A Web Tool for Generating High Quality Machine-readable Biological Pathways

PathWhiz is a comprehensive, online pathway drawing tool for generating biochemical and biological pathways. It uses publicly accessible databases and easily expandable palettes consisting of pre-drawn pathway components. This protocol describes how to easily build new pathways, replicate and edit existing pathways, and propagate previously drawn pathways to different organisms.

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The overall goal of this protocol is to use PathWhiz and the internet to easily create, replicate and propagate biochemical pathways for a variety of purposes and applications. This tool allows scientists, educators and students to create visually pleasing and accurate biochemical pathways with a high level of biological detail and complexity. PathWhiz is a free public gallery with thousands of pathways and pathway components, which is compatible with essentially any operating system and can be accessed and expanded upon by all users.

Begin by loading the PathWhiz page in any modern web browser and clicking on the Draw menu. Click the New Pathway button to start a new pathway and enter the name of the pathway to be drawn. Choose the type of pathway from the dropdown list.

Then enter the scientific name of the organism into the auto complete box to search for the organism of interest, followed by the scientific name of the species and the common name. Select the species classification from the dropdown list as Eucaryote or Procaryote and enter the taxonomy ID from the NCBI taxonomy. Click Create Species and enter a comprehensive description for the pathway.

Clicking Add Reference to add external references to the pathway as appropriate. Next, click Create Pathway. A white gridded canvas will appear with a gray menu bar.

Click the Add Process link and select Add Reaction to add the first process visualization. Enter the reactants, products or enzymes of interest in the auto complete box to search the existing reactions. Then scroll through the existing reactions.

When the desired reaction is found, select it. Followed by entrance of the corresponding element name in the auto complete box to select the appropriate stoichiometry and element type. After all of the elements on the left side of the reaction have been added, select the direction of the pathway from the dropdown list and click Add Right Element to add a product.

Select the stoichiometry and element type, as just demonstrated, for all the elements on the right side of the reaction. Then click Add Enzyme to add an enzyme to the reaction. Type the name of the enzyme into the auto complete box and select the appropriate enzyme.

When all of the elements of the reaction have been added, click the Create Reaction button to save the new reaction and select the orientation desired for the initial rendering of the reaction from the dropdown lists. Then click the Create Reaction button again. The newly created reaction will be displayed on the drawing canvas.

To edit the reaction as appropriate, drag the reaction elements on the canvas to reposition them as desired. Then single-click each element to add them to the current selection. When all of the elements have been selected, drag them to the appropriate area of the canvas and click on the elements again to deselect them.

To access a pop-up editing sidebar, double click a chemical and edit the template, biological state, Z-index and complete reaction details of the reaction as appropriate. To edit the information for an entire process, double click any of its elements. Under the gray secondary menu bar, click the Edit Selected link and select Edit Element or Edit Process as appropriate.

Reposition the elements on the canvas to the desired positions. Select the reaction edges of interest and edit them as just demonstrated for the reaction compounds and proteins. Once the first reaction has been drawn as desired, click a product of the reaction to select it.

Then, under the Add Process tab, select Add Reaction. When the pathway is complete, click the Pathway link and select Export and View. Select the Background Color for Images option to choose either blue or white as the background color for the image and select yes or no for the Also Generate Simplified Version option.

Then click Generate Image Files. When the image as been generated, click Show in Viewer to generate a fully hyperlinked, high resolution pathway image in the browser. To duplicate an existing pathway, click the Pathways menu and enter the name of the pathway of interest in the search bar.

Locate the pathway to be replicated and click Replicate. Edit the name of the pathway and enter a new description of the pathway as appropriate. Then click Create Pathway to generate the duplicate pathway.

To view or Download a pathway, enter the Pathways menu, locate the pathway of interest as just demonstrated and click Show. Next, click on the button with the desired PathWhiz ID next to the Show in Viewer label and open the Downloads tab. Then click the hyperlinks to download the pathway in various file formats.

PathWhiz can be used to generate pathways with various content types and styles. Including traditional metabolic pathways, disease and drug pathways to illustrate side effects and drug responses, as well as protein signaling pathways. The pathways may be richly colored with considerable biological detail or they may be converted to simple black and white representations.

Once completed, these pathways may viewed in the interactive pathway viewer, downloaded as images or exported in several different machine readable data exchange formats for further analysis. Once mastered, it is possible to generate a standard internet ready pathway in about 15 minutes. Although, more complex pathways could take longer to complete.

While attempting this procedure, it's important to remember that the species chosen for each individual reaction always matches the pathway species and to confirm that the direction of the reaction arrows is correct. Following this procedure, other methods such as metabolic analysis, can be performed to answer additional questions about the dynamics or quantification of metabolites of interest. After its development, this technique paved the way for researchers in the field of metabolomics and biology to create thousands of internet ready pathways, illustrating a wide range of human, east and E.Coli biochemistries.

After watching this video, you should have a good understanding of how to build new pathways, replicate and edit existing pathways, as well as propagate previously drawn pathways to different organisms. Don't forget that locking a pathway renders it uneditable. Also, be aware that you can choose to create either public or private pathways, depending on your preference.

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Journal (Biology)

Journal (Biology)

A Web Tool for Generating High Quality Machine-readable Biological Pathways

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