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Pathways with PathWhiz.

Pon A, Jewison T, Su Y, Liang Y, Knox C, Maciejewski A, Wilson M, Wishart DS - Nucleic Acids Res. (2015)

Bottom Line: PathWhiz's pathway replication and propagation functions allow for existing pathways to be used to create new pathways or for existing pathways to be automatically propagated across species.PathWhiz pathways can be saved in BioPAX, SBGN-ML and SBML data exchange formats, as well as PNG, PWML, HTML image map or SVG images that can be viewed offline or explored using PathWhiz's interactive viewer.PathWhiz has been used to generate over 700 pathway diagrams for a number of popular databases including HMDB, DrugBank and SMPDB.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.

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Related in: MedlinePlus

Examples of the different types of pathway diagrams that PathWhiz can produce: (a) a detailed small-molecule pathway (Irinotecan Metabolism in Homo sapiens), (b) a simplified pathway (Folate Metabolism in Mus musculus), (c) a disease pathway (Sepiapterin Reductase Deficiency in Homo sapiens) and (d) a protein–protein signalling pathway (intracellular signalling through adenosine receptor A2a and adenosine in Homo sapiens).
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Figure 2: Examples of the different types of pathway diagrams that PathWhiz can produce: (a) a detailed small-molecule pathway (Irinotecan Metabolism in Homo sapiens), (b) a simplified pathway (Folate Metabolism in Mus musculus), (c) a disease pathway (Sepiapterin Reductase Deficiency in Homo sapiens) and (d) a protein–protein signalling pathway (intracellular signalling through adenosine receptor A2a and adenosine in Homo sapiens).

Mentions: The PathWhiz drawing system also contains a membrane tool that allows the free-form rendering of simple or complex membranes colour-coded to indicate different membrane types. Pathways can be further augmented with the drawing system's library of stock images, which correspond to other kinds of biological elements such as organs, cell organelles, or biological ‘states’ such as mutated proteins. There are also non-biological visualization components that can be utilized to aid pathway depiction, including customizable labels, lines, and zoom boxes. In effect, the large variety of visualization options available in the drawing system's library allows the generation of pathway representations from very simple, black and white wire depictions to very detailed, colourful and image-rich diagrams (Figure 2). Quick start and detailed user manuals for the PathWhiz Editor are available online (http://smpdb.ca/pathwhiz/guides). Once a pathway diagram is completed it can be exported to various graphical and data exchange formats, as well as viewed in the interactive Pathway Viewer, which is described later.


Pathways with PathWhiz.

Pon A, Jewison T, Su Y, Liang Y, Knox C, Maciejewski A, Wilson M, Wishart DS - Nucleic Acids Res. (2015)

Examples of the different types of pathway diagrams that PathWhiz can produce: (a) a detailed small-molecule pathway (Irinotecan Metabolism in Homo sapiens), (b) a simplified pathway (Folate Metabolism in Mus musculus), (c) a disease pathway (Sepiapterin Reductase Deficiency in Homo sapiens) and (d) a protein–protein signalling pathway (intracellular signalling through adenosine receptor A2a and adenosine in Homo sapiens).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489271&req=5

Figure 2: Examples of the different types of pathway diagrams that PathWhiz can produce: (a) a detailed small-molecule pathway (Irinotecan Metabolism in Homo sapiens), (b) a simplified pathway (Folate Metabolism in Mus musculus), (c) a disease pathway (Sepiapterin Reductase Deficiency in Homo sapiens) and (d) a protein–protein signalling pathway (intracellular signalling through adenosine receptor A2a and adenosine in Homo sapiens).
Mentions: The PathWhiz drawing system also contains a membrane tool that allows the free-form rendering of simple or complex membranes colour-coded to indicate different membrane types. Pathways can be further augmented with the drawing system's library of stock images, which correspond to other kinds of biological elements such as organs, cell organelles, or biological ‘states’ such as mutated proteins. There are also non-biological visualization components that can be utilized to aid pathway depiction, including customizable labels, lines, and zoom boxes. In effect, the large variety of visualization options available in the drawing system's library allows the generation of pathway representations from very simple, black and white wire depictions to very detailed, colourful and image-rich diagrams (Figure 2). Quick start and detailed user manuals for the PathWhiz Editor are available online (http://smpdb.ca/pathwhiz/guides). Once a pathway diagram is completed it can be exported to various graphical and data exchange formats, as well as viewed in the interactive Pathway Viewer, which is described later.

Bottom Line: PathWhiz's pathway replication and propagation functions allow for existing pathways to be used to create new pathways or for existing pathways to be automatically propagated across species.PathWhiz pathways can be saved in BioPAX, SBGN-ML and SBML data exchange formats, as well as PNG, PWML, HTML image map or SVG images that can be viewed offline or explored using PathWhiz's interactive viewer.PathWhiz has been used to generate over 700 pathway diagrams for a number of popular databases including HMDB, DrugBank and SMPDB.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada.

Show MeSH
Related in: MedlinePlus