraph{Funding\textcolon} %Spher4Sys, BMBF, MARCAR, Virtualliver, NGFN
 \paragraph{Conflict of Interest\textcolon} none declared.
@@ -193,6 +197,7 @@ \section*{Acknowledgement}
 %XXX: Uncomment for dynamic reference addition
 %\bibliography{KEGGtranslator}
 
+\vspace{-.1cm}
 
 \begin{thebibliography}{}
 
@@ -250,6 +255,11 @@ \section*{Acknowledgement}
   {(MIRIAM)}.
 \newblock {\em Nat Biotechnol\/}, {\bf 23}(12), 1509--1515.
 
+\bibitem[Swainston {\em et~al.}(2011)]{Swainston2011}
+Swainston, N. \emph{et al.} (2011).
+\newblock {The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks}.
+\newblock {\em Submitted to Journal of Integrative Bioinformatics\/}. %Integr. Bioinf. ?
+
 \bibitem[Wiese {\em et~al.}(2001)Wiese, Eiglsperger, and Kaufmann]{yFiles}
 Wiese, R. \emph{et al.} (2001).
 \newblock {yFiles: Visualization and Automatic Layout of Graphs}.

src/de/zbit/kegg/io/KEGG2SBGN.java

@@ -38,7 +38,7 @@
  * A (not yet fully implemented) implementation of KEGG2SBGN.
  * 
  * <p> Note:<br/>
- * Martijn want to be mentioned in 'Acknowledgments', in case of a publication
+ * Martijn should be mentioned in 'Acknowledgments', in case of a publication
  * of this method.</p>
  * 
  * @author Martijn van Iersel