Body: <p>For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (<a href="http://sideeffects.embl.de/download/" rel="nofollow noreferrer">http://sideeffects.embl.de/download/</a>). If you open the README file, the first description you'll see is:</p>
  <blockquote>
  <p>meddra_all_se.tsv.gz<br />
  1 &amp; 2: STITCH compound ids (flat/stereo, see above)<br />
  3: UMLS concept id as it was found on the label<br />
  4: MedDRA concept type (LLT = lowest level term, PT = preferred term; in a few cases the term is &gt;neither LLT nor PT)<br />
  5: UMLS concept id for MedDRA term<br />
  6: side effect name</p>
  </blockquote>
  <p>I can not really understand what is the difference between flat and stereo compound ID; is it a chemical descriptor? Is it a notation issue? Moreover, I thought that the two IDS for the same compound could yield to similar results on PubChem but they don't. For example, in the dataset the STITCH ids for the first compound are CID100000085 and CID000010917; on PubChem the first is an aromatic compound and the second is not, they are widely different.<br />
  Thanks to everyone who will take the time to help me.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T10:32:41.860Z
Comments.Text: Hey, welcome to Bioinformatics. I see you [asked](https://stackoverflow.com/questions/71156020/what-is-the-difference-between-flat-and-stereo-stitch-compound-ids-sider-datas) the same question on another SO! Please try to avoid posting the question on multiple communities.
Comments.UserDisplayName: user324810
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-18T10:36:51.817Z
Comments.Text: As for your questions, I may be wrong but I think those terms refer to the chemistry 3D representation in space. I think `Stereo` should stand for `Stereoisomers`. You can read more about it [here](http://iverson.cm.utexas.edu/courses/310M/Handouts/Handoutsfl05/stereohand.html). As for `flat`, it is how you would represent a compound on a 2D space.
  The same compound arranged differently in 3D space can be different molecules and thus yield different results.
Comments.UserDisplayName: user324810
Tags: <database><public-databases><computational-biochemistry>
Title: What is the difference between flat and stereo stitch id?
ThreadText: # What is the difference between flat and stereo stitch id?
  
  (Asked by: username_0 on 2022-02-17)
  
  For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (<http://sideeffects.embl.de/download/>). If you open the README file, the first description you'll see is:
  
  > meddra\_all\_se.tsv.gz  
  > 1 & 2: STITCH compound ids (flat/stereo, see above)  
  > 3: UMLS concept id as it was found on the label  
  > 4: MedDRA concept type (LLT = lowest level term, PT = preferred term; in a few cases the term is >neither LLT nor PT)  
  > 5: UMLS concept id for MedDRA term  
  > 6: side effect name
  
  I can not really understand what is the difference between flat and stereo compound ID; is it a chemical descriptor? Is it a notation issue? Moreover, I thought that the two IDS for the same compound could yield to similar results on PubChem but they don't. For example, in the dataset the STITCH ids for the first compound are CID100000085 and CID000010917; on PubChem the first is an aromatic compound and the second is not, they are widely different.  
  Thanks to everyone who will take the time to help me.
  
  **Tags:** database, public-databases, computational-biochemistry
  
  > **Comments:**
  > **username_1**: Hey, welcome to Bioinformatics. I see you [asked](https://stackoverflow.com/questions/71156020/what-is-the-difference-between-flat-and-stereo-stitch-compound-ids-sider-datas) the same question on another SO! Please try to avoid posting the question on multiple communities.  
  > **username_1**: As for your questions, I may be wrong but I think those terms refer to the chemistry 3D representation in space. I think `Stereo` should stand for `Stereoisomers`. You can read more about it [here](http://iverson.cm.utexas.edu/courses/310M/Handouts/Handoutsfl05/stereohand.html). As for `flat`, it is how you would represent a compound on a 2D space. The same compound arranged differently in 3D space can be different molecules and thus yield different results.  
  
  ---
  
  ## 0 answers
  
  