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pathways [2024/03/20 09:45] – [Additional Information] shankarpathways [2024/04/23 11:32] (current) – shankar
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 ====== Pathways ====== ====== Pathways ======
  
-Basically a pathway is a set of [[compounds|compounds]] and [[reactions|reactions]].+A pathway is a set of [[compounds|compounds]] and [[reactions|reactions]].
  
 A pathway stores the biodegradation of compounds. A pathway can either be predicted or created manually by adding compounds and reactions. When predicting a pathway enviPath tries to apply a set of [[rules|transformation rules]] to the compound at hand, starting with the root compound, and will add the transformation product(s) to the pathway. If two different rules predict the same compound the pathway will only have one compound but there will be two connections from the educt to the product. Each connection represents a reaction. For every product a compound will be generated and added to package unless it is already present there. Descending from the root compound enviPath recursively transforms its products until no further transformation is possible or the pathway prediction reaches one of the limits defined in the [[settings|settings]]. A pathway stores the biodegradation of compounds. A pathway can either be predicted or created manually by adding compounds and reactions. When predicting a pathway enviPath tries to apply a set of [[rules|transformation rules]] to the compound at hand, starting with the root compound, and will add the transformation product(s) to the pathway. If two different rules predict the same compound the pathway will only have one compound but there will be two connections from the educt to the product. Each connection represents a reaction. For every product a compound will be generated and added to package unless it is already present there. Descending from the root compound enviPath recursively transforms its products until no further transformation is possible or the pathway prediction reaches one of the limits defined in the [[settings|settings]].
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 +{{ :screenshot_2024-04-22_at_14.03.01.png?nolink |}}      
  ====== Create new pathway from scratch ======  ====== Create new pathway from scratch ======
    
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 There are three locations where a user can trigger the creation of a pathway. There are three locations where a user can trigger the creation of a pathway.
  
-1. By entering a smiles or drawing a structure on the [[https://envipath.org|homepage]].+1. By entering a smiles or drawing a structure as an input in the dialog box on the [[https://envipath.org|homepage]] of enviPath.
  
-2. By entering a smiles or drawing a structure on the [[https://envipath.org/pathway|pathway overview]] (package independent).+{{ :h16srng.png?nolink&600 |}}
  
-3. Inside a specific package by clicking on pathway.+2. On the [[https://envipath.org/pathway|Pathway]] page, click on “Actions” then “+ New Pathways”,and then enter a smiles or draw a structure as an input in the dialog box. Pathways created using this method are stored in the [[Packages#Default Package | default package]] of the user.
  
-When using the first option the currently associated [[settings|setting]] of the logged in user will be taken into account.+3. Inside a specific package by clicking on "Pathways" and following the same steps as Option 2.
  
 Options 2. and 3. are very much alike. But in option 2 the package is implicitly set to the default package of the user whereas in option 3 it is set to the selected pathway. Options 2. and 3. are very much alike. But in option 2 the package is implicitly set to the default package of the user whereas in option 3 it is set to the selected pathway.
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 Whether a rule will be applied depends on different aspects: Whether a rule will be applied depends on different aspects:
  
-  * Rule likelihood +  * Rule likelihood: A rule can be tagged with a likelihood by assigning a [[scenarios|scenario]]. The user can adjust the minimum likelihood in a setting and only rules with a likelihood greater or equal will be used.
-      A rule can be tagged with a likelihood by assigning a [[scenarios|scenario]]. The user can adjust the minimum likelihood in a setting and only rules with a likelihood greater or equal will be used.+
  
 The prediction can also be enhanced by[[settings| setting]] up a setting with a [[relative_reasoning|Machine learning based Relative Reasoning]]. The prediction can also be enhanced by[[settings| setting]] up a setting with a [[relative_reasoning|Machine learning based Relative Reasoning]].
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 A pathway can be edited by manually adding compounds or reactions. A pathway can be edited by manually adding compounds or reactions.
  
-====== Adding compounds ======+===== Adding compounds =====
  
  
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 Analogously when typing or drawing a structure the corresponding compound will be created if necessary and added to the pathway. Analogously when typing or drawing a structure the corresponding compound will be created if necessary and added to the pathway.
  
-======  Adding reactions ======+=====  Adding reactions =====
  
  
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 To attach scenarios to a reaction shown in a pathway (an edge), go to //Edit reaction// information on the Pathway page, specify the reaction (or edge) in the pathway, and then select scenarios for it from those available. In contrast, use the Reaction (//Actions->Update// scenario) or Scenario (A//ctions->Attach//) pages to attach scenarios to a reaction object in a more general way and not to a specific edge (reaction step) within a specific pathway. To attach scenarios to a reaction shown in a pathway (an edge), go to //Edit reaction// information on the Pathway page, specify the reaction (or edge) in the pathway, and then select scenarios for it from those available. In contrast, use the Reaction (//Actions->Update// scenario) or Scenario (A//ctions->Attach//) pages to attach scenarios to a reaction object in a more general way and not to a specific edge (reaction step) within a specific pathway.
  
-======  Studies ======+=====  Studies =====
    
  
  
 The user has also the possibility to upload an Excel-sheet. Therefore the [[packages|package]] provides an option called //Import scenarios// located in the //Actions// menu. When uploading an Excel-sheet containing some scenarios a pathway (without reactions) will be created according to the information provided in the Excel-sheet. The user has also the possibility to upload an Excel-sheet. Therefore the [[packages|package]] provides an option called //Import scenarios// located in the //Actions// menu. When uploading an Excel-sheet containing some scenarios a pathway (without reactions) will be created according to the information provided in the Excel-sheet.
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-Retrieved from "https://wiki.envipath.org/index.php?title=Pathways&oldid=580" 
  
pathways.1710927909.txt.gz · Last modified: 2024/03/20 09:45 by shankar