Answers.Body: <p>Pathways are generally directed graphs, which can be implemented in python using the <code>networkx</code> package. Note that there will be cycles in graphs.</p>
  
  <p>Please note that there are large numbers of pathways analysis packages that already exist (both python and R packages but also just webservers), so I strongly recommend searching to see if something already exists before wasting time and implementing it yourself.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-29T12:18:42.943Z
Answers.Text: Pathways aren’t exactly directed graphs. There are different relationships (inhibition, enhancement,...) how to build a netwrokx’s graph out of it isn’t clear. And that is my main issue, how to build a graph given a KEGG pathway.
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-29T15:16:05.507Z
Answers.Text: Basically my original question is how to transfer a KEGG pathway to a networkx object?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-29T19:17:45.490Z
Answers.Text: Inhibition and enhancement would be weights with different signs. For more complicated interactions standard graph representations simply wouldn't suffice.
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2020-01-29T07:21:52.870Z
Answers.LastActivityDate: 2020-01-29T07:21:52.870Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I would like to construct a mathematical graph: <span class="math-container">$G = (E,V, w(E))$</span> a graph with vertices, edges with weight on them <a href="https://www.biostars.org/p/85763/" rel="nofollow noreferrer">based on a KEGG pathway</a>.  </p>
  
  <p>Is there a way to do that with existing tools? If not I will start to implement a Python module for that. My main question is what is the mathematical graph representation of pathways? Assuming the possible node types and the different connections? </p>
  
  <p>I would like to transform a pathway to a graph because then one can run min-cut-max-flow algorithms and stuff like that as part of my <a href="https://en.wikipedia.org/wiki/Pathway_analysis" rel="nofollow noreferrer">pathway analysis</a>. </p>
  
Tags: <python><pathway><kegg>
Title: How to represent pathways as mathematical graphs?
ThreadText: # How to represent pathways as mathematical graphs?
  
  (Asked by: username_0 on 2020-01-28)
  
  I would like to construct a mathematical graph: $G = (E,V, w(E))$ a graph with vertices, edges with weight on them [based on a KEGG pathway](https://www.biostars.org/p/85763/).
  
  Is there a way to do that with existing tools? If not I will start to implement a Python module for that. My main question is what is the mathematical graph representation of pathways? Assuming the possible node types and the different connections?
  
  I would like to transform a pathway to a graph because then one can run min-cut-max-flow algorithms and stuff like that as part of my [pathway analysis](https://en.wikipedia.org/wiki/Pathway_analysis).
  
  **Tags:** python, pathway, kegg
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-29. Score: 1
  
  Pathways are generally directed graphs, which can be implemented in python using the `networkx` package. Note that there will be cycles in graphs.
  
  Please note that there are large numbers of pathways analysis packages that already exist (both python and R packages but also just webservers), so I strongly recommend searching to see if something already exists before wasting time and implementing it yourself.
  
  > **Comments:**
  > **username_0**: Pathways aren’t exactly directed graphs. There are different relationships (inhibition, enhancement,...) how to build a netwrokx’s graph out of it isn’t clear. And that is my main issue, how to build a graph given a KEGG pathway.  
  > **username_0**: Basically my original question is how to transfer a KEGG pathway to a networkx object?  
  > **username_1**: Inhibition and enhancement would be weights with different signs. For more complicated interactions standard graph representations simply wouldn't suffice.  
  
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