Differences

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--- rules [2024/01/22 07:05] – anguerasempere
+++ rules [2024/05/03 12:38] (current) – [Available Rules] strich
@@ Line 8: / Line 8: @@
-A list of all available rules is provided here. To view all rules of a particular package, select the package first, then the rules within his package (http://evipath.org/package/<id>/rule).
+A list of all available rules in enviPath can be found [[https://envipath.org/rule|here]]. To view all rules of a particular [[package|package]], select the package start page and click on the rules tab.
  ===== Description =====
@@ Line 20: / Line 22: @@
-A rule consists of one (simple rule) or several (composite rule) reaction patterns. Each pattern is represented by a SMIRKS string. enviPath can import or export transformation rules using this format. Additionally, the web interface offers the graphical molecule editor Ketcher, which can create transformation rules that can be stored directly from the editor.
+A rule consists of one (simple rule) or several (composite rule) reaction patterns. Each pattern is represented by a [[https://www.daylight.com/dayhtml/doc/theory/theory.smirks.html|SMIRKS]] string. enviPath can import or export transformation rules using this format. Additionally, the web interface offers the [[https://lifescience.opensource.epam.com/ketcher/|graphical molecule editor Ketcher]], which can create transformation rules that can be stored directly from the editor.
 ===== EC numbers =====
-Here, 4th level EC (Enzyme Commission) numbers (see numerical classification scheme for enzymes recommended by IUBMB) are listed for enzymes known to catalyze reactions that are consistent with the respective rule. Details on how these rule-enzymes linkages were generated are described in Schmid, Fenner, enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining, submitted to Biofinformatics, 2020.
+Here, 4th level EC (Enzyme Commission) numbers (see [[http://en.wikipedia.org/wiki/Enzyme_Commission_number|numerical classification scheme for enzymes]] recommended by [[https://iubmb.org/|IUBMB]]) are listed for enzymes known to catalyze reactions that are consistent with the respective rule. Details on how these rule-enzymes linkages were generated are described in [[https://www.biorxiv.org/content/10.1101/2021.05.20.442588v1|Schmid, Fenner, enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining, submitted to Biofinformatics, 2020]].
 ===== Additional fields =====
-A rule can have additional SMARTS filter that exclude matching products or reactants when applying the rule.
+  * A rule can have additional [[https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html|SMARTS]] filter that exclude matching products or reactants when applying the rule.
-In the core data provided in enviPath, the aerobic rule likelihood is stored as additional information. This information can be used to apply a truncation strategy when predicting a pathway, e.g. to suppress reactions that are unlikely under aerobic conditions.
+  * In the core data provided in enviPath, the aerobic rule likelihood is stored as additional information. This information can be used to apply a [[settings|truncation strategy]] when predicting a [[pathways|pathway]], e.g. to suppress reactions that are unlikely under aerobic conditions.
-Retrieved from "https://wiki.envipath.org/index.php?title=Rules&oldid=576"