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Pathway Editor Brief Tutorial - version 1.0 beta 2

Introduction
Start the Pathway Editor
Open a pathway from a file
Open a LIPID MAPS pathway from the database
Open a KEGG pathway from the database
View some selected pathway information
Create a new pathway
    Create a  node 
    Show node information 
    Change the node's compound 
    Change the node's label 
    Add more nodes 
    Connect nodes to form a process 
    Rearrange nodes and processes 
    Change the appearance of an individual node
    Change the appearance of all nodes in a pathway or subpathway
    Change the appearance of all processes (interactions) in a pathway or subpathway
    Change the appearance of an individual process (interaction)
    Change pathway display settings 
Manage data display
Obtain an expanded chart for printing and saving to file
Animate charts
Save a pathway as a *.path file
Save a pathway as an image
Search for experimental lipidomics data 
Search for microarray or protein array experiment data
Using Pathway Editor to view user-defined data

Introduction

This is a brief tutorial for the beta 2 Pathway Editor.

The Pathway Editor is drawing application that draws in three dimensions. Icons are drawn with shadows on the lower right to suggest raised features.

There are separate Pathway file open and Pathway file save windows (dialogs) that operate independently of each other. These features allow the two dialogs to open onto different file locations and may thus minimize repeated navigation betwen folders.

Some program windows allow the user to interact with the program and to set properties using "Apply" and "Reset" buttons. In addition, on Windows, many viewing properties are set by pressing a "Done" button that also closes the window. On Apple computers, instead of a "Done" button, properties may be set by exiting the current window.

Start the Pathway Editor

From the Pathway Editor tutorial (this page) or from the LIPID MAPS Pathway Editor webpage, click the link Download and launch Pathway Editor to start the application. Click on "yes" each time you are asked if you trust our downloads (we assume you do). The Editor asks if you want to associate files ending in “.path” with this program. If you do, click "yes" on the PC, or check the box next to "Do this automatically for files like this from now on" on the Mac. This allows Pathway Editor to be placed on a list of programs that opens this file type.

When the download completes, the editor will start up and look like this:

The 3 leftmost buttons in the toolbar at the top allow entry into node select mode, node creation mode, and node connect mode. The next two buttons allow you to zoom in and out, repectively, with the current zoom level shown in the 'Current' button. The 'Fit to screen' button fits the current pathway to the canvas. The last two buttons, 'Tilt up' and 'Tilt down', allow you to tilt the pathway plane. The scrollbars on the right and bottom of the drawing canvas allow you to move the viewing area vertically and horizontally over the drawing plane. The mouse scroll wheel allows fine-grained zooming in and zooming out in small increments.

Open a pathway from a file

Go to the "File" menu and select "Open pathway file..." to get a file-opening window. Select a file, click "Open" and the pathway will load.

Pathway files must end with ".path". If you do not already have a .path file saved to your local environment, you can download the .path file for Arachodonic Acid metabolism: AApathway9genes.path

A .path file contains descriptions of the components of a pathway and their appearance in the Editor display. It contains database IDs (identifiers) and other material that identify specific molecules. This information is checked when the Editor opens the file and is updated from the database automatically. The file may also contain experiment IDs that reference experiment data in the LIPID MAPS database. The presence of experiment IDs instructs the Pathway Editor to download experimental data. All of the data for a time course (lipidomics) experiment is downloaded. For a microarray or protein array experiment, only the data for the microarray or protein array molecule identifiers currently being used in the file and in the currently displayed pathway are downloaded.

Additional .path files may be downloaded from http://www.lipidmaps.org/pathways/pathwayeditor.html, or accessed from within the Pathway Editor application, as described below in "Open a LIPID MAPS pathway from the database".

If .path files are sent by email, some email programs have problems with the file format. If email is necessary, it is best to zip the files before emailing.

Open a LIPID MAPS pathway from the database

Go to the "File" menu and select "Open LIPID MAPS Pathway..." to show a search window:

Press the 'List' button to display the complete list of LIPID MAPS Pathways. These are highly curated pathways, developed based on LIPID MAPS experimental data. The list of pathways is drawn from the URL indicated, http://www.lipidmaps.org/pathways/pathwayeditor.html

Select the "Arachidonic acid metabolism" pathway. The .path file will automatically be downloaded from the LIPID MAPS website, and loaded into the Pathway Editor.

You can also visit the LIPID MAPS website, and view and download these .path files to your local hard drive. You can then load them following the above instructions for opening a pathway from a file.

Open a KEGG pathway from the database

Go to the "File" menu and select "Open pathway database ..." to show a search window:

By default, the search looks for all pathways of any type. Constrain the search by typing a keyword and/or selecting a pathway type. Click "Search" to search the database for matching pathways.

Select the "Arachidonic acid metabolism" pathway and press the "Select" button. The pathway will load:

View some selected pathway information

Go to the "File" menu and select "Show pathway information" to get a Pathway information window.

The window contains information that may be edited and saved to a .path file. This includes pathway title, type of pathway, comments, authors, and history.

Create a new pathway

Go to the "File" menu and select "New pathway " to create a new empty pathway.

Create a node

On the toolbar, select the box-shaped icon (2nd from left) to enter node creation mode, then click in the drawing area to drop a new node at the cursor. Nodes are always box-shaped icons.

The blue outline shows that the node is selected.

Show node information

You can show information about a selected node by doing any of the following (they are all equivalent):

• Select "Show node info..." from the "Edit" menu.
• Press the right mouse button and select "Show info..." from the context menu that pops up.
• Double-click on the node or heatmap/chart.

All of these bring up a window about the node. From this window you can change the node's label, compound, and other attributes.

Change the node's compound

To assign a compound to the node, select the "Compound" tab and press the "Select compound..." button. This shows a compound search window.

Constrain the search by selecting the compound type and category and/or entering a keyword. Radio buttons provide further constraints on the text that is searched. Then press "Search" to get a list of results.

Select one of the compounds from the list and press the "Select" button. The compound is loaded from the database and assigned to the node. You can view the compound's details by pressing the "Show info..." button on the node's information window.

Change the node's label

Change the node's label to anything you want by typing a new value in the "Label:" box in the node's information window. Up to 3 lines may be entered. Additional lines will not be saved. To set line indents, see "Change the appearance of an individual node"

This changes the label on the node's box in the drawing area.

Add more nodes

Continue using the "box" icon. Drop more nodes into the pathway and assign compoundes to them.

Connect nodes to form a process

Click on the dot-and-arrows icon on the toolbar (third from the left) and click-and-drag to draw connections between nodes.

A process or interaction is a connection between two or more nodes. The process is drawn as a square withe arrows connecting the square to nodes. Nodes with arrows into the square are reactants. Nodes with arrows from the square are products.

The first time you connect two nodes, you create the process. After that, you can drag a connection from a node to the dot, or from the dot to a node to add the node to the process.

You can show information about a process by selecting the process square and then performing one of the following:

• Select "Show node info..." from the "Edit" menu.
• Press the right mouse button and select "Show info..." from the context menu that pops up.
• Double-click on the square.

All of these show an information window about the process.

From this window you can enter information on the process in the "Label" field, change its process type, and see a list of the nodes connected to the process. For each of these nodes, you can change their role in the process and their stoichiometry. A node's role can be a reactant, a product, a catalyst, an inhibitor, and so on. Inhibitor nodes are drawn with a "bar" on their connection line. The rest are shown with arrows.

Rearrange nodes and processes

Click on the arrow icon on the toolbar (the left-most button) to enter selection mode. Click and drag to move any node. Process arrows stay attached. Click and drag a process square to move the square.

Shift-click to select multiple nodes. Or click on the background and drag open a selection box around nodes and processes to select a group, then move them as a group.

Change the appearance of an individual node

Right-click on a node. Select "Node preferences..". The "Edit viewing preferences" window appears, with the tab for the type of node selected. The tab contains current viewing preferences for the node. Change any of the settings and press "Apply". Then press "Done" or exit the window.

"Automatically resize" means to let the application change node size when typing in a label. If the setting is No, the Node height and Node width may be changed using the drop-down lists. In addition, the handles on the sides of the node are then activated, allowing the user to drag out the sides to a desired position.

The left indent positions of label text may be set using the "Indents" tab.

Change the appearance of all nodes in a pathway or subpathway

Until experience is gained with the Editor, it may be best to limit use of this feature to the very first step in creating a pathway.

Select a region of the drawing area by clicking in the drawing panel and dragging to create a rectangle enclosing the nodes to be changed. Then right-click on any node. The "Edit viewing preferences" window appears. The window contains current viewing preferences for the first of each kind of node in the selection. Changes made to any of the tabs in this window will affect all the nodes in the selection (not just the first node).

Alternatively, select all nodes by accessing the Edit | Node preferences menu. An "Edit viewing preferences" window appears. Changes made on this window will affect all current and new future nodes in the pathway.

Make the desired changes and press "Apply" followed by exiting the window or by clicking "Done". The changes should appear in the drawing panel.

Change the appearance of all processes (interactions) in a pathway or subpathway

Until experience is gained with the Editor, it may be best to limit use of this feature to the very first step in creating a pathway.

Make sure that no processes are selected and go to the Edit menu and select "Interaction preferences...". Alternatively, select a region of the drawing area by clicking in the drawing panel and dragging to create a rectangle enclosing the processes to be changed. Then right-click on any process and select "Interaction preferences". The "InteractionEdit viewing preferences" window appears. The window contains current default viewing preferences for the program, or for the first interaction in the selection. Changes made to any of settings in the window will affect all the interactions in the selection and all interactions that are added later.

Make the desired changes and press "Apply" followed by exiting the window or by clicking "Done". The changes should appear in the drawing panel.

Change the appearance of an individual process (interaction)

Right-click on a process square. Select "Interaction preferences..". The "Edit interaction preferences" window appears. Change any of the settings and press "Apply". Then press "Done"

Change pathway display settings

The Editor uses different sets of settings for displaying pathways, depending upon the type of file. Both sets can be inspected by selecting "Pathway preferences" on the Edit menu.

Changes to pathway settings must be made before reading a file or downloading a pathway.

For .path files, the Editor automatically fits the pathway to the screen dimensions. It automatically uses the zoom setting that was set when the file was saved. Alternatively, the file zoom may be ignored, or a different zoom may be applied, using the Pathway preferences window.

For KEGG file downloads, the same features are available, with the exception of using a file zoom setting. KEGG pathways files do not contain zoom levels.

Manage data display

Construct a pathway and load one or more experiments that contain data to be displayed. Go to the Tools menu and select "Manage data display".

The window that appears contains controls that allow changes to default display settings for data. Make the desired changes on each tab and press "Apply". The changes should appear instantly.

Data may be displayed in the form of heat maps or line charts, separately for each type of node. If heat maps are selected on the first tab of the window, the treatment ratio may then be selected. The default treatment ratio is Kdo/Control.

Alternatively, line charts may be set on the first tab, and line chart settings may be set on the "Chart settings" and "Series colors" tabs.

The changes apply both to data displays in the drawing panel as well as in node information windows.

Obtain an expanded chart for printing and saving to file

On the drawing panel, double-click a chart. In the window that appears, select the "Plot" tab and double-click the chart. Yet another window containing a chart appears, that may be resized. Right-click on the chart and select one of the menu items. "Save as" leads to a window that permits saving a chart in a .png image file. "Print" leads to a window that allows access to the local printing network.

The display properties of the resizable window may be changed using the "Properties" menu item.

Animate charts

Ensure that display settings specify line charts for small molecules, proteins, or both. In the View menu, select "Animate" and then "Play". The line charts become bar charts that change with time.

The animation may be stopped by accessing the View menu, selecting "Animate" and then "Stop". The bar charts return to XY charts.

Animation settings may be changed using the "Manage data display" window that is accessed by selecting the "Manage data display" menu item in the Tools menu.

Save a pathway as a *.path file

Go to the "File" menu and select "Save pathway as..." to get a save window. Enter a file name, select the "PATH" file type and click "Save." The PATH format is our own file format that supports saving display parameters for the pathway and its assigned compounds.

Experiments are also referenced in the .path file if experiments were previously downloaded from the database. The data for these referenced analyte (lipidomic), microarray, and protein array experiments are automatically downloaded from the LIPID MAPS database when the file is read back into the program.

Save a pathway as an image

Go to the "File" menu and select "Save image as..." and select any of 'bmp', 'jpg', 'jpeg', 'png'. Please note that on the Mac, before saving your pathway as an image, you must first select any node in the pathway. If you do not first select a node, the image will be saved, but if experimental data is shown in the pathway, some of this data may be missing from the saved image.

Search for experimental lipidomics data

Go to the "Tools" menu and select "Manage time course experiments..." to get a list of loaded experimental data (initially empty).

Click on the "Add" button to add an experiment from the database.

In the window that opens, optionally enter a keyword or keyword fragment and press the "Search" button to search descriptions and lab titles in the database.

Select an experiment from the list and press the "Add" button to load it into the program. Relevant experimental data is automatically shown in heat maps or line charts under each node in the pathway.

To view an experiment's data, select the experiment and press the "Show info..." button.

Select any of the compounds in the Manage time course experiments window to show their heat map or line chart and raw data to the right.

You can add more experiments to the Manage time course experiments window by clicking the "Add" button and searching the database again. Click the "Remove" button to remove an experiment. Click on the checkbox beside an experiment to show it in the pathway (checked) or hide it (unchecked).

Check the "Average experiments" checkbox to average the data in the list of experiments for purposes of display.

If the "Average experiments" checkbox is not checked, then only the data of the first checked experiment in the list is displayed. The rest of the experiments are ignored.

Search for microarray or protein array experiment data

Go to the "Tools" menu and select "Manage microarray experiments..." or "Manage protein array experiments..." to get a list of experimental data.

The next steps are nearly identical to those in "Search for experimental lipidomics data". The exception is that data is downloaded only for these gene symbols that are currently assigned to existing nodes.

The database is checked for data assigned to gene symbols when an array experiment is selected and the "Refresh" button in the "Manage microarray experiments" or "Manage protein array experiments" windows is pressed, and also when a .path file referencing an array experiment is opened.

P-values for a microarray experiment may be searched using the window that appears when a microarray experiment is selected and the "P-values" button is pressed.

To search P-values, select a type of P-value and enter the upper P-value of the range to be used.Press "Search". A list of gene symbols and their P-values are shown.

The gene symbols and P-values can be sorted by using the "Sort" buttons, or by pressing a column header.

Using Pathway Editor to view user-defined data

The Pathway Editor loads CSV (Comma Separated Value) data files generated by Microsoft Excel. CSV files may be opened using Excel for editing, if desired. Data files may also be created using a text editor. Below is a description of a CSV data file.

Using CSV data files

Note that steps 1 and 2 can be performed any number of times and in any order.

1. Go to File | Open CSV data file and load a file ending with the extension .csv. When loaded in Pathway Editor, the data can be viewed using the menu items in the Tools menu.
2. Go to File | Open pathway file and load a .path file. The nodes in the file may have database compounds assigned, or not, as desired.
3. The data will be displayed in the Pathway Editor.
4. When generating a new node, the Editor will automatically assign data to nodes: First, create a node and assign a node type (Small molecule, nucleic acid, or protein) using the Node information window. Next, assign a label name that is a compound name from the data file. On a Windows desktop, press the "Done" button. On a Mac, close the dialog. If the information has been typed correctly, the data will automatically be associated with the node and displayed.

Rules for writing CSV data files

Each data file may contain one or more experiments. Each experiment may contain Analytes (metabolites, comprised of Small molecules, Proteins, or Nucleic acids), Microarray, or Proteinarray compound types. However, an experiment may not contain a mixture of compound types.

1. Start the file with a line beginning "Experiment list".
2. The next line should contain at least one leading comma.
3. Lines 3 through 10 describe an experiment and should contain:
   1. A line beginning with the word Experiment.
   2. A line beginning with the word Date, a comma, and the date in month-day-year format (mm-dd-yyyy). The date in this format must also be surrounded by quotes (that is, July 12, 2008 may be written "07-12-2008"). The date may also be written as mm/dd/yyyy, without quotes (written as 07/12/2008).
   3. A line beginning with the word Type, a comma, and the type of experiment (Analyte for a metabolite, Microarray for a microarray experiment, or Proteinarray for a protein array experiment).
   4. A line beginning with the word Ratios, a comma, and a list of treatment type ratios to be used by the program. The ratios will appear on the Manage data display dialog.
   5. A line beginning with the word Description, a comma, and a brief description of the experiment.
   6. A line beginning with the phrase Time units, followed by the time units for the experiment (h for hours, etc. These must be the same for all compounds.)
   7. A line beginning with the word Lab, followed by a description of the lab.
   8. A line beginning with word System, followed by a description of the biological system.
   Note that the description of the lab should be contained with quotes to allow use of commas in the description.
4. Line 11 should contain a leading comma.
5. The next 7 lines should contain the description of the compound. The compound should be of the same type as a node in the pathway to which the data is to be assigned.
   1. A line beginning with the word Label, a comma, and the compound name.
   2. A line beginning with the word Type, a comma, and Small molecule, Protein, or Nucleic acid.
   3. A line beginning with the phrase Gene symbol and a comma. If the compound is a protein, the text symbol for the microarray or protein array spot should be next. Leave the symbol empty for other compound types.
   4. A line beginning with the phrase Data units, followed by the units for the data. This should be the same for all compounds within the experiment.
   5. A line beginning with the word Treatment, a comma, and the type of treatment. Treament types may be the same as listed in the LIPID MAPS pathway database. Alternatively, a different treatment type may be used on this line, as desired.
   6. A line beginning with the word Times, a comma, and all the measurement times for the compound, separated by commas. It is not necessary to enter values for time 0.
   7. A line beginning with the word Measurements, a comma, and all the measurement values for the compound, separated by commas. It is not necessary to enter values for time 0.
   8. Each compound description should be separated by a line beginning a leading comma.
   9. Additional guides:
      1. If the compound is a Small molecule, Protein, or Nucleic acid analyte, the label name in the CSV file must be the same as the label name for the node in the pathway diagram.
      2. If the compound is part of an array experiment, the compound in the CSV file must have a label name that is the same as the label name for the node. If the node has one or more gene symbols assigned, the compound in a the CSV file must possess one of the gene symbols. If the node does not have a gene symbol assigned, the gene symbol of the compound can be any desired text. In either case, data will be automatically associated with the node.
6. Repeat 4 and 5 for each compound in the .csv file.