Body: <p>I'm currently doing an internship with my professor and we were using a few Protein-Protein Interaction Networks (PPIN) on a community detection algorithm MONET. The PPINs we used were unweighted, but we are curious how our results would change by adding weighted interactions between our proteins. I tried using the <a href="https://pubmed.ncbi.nlm.nih.gov/22649056/" rel="nofollow noreferrer">IntScore</a> website (<a href="http://intscore.molgen.mpg.de" rel="nofollow noreferrer">http://intscore.molgen.mpg.de</a>) but unfortunately that's down. I also tried using some tools from the <a href="https://cbdm-01.zdv.uni-mainz.de/%7Emschaefer/hippie/" rel="nofollow noreferrer">HIPPIE</a> website, but the PPIN I am using has over 300,000 interactions which it can't process, even when using the API documentation.</p>
  <p>Can anyone recommend any tools that I can use to get the edge weights for my interactions? I'll link an example of what I want my PPIN to look like. Thank you very much!</p>
  <p>I am working with human data, specifically I am using NCBI gene entrez ID's as my main format for the algorithm I am using. We wanted the weights to represent the first one you mention, ie 'he reliability of the interaction prediction based on the experimental method used to predict it'. if experimental evidence isnt available for a given interaction, we would not mind an interaction score / confidence score given from text mining. If there is such a tool I can use, please let me know.</p>
  <p>The first few lines are:</p>
  <pre><code>1785    26060   0.958126
  1785    5747    0.999472
  1994    2624    0.876802
  988 1459    0.976516
  7530    64837   0.0153325
  5885    5901    0.997154
  9318    122769  0.0171704
  3091    7975    0.946822
  3014    5351    0.464768
  2099    10574   0.683967
  </code></pre>
  <p>Link to full network example: <a href="https://jumpshare.com/s/PScmwTMPTQTlDJGxf8fy" rel="nofollow noreferrer">https://jumpshare.com/s/PScmwTMPTQTlDJGxf8fy</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-09T09:02:08.213Z
Comments.Text: I don't know of any NCBI numerical ID system for proteins. Could those be NCBI _gene_ IDs? I tried a couple and they seem to resolve to human genes, are you working with human data?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-09T09:04:20.327Z
Comments.Text: Also, where would the weights come from? What do you want the weights to represent? Would it be the reliability of the interaction prediction based on the experimental method used to predict it? Would it be the likelihood of interaction? Or maybe the frequency of interaction? You can use weights for very many things, what do you want yours to be?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-13T15:07:52.103Z
Comments.Text: Hey Terdon, thanks for responding. So i am working with human data, specifically I am using NCBI gene entrez ID's as my main format for the algorithm I am using. We wanted the weights to represent the first one you mention, ie 'he reliability of the interaction prediction based on the experimental method used to predict it'. if experimental evidence isnt available for a given interaction, we would not mind an interaction score / confidence score given from text mining. If there is such a tool I can use, please let me know. Thank you so much!
Comments.UserDisplayName: Ruhan Gandhi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-13T15:30:47.993Z
Comments.Text: Please add this to your question so everyone can see it. I haven't worked on this kind of thing for more than a decade, but when I did, I made a list of the methods I found acceptable (I needed direct evidence of interaction) and used that. You need to know where each of the interactions you have came from and how they were derived. I expect you will need to build a new network.
Comments.UserDisplayName: terdon
Tags: <protein-protein-interaction>
Title: Tools for Protein-Protein interaction prediction?
ThreadText: # Tools for Protein-Protein interaction prediction?
  
  (Asked by: username_0 on 2024-07-08)
  
  I'm currently doing an internship with my professor and we were using a few Protein-Protein Interaction Networks (PPIN) on a community detection algorithm MONET. The PPINs we used were unweighted, but we are curious how our results would change by adding weighted interactions between our proteins. I tried using the [IntScore](https://pubmed.ncbi.nlm.nih.gov/22649056/) website (<http://intscore.molgen.mpg.de>) but unfortunately that's down. I also tried using some tools from the [HIPPIE](https://cbdm-01.zdv.uni-mainz.de/%7Emschaefer/hippie/) website, but the PPIN I am using has over 300,000 interactions which it can't process, even when using the API documentation.
  
  Can anyone recommend any tools that I can use to get the edge weights for my interactions? I'll link an example of what I want my PPIN to look like. Thank you very much!
  
  I am working with human data, specifically I am using NCBI gene entrez ID's as my main format for the algorithm I am using. We wanted the weights to represent the first one you mention, ie 'he reliability of the interaction prediction based on the experimental method used to predict it'. if experimental evidence isnt available for a given interaction, we would not mind an interaction score / confidence score given from text mining. If there is such a tool I can use, please let me know.
  
  The first few lines are:
  
  ```
  1785    26060   0.958126
  1785    5747    0.999472
  1994    2624    0.876802
  988 1459    0.976516
  7530    64837   0.0153325
  5885    5901    0.997154
  9318    122769  0.0171704
  3091    7975    0.946822
  3014    5351    0.464768
  2099    10574   0.683967
  
  ```
  
  Link to full network example: <https://jumpshare.com/s/PScmwTMPTQTlDJGxf8fy>
  
  **Tags:** protein-protein-interaction
  
  > **Comments:**
  > **username_1**: I don't know of any NCBI numerical ID system for proteins. Could those be NCBI _gene_ IDs? I tried a couple and they seem to resolve to human genes, are you working with human data?  
  > **username_1**: Also, where would the weights come from? What do you want the weights to represent? Would it be the reliability of the interaction prediction based on the experimental method used to predict it? Would it be the likelihood of interaction? Or maybe the frequency of interaction? You can use weights for very many things, what do you want yours to be?  
  > **username_0**: Hey username_1, thanks for responding. So i am working with human data, specifically I am using NCBI gene entrez ID's as my main format for the algorithm I am using. We wanted the weights to represent the first one you mention, ie 'he reliability of the interaction prediction based on the experimental method used to predict it'. if experimental evidence isnt available for a given interaction, we would not mind an interaction score / confidence score given from text mining. If there is such a tool I can use, please let me know. Thank you so much!  
  > **username_1**: Please add this to your question so everyone can see it. I haven't worked on this kind of thing for more than a decade, but when I did, I made a list of the methods I found acceptable (I needed direct evidence of interaction) and used that. You need to know where each of the interactions you have came from and how they were derived. I expect you will need to build a new network.  
  
  ---
  
  ## 0 answers
  
  