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doc/publication/draft/document.tex

@@ -77,7 +77,7 @@ \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} 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.
 

src/de/zbit/kegg/gui/TranslatorUI.java

@@ -103,7 +103,7 @@ public static enum Action implements ActionCommand {
 		TRANSLATION_DONE;
 		/**
 		 * Invisible {@link Action} that should be performed, whenever a file
-		 * has been droppen on this panel.
+		 * has been dropped on this panel.
 		 */
 		//FILE_DROPPED
 
@@ -690,6 +690,7 @@ public URL getURLOnlineHelp() {
 	  return Translator.class.getResource("html/help.html");
 	}
 
+
 	/*
 	 * (non-Javadoc)
 	 * 

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

@@ -32,24 +32,24 @@
 public interface KEGGtranslator {
 
   /**
-   * The name of the appplication.
+   * The name of the application.
    */
   public final static String APPLICATION_NAME = "KEGGtranslator";
 
   /**
    * Version number of this translator
    */
-  public static final String VERSION_NUMBER = "1.0.0";
+  public static final String VERSION_NUMBER = "1.1.0";
 
   /**
    * Filename of the KEGG cache file (implemented just
-   * like the browser cache). Must be loded upon start
+   * like the browser cache). Must be loaded upon start
    * and saved upon exit.
    */
   public static String cacheFileName = "keggdb.dat";
   /**
    * Filename of the KEGG function cache file (implemented just
-   * like the browser cache). Must be loded upon start
+   * like the browser cache). Must be loaded upon start
    * and saved upon exit.
    */  
   public static String cacheFunctionFileName = "keggfc.dat";