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From PathVisio Wiki
Overview
PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as though you are drawing them in powerpoint. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological components (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing (Note: mapping experimental data is not yet a feature of PathVisio 1.1, but you can do this in combination with GenMAPP or with additional plug-ins for PathVisio).
Here is a screenshot of the program in action:
Editing pathways
How do I ... Create a new pathway?
- Create a new pathway by pressing Ctrl+N or going to File > New.
- A blank drawing area will open where you can start adding and editing new elements. Specific editing features are described below.
Placing new objects
Add new objects by selecting one of the object icons in the toolbar, then drag and drop the object in the desired location in the drawing area. If you're unsure what a certain icon does, you can hover over it with the mouse cursor to get a description.
Selecting objects
Single or multiple objects can be selected in two ways:
- Click-and-drag anywhere in the drawing area and drag to select any number of objects using a rectangular selection tool.
- Click on any object to select it. Holding down the Ctrl key or Shift key and click on additional items to add these to the selection.
Moving objects
You can move objects in two ways:
- Click and drag: Select one or more objects and then click and drag the selection to the desired location.
- Arrow keys: Select one or more objects and click any of the keyboard arrow keys to move the selected objects. Holding down the shift key while pressing the arrow keys will move the objects with a larger increment.
Changing the size of objects
You can change the size of objects in two ways:
- Click on an object and drag the handles to resize or move objects.
- Open the properties tab in the panel on the right side of the window. Change the size of the object by entering information for Width and Height.
Pathvisio in edit mode:
Grouping objects
PathVisio supports the notion of groups, to facilitate editing and for describing biological entities. Any selection of objects can be grouped in PathVisio:
- Select the group of objects to be grouped.
- Click Ctrl+G to group the objects. The objects can now be moved as a group and the group can also be linked to other objects. Clicking Ctrl+G again ungroups the group.
Aligning, scaling and stacking objects
To facilitate editing, objects can be aligned, scaled and stacked using a set of buttons in the toolbar.
- Align vertically: Center of objects are aligned vertically based on the location of the top selected object
- Align horizontally: Center of objects are aligned horizontally based on the location of the top selected object
- Set common width: Widths of selected objects are set to the width of the widest selected object
- Set common height: Heights of selected objects are set to the height of the tallest selected object
- Stack vertically: Objects are are arranged into a vertical stack based on the top selected object
- Stack horizontally: Objects are are arranged into a horizontal stack based on the top selected object
Zoom
Pathways can be zoomed using the zoom drop-down in the toolbar or by going to View > Zoom. The Zoom to fit option sizes the pathway to fit in the current drawing area.
Copy and paste
Copy and paste works for objects within a given pathway as well as between pathways open in different windows of PathVisio, and between PathVisio and WikiPathways. Copy and Paste can be accessed in the Edit menu as well as with shortcut keys, Ctrl+C copies selected objects and Ctrl+V pastes copied objects.
Linking two biological entities together
You can link any line endpoint to a shape, gene product or brace in the following way:
- Click on the line and select the end point handle
- Drag the end point to the object you want to the object you want to link it to. When you come near the object, little round "snap targets" appear. When you move close to a snap target, the line snaps to it and the target shows a green line. When this happens, release the handle.
The end point of the line is now tied to the object. If you move the object, the endpoint of the line follows. However, you can still move the line independently of the shape.
Changing line and arrow type
There are three possible line styles for connectors:
- Straight, a direct line
- Elbow, connects points with straight angles
- Curved, connects points with a smooth curve
Make the connection line or arrow first, then right-click to bring up the line style pop-up menu.
Pointing arrows to other arrows
It is create an arrow that points to another arrow. This is useful for e.g. one arrow representing a reaction and another arrow representing catalysis of that reaction by an enzyme.
First you need to create an anchor on the target line. There are two ways to do this:
- Select the line and press Ctrl+R
- Right-click on the line and select "add anchor" from the pop-up menu.
You can choose two different anchor styles,
- Circle, a big, visible dot.
- None, represented as a tiny dot.
To select an anchor style, right-click on it and choose from the anchor type menu.
Changing the drawing order
You can change the drawing order of objects in a Pathway by right-clicking on an element. However, in the current version of PathVisio the drawing order is lost after saving and re-opening a pathway. This is a known issue and we're working to resolve this.
Adding references to database identifiers
When creating a pathway, it is useful to link the genes to public database identifiers. To do this, you must first select one the synonym databases distributed by PathVisio:
- Download and install the synonym database you want to use (How?).
- Go to Data > Select Gene Database and choose the database file you want to use. The status bar at the bottom of the PathVisio window will show which gene database is currently used.
- Select the gene product for which you want to enter an identifier.
Now there are two ways to set the right identifier
- Double-click on the gene. This opens a dialog. Enter a gene identifier or (partial) gene name and click "search". If there is one or more result found, you can select it from a list.
- In the property panel on the right side of the PathVisio main window, enter the database identifier in the "Name" property, and select the database the identifier belongs to from the System Code property.
Certain genes may not be found in the synonym databases that come with PathVisio. You may still fill out the gene name and identifier of your choosing, but PathVisio will not be able to cross-reference this to online databases.
Adding Comments
To add comments to any element, double-click on it to open a properties dialog. Click on the "comments" tab, and click "add comment", to create a new comment. You can add unlimited separate comments to any element in a pathway.
Adding Literature References
To add a literature reference to any element, double click on it to open a properties dialog. Click on the "Literature" tab and click the "add" button. The easiest way to enter a reference is to enter a pubmed identifier if you know it, and click the "Query pubmed" button. PathVisio will connect with pubmed over the internet and obtain the full reference info. Alternatively, you can fill in the fields for Title, Year, Author and Journal manually.
Editing object properties
In the property panel on the right side of the PathVisio window you have precise control over all the properties of the object you have currently selected. For example, you can position objects by entering exact coordinates, change their color or size. You can also change the font and style of labels, or add notes to any object. For a lot of properties, editing them in the property panel is the only way to change them. Not all object types have the same set properties, for example, only Gene products have the "Gene ID" property.
To edit a certain property, double-click on the entry in the table of properties to make the field editable, then enter the desired value.
It is possible to select multiple objects at once, and edit one property for all of them.
Changing general pathway information
To access the general pathway properties, click on the info box that is always present in the top-left of every pathway. When the info box is selected, you can edit pathway properties in the property pane on the right. You can set the following properties:
- Pathway Name
- Author, you could fill out more than one author here if you like
- Email, email address of the contact person for this pathway (usually the maintainer)
- Maintainer, full name of the maintainer of this pathway
- Data-Source, source where this pathway is derived from such as another pathway database. May be left empty if there is no suitable data source.
- Organism, the organism that this pathway is designed for.
- Availability, this should describe the terms of usage for this pathway. We encourage the use of Creative Commons licenses for pathway data.
Importing and exporting to / from GenMAPP
You can import/export your pathway from and to the GenMAPP format (.mapp).
- To import a GenMAPP pathway, go to File > Import and select the GenMAPP file you want to import. The pathway will now be loaded in PathVisio where you can edit it and save it to the GPML format, or export it back to a GenMAPP file.
- To export your PathVisio pathway to a pathway file that can be read by GenMAPP, go to File > Export. Specify the GenMAPP file you want to save the pathway to.
NOTE: Importing / exporting GenMAPP format is only available on the Microsoft Windows operating system.
Browsing Pathways
Searching pathways for genes
PathVisio allows you to search for pathways that contain a given gene product. You can search pathways in two ways:
- Gene symbol (gene name)
- Gene identifier (as defined in the synonym database)
Search by gene symbol
This method searches for all pathways containing one or more gene products for which the gene symbol contains the specified search text. To find only gene products where the symbol exactly matches the search text, add "\b" before and after the text (e.g. "\bTP53\b" to search for exact matches of "TP53"). To start the search, go to the Pathway search tab in the side panel:
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You can choose to search by gene symbol or gene id using the drop-down list (red arrow). This screen shot shows how to search by gene symbol:
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Search by gene identifier
This method searches for all pathways containing one or more gene products that correspond to the given identifier. Gene products that are linked via cross references in the synonym database are also included. To start the search, go to the Search tab in the side panel:
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You can choose to search by gene identifier using the drop-down list (red arrow). This screen shot shows how to search by gene identifier:
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Browsing search results
The search results will be displayed in the side panel. For example, results of a gene symbol search for "TNF" in all human pathways will look like this:
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The results table (yellow box) shows the pathway that have one or more gene-products with a symbol that contains "TNF". If you double-click on a pathway in the table, PathVisio will open this pathway and highlight the gene products that were found (here the gene products are highlighted with a green box). You can disable this highlighting by unchecking highlight found genes (red arrow). |
Retrieving Databases and Pathways
Downloading and Installing pathways
In the download section on the Main Page you can find a link to zip files containing available pathways converted from GenMAPP. After you download one or more of these zip files, unpack them to the PathVisio\pathways folder in your user directory (e.g C:\Documents and Settings\Username\Pathvisio\pathways on windows XP). This is the default folder where Pathvisio looks for pathway files.
Downloading and Installing synonym databases
Gene Databases provide PathVisio with cross references between gene identifiers in pathways and other database identifiers. Databases are downloaded and installed locally for use with PathVisio. In step 3 in the download section you can find a link to these databases. Download and unzip databases to the Pathvisio\gene databases directory in your user directory on your computer. Be warned: gene databases can take up a lot of disc space. For the human gene database you need at least 400 Mb of free disk space.
Available synonym databases
Our synonym databases contain the latest information from Ensembl. A synonym database for any species that is in Ensembl can be generated. You can get the available synonym databases from the download page. If you would like to have a PathVisio synonym database for another species that is present in Ensembl, please contact us.
Supported database systems
Each supported public database supported in PathVisio synonym databases has a specific system code that is used to identify which system a particular identifier belongs to in PathVisio. The following list displays the proper system codes for PathVisio:
system codes for genes and proteins:
system codes for metabolites:
| Ca | Chemical Abstracts (CAS) |
| Ce | ChEBI |
| Ch | HMDB |
| Cp | PubChem |
| Cs | Chemspider |
*** = Organism name is also required as a variable in url for linkout
Other Features
Setting Preferences
Several preferences can be set in PathVisio to customize the appearance and usage of the program. The Preferences menu can be accessed from the View menu. Options in the Preferences menu are:
Display
- The initial size of the right side panel when PathVisio is first opened can be set. The default value for this is 30.
- Gene product rectangles (data nodes) can be displayed with rounded or squared edges. The default is squred edge display.
- Movement of lines on the drawing board can be either be free or lines can be set to "snap-to-angles" to facilitate drawing. The default is free movement. The degree of angles for "snap-to-angle" is user-defined as well, the default is 15.
- Support for MIMs (Molecular Interaction Maps) can be loaded automatically when PathVisio starts. MIMs support is not loaded by default.
- Advanced object attributes, such as references, can be displayed. Advanced attributes are hidden by default.
- Coloring preferences for managing the coloring of highlighted and selected objects, as well as options for coloring related to displaying data.
- Default color for "no criteria met"
- Default color for "gene not found"
- Default color for "no data found"
- Outline color for selected objects
- Outline color for highlighted objects
NOTE: You need additional plug-ins for displaying data on pathways with PathVisio 1.1
Directories
Preferences for file locations determine in which directories PathVisio will look for files by default. The following file locations can be set:
- gpml pathways
- Gene databases
- Expression Datasets
NOTE: You need additional plug-ins to display data on pathways in PathVisio 1.1
Files
The location of where the PathVisio log file will be stored can be set as a preference.
Database
The type of database connector for gene databases and expression datasets can be stored as a preference.
NOTE: PathVisio 1.1 requires additional plug-ins to support display of microarray data on pathways.
Keyboard shortcuts
Ctrl + N: Create a new pathway
Ctrl + O: Open a pathway
Ctrl + S: Save pathway
Ctrl + C: Copy
Ctrl + V: Paste
Ctrl + left mouse click: Add or remove object from selection
Ctrl + A: Select all gene products on the pathway
Ctrl + G: Create a group of selected objects
Ctrl + Z: Undo
Using Molecular Interaction Map styles
PathVisio has limited support for Molecular Interaction Map styles (aka Kohn Maps). See the following link for a legend of MIM symbols: [1]
