Working with pathways

 

Help
Creating a new pathway
Opening a pathway in the database
Opening a pathway file
Saving a pathway to the same file
Saving a pathway to a new file
Getting pathway information
Setting a pathway title
Assigning a pathway type
Adding comments

 

Creating a new pathway

You can create a pathway from scratch:

  • From the "File" menu, select "New pathway". If the file you are working on needs to be saved, you will be prompted to save it first.
  • The pathway window will clear, leaving you a blank canvas on which to add nodes and draw process edges.

Opening a pathway in the database

You can view and edit a pathway in the LIPID MAPS database:

  • From the "File" menu, select "Open pathway database..." to show the pathway search window.
  • Optionally, select the type of pathway to search for using the pull-down menu labeled "Type:". The choices are "Gene regulation", "Metabolic", "Signaling", "Other", or "Any".
  • Optionally, type in part of a pathway's name to look for using the
  • Press the "Search" button. The Pathway Editor will search the database and show a list of pathways.
  • Select a pathway in the list and press the "Select" button. The Pathway Editor will load the pathway and show it in the pathway window.

Opening a pathway file

You can view and edit a pathway read from a file:

  • From the "File" menu, select "Open pathway file..." to show the file selection window.
  • Find the file you want on your hard disk. The Pathway Editor reads KEGG KGML and Biopathways PATH files.
  • Press the "Open" button. The Pathway Editor will load the pathway and show it in the pathway window.

Saving a pathway to the same file

If you opened a pathway file, you can save your changes back to that file:

  • From the "File" menu, select "Save pathway".
  • The pathway will be saved to the same file it was read from.

Saving a pathway to a new file

You save a pathway to a new file:

  • From the "File" menu, select "Save pathway as... ". You will be presented with a window from which to select the name of a new file, and where to put the file.
  • Type in a file name.
  • Click on the "Save" button to save the file.

Getting pathway information

The pathway information window shows the pathway's title, type, comments, and history.

  • From the "File" menu, select "Show pathway info... ".

Setting a pathway title

Assigning a pathway type

You select the type for a pathway, such as "Signaling" or "Metabolic". The pathway's type is useful documentation about the pathway, and helps the Pathway Editor present default choices when setting a node's role in a process.

  • Get the pathway information window.
  • Use the pull-down menu labeled "Type:" to select between "Gene regulation", "Metabolic", "Other", "Signaling", or "Undefined." The default is "Metabolic."

Adding comments

You can add your own comments about a pathway: