Answers.Body: <p>Some information seems to be available on the module level utilising the API. </p>
  
  <p>Reaction <a href="http://www.genome.jp/dbget-bin/www_bget?rn:R00352" rel="nofollow noreferrer">R00352</a> points to the module <a href="https://www.genome.jp/kegg-bin/show_module?M00173" rel="nofollow noreferrer">M00173</a>. While some information is in the <code>Definition</code>, it's not trivial to link it to the particular reaction. This linkage is however easier accessible via <a href="http://rest.kegg.jp/get/md:M00173" rel="nofollow noreferrer">API</a>: </p>
  
  <p><a href="https://i.sstatic.net/orSvB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/orSvB.png" alt="Reaction orthology defined on module level"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-25T21:56:13.680Z
Answers.Text: Thanks. There are two issues with this as far as I can see: i) the third KO (K01648) is missing in the list and ii) it is not clear which logical relationship exists between these KOs; it seems it is always an AND but it is not entirely clear (e.g. from the link you provide: `K00239,K00240,K00241,K00242,K00244,K00245,K00246,K00247` - do I need all of these or not?.
Answers.UserDisplayName: Cleb
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-25T23:17:40.413Z
Answers.Text: This table seems to point where the indicated members should all be required as one. In a couple of cases I looked it is indeed the case. Hence ad i) K01648 is separate so should not be noted ad ii) a very detailed decomposition to subunits, but yes.
Answers.UserDisplayName: ellimilial
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-25T21:34:11.070Z
Answers.LastActivityDate: 2019-05-26T07:07:10.983Z
Answers.LastEditDate: 2019-05-26T07:07:10.983Z
Answers.UserDisplayName: ellimilial
Body: <p>The completeness of a module can easily be checked by looking at the <code>Definition</code> entry associated with the module. For example, in module <a href="http://www.genome.jp/kegg-bin/show_module?M00010" rel="nofollow noreferrer">M00010</a>, it is given as:</p>
  
  <pre><code>Definition  K01647 (K01681,K01682) (K00031,K00030)
  </code></pre>
  
  <p>which can be translated to:</p>
  
  <pre><code>K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)
  </code></pre>
  
  <p>If this expression evaluates to <code>TRUE</code>, the module is considered complete.</p>
  
  <p>I am wondering whether analogous information exists for a single <em>reaction</em>. For example, when looking at reaction <a href="http://www.genome.jp/dbget-bin/www_bget?rn:R00352" rel="nofollow noreferrer">R00352</a>, one finds the following information about its Orthology:</p>
  
  <p><a href="https://i.sstatic.net/9jRBq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/9jRBq.png" alt="enter image description here"></a></p>
  
  <p>But I can't easily find the logical relation that correspond to the KOs for this reaction. It could be:</p>
  
  <pre><code>K01648 AND K15230 AND K15231 
  </code></pre>
  
  <p>or:</p>
  
  <pre><code>K01648 OR K15230 OR K15231
  </code></pre>
  
  <p>or:</p>
  
  <pre><code>K01648 OR (K15230 AND K15231)
  </code></pre>
  
  <p>and so on.</p>
  
  <p>In the above example, I know that the correct expression is:</p>
  
  <pre><code>K01648 OR (K15230 AND K15231)
  </code></pre>
  
  <p>i.e. one either needs either <code>K01648</code> or both of the other two subunits.</p>
  
  <p>Can this information be retrieved from KEGG for each reaction and if so, how?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-21T08:17:16.087Z
Comments.Text: You might need to look into the FTP dump; I looked into the KEGG REST API (http://www.kegg.jp/kegg/rest/keggapi.html) and couldn't find anything related to your question...
Comments.UserDisplayName: mgalardini
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-30T21:17:32.927Z
Comments.Text: Have you tried to asked KEGG directly via http://www.kegg.jp/feedback/ ? If anything, that might give them the information that there's something missing which people need.
Comments.UserDisplayName: BaCh
Tags: <kegg><database><data-retrieval>
Title: How to retrieve logical expressions (KO based) for reactions from KEGG?
ThreadText: # How to retrieve logical expressions (KO based) for reactions from KEGG?
  
  (Asked by: username_0 on 2017-05-20)
  
  The completeness of a module can easily be checked by looking at the `Definition` entry associated with the module. For example, in module [M00010](http://www.genome.jp/kegg-bin/show_module?M00010), it is given as:
  
  ```
  Definition  K01647 (K01681,K01682) (K00031,K00030)
  
  ```
  
  which can be translated to:
  
  ```
  K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)
  
  ```
  
  If this expression evaluates to `TRUE`, the module is considered complete.
  
  I am wondering whether analogous information exists for a single *reaction*. For example, when looking at reaction [R00352](http://www.genome.jp/dbget-bin/www_bget?rn:R00352), one finds the following information about its Orthology:
  
  [![enter image description here](https://i.sstatic.net/9jRBq.png)](https://i.sstatic.net/9jRBq.png)
  
  But I can't easily find the logical relation that correspond to the KOs for this reaction. It could be:
  
  ```
  K01648 AND K15230 AND K15231 
  
  ```
  
  or:
  
  ```
  K01648 OR K15230 OR K15231
  
  ```
  
  or:
  
  ```
  K01648 OR (K15230 AND K15231)
  
  ```
  
  and so on.
  
  In the above example, I know that the correct expression is:
  
  ```
  K01648 OR (K15230 AND K15231)
  
  ```
  
  i.e. one either needs either `K01648` or both of the other two subunits.
  
  Can this information be retrieved from KEGG for each reaction and if so, how?
  
  **Tags:** kegg, database, data-retrieval
  
  > **Comments:**
  > **username_2**: Have you tried to asked KEGG directly via http://www.kegg.jp/feedback/ ? If anything, that might give them the information that there's something missing which people need.  
  > **username_1**: You might need to look into the FTP dump; I looked into the KEGG REST API (http://www.kegg.jp/kegg/rest/keggapi.html) and couldn't find anything related to your question...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-05-25. Score: 1
  
  Some information seems to be available on the module level utilising the API.
  
  Reaction [R00352](http://www.genome.jp/dbget-bin/www_bget?rn:R00352) points to the module [M00173](https://www.genome.jp/kegg-bin/show_module?M00173). While some information is in the `Definition`, it's not trivial to link it to the particular reaction. This linkage is however easier accessible via [API](http://rest.kegg.jp/get/md:M00173):
  
  [![Reaction orthology defined on module level](https://i.sstatic.net/orSvB.png)](https://i.sstatic.net/orSvB.png)
  
  > **Comments:**
  > **username_0**: Thanks. There are two issues with this as far as I can see: i) the third KO (K01648) is missing in the list and ii) it is not clear which logical relationship exists between these KOs; it seems it is always an AND but it is not entirely clear (e.g. from the link you provide: `K00239,K00240,K00241,K00242,K00244,K00245,K00246,K00247` - do I need all of these or not?.  
  > **username_3**: This table seems to point where the indicated members should all be required as one. In a couple of cases I looked it is indeed the case. Hence ad i) K01648 is separate so should not be noted ad ii) a very detailed decomposition to subunits, but yes.  
  
  ---
  
  