Import Notes plugin Release date: 2008/6/18 Version: 1.1 ================================================================== "Import Notes plugin" can import notes data for components/reactions from CSV file into CellDesigner model. The CSV file format used by this plugin is same as CellDesigner's exported list file format. You need to prepare separate CVS file for different type of components/reactions; [Species][Proteins][Genes][RNAs][asRNAs] [Reactions] [Compartments]. Each CVS file should include essential columns as described below. x : essential column +---------------+--------------++-------+-------+-------+-------+-------+ | CSV file type | matching key || id | notes | name | class | type | +===============+==============++=======+=======+=======+=======+=======+ | ALL | ID || x | x | | | | +---------------+--------------++-------+-------+-------+-------+-------+ | Species | NAME || | x | x | x | | +---------------+--------------++-------+-------+-------+-------+-------+ | Proteins | NAME || | x | x | | x | +---------------+--------------++-------+-------+-------+-------+-------+ | Genes | NAME || | x | x | | | +---------------+--------------++-------+-------+-------+-------+-------+ | RNAs | NAME || | x | x | | | +---------------+--------------++-------+-------+-------+-------+-------+ | asRNAs | NAME || | x | x | | | +---------------+--------------++-------+-------+-------+-------+-------+ | Reactions | NAME || | x | x | | x | +---------------+--------------++-------+-------+-------+-------+-------+ | Compartments | NAME || | x | x | | | +---------------+--------------++-------+-------+-------+-------+-------+ CSV file format example: ----------------------------------- 1. Startup CellDesigner. 2. Open "database.xml" file from "celldesigner_install_dir/samples" folder. 3. Click target component tab from List area and click [Export] button. You can select the tab below: [Species][Proteins][Genes][RNAs][asRNAs] [Reactions] or [Compartments] 4. "Export Setting" dialog is displayed. Click "id","name" and "notes" check box. * You can check other attributes as well, but the irrelevant data would be ignored when importing notes. 5. Click [OK] button. 6. "Save dialog" is displayed. Input file name and click [Save] button. 7. Open CSV file and check the format. In the CVSV file, the first row is columnfs title. You can make a CSV file for importing notes using this format. How to import Notes data: ----------------------------------- 1. Deploy "import_notes_plugin.jar" file to "celldesigner_install_dir/plugin/" directory. 2. Startup CellDesigner and open Model file. 3. Select [Plugin] - [Import Notes 1.1] - [Select Notes filec] menu. "Import Notes 1.1" dialog is displayed. 4. Select CSV file type and click [Importc] button. 5. "Open" dialog is displayed. Select CSV file and click [Open] button. 6. Select matching key. 7. Notes data is imported. The log file ".csv.ImportNotes.log" is created in same directory.