Answers.Body: <p>Support for distinguishing replicates was added in SBOL 2.2, along with other support for linking data throughout the experiment cycle.  I will explain this in terms of SBOL 3, which is simpler, then give the SBOL 2 translation at the end.</p>
  <p>For SBOL 3, all designs, including those for a plasmid, a strain, etc, are specified in terms of the <code>Component</code> class. This is just a &quot;paper&quot; design, however, and may or may not actually exist. When you have a real physical aliquot that you want to talk about, this is represented by an <code>Implementation</code> object: this is your biological replicate.</p>
  <p>The <code>Implementation</code> doesn't really have any content of its own; its nature is defined by linking back to the intended design with a <code>prov:wasDerivedFrom</code> link. If you've verified that what you got is what you intended, you can supplement that with a <code>built</code> link as well.</p>
  <p>One additional note, however: when you're representing a colony, you're probably not actually representing just a plasmid, but rather are representing a particular strain that has been transformed by a plasmid. The actual data you have may then be one level further removed, since the data has been gathered from a sample under particular growth conditions. SBOL can represent that as well, by describing the sample as a mixture of particular media, inducers, etc., with a transformed strain, which is itself a cell type containing your plasmid.</p>
  <p>Here is an example diagram showing just this sort of relationship, of data associated with three replicates of a sample.</p>
  <p><a href="https://i.sstatic.net/ajATx.png" rel="noreferrer"><img src="https://i.sstatic.net/ajATx.png" alt="SBOL representation of three replicates of a sample" /></a></p>
  <p>You can find this example in <a href="https://github.com/SynBioDex/Community-Media/tree/master/2020/COMBINE20" rel="noreferrer">the SBOL3 tutorial from COMBINE 2020</a>.</p>
  <p>Finally, in SBOL 2, this works exactly the same way, except that instead of a <code>Component</code> your implementation points to a <code>ComponentDefinition</code> or a <code>ModuleDefinition</code>, depending on the nature of the design you're representing. I won't go into that distinction, because it was a bad idea and there's a reason we got rid of it for SBOL 3.</p>
  
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Answers.CreationDate: 2021-03-16T21:17:03.033Z
Answers.Text: Indeed, as @jakebeal says, the "colony" is a strain transformed with a plasmid, and then this `Implementation` can be used in experiments with different media and inducers.
Answers.UserDisplayName: Alejandro Vignoni
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Answers.Text: Exactly, @AlejandroVignoni: you can end up with trees of replicate derivation. I personally value that quite a bit, because the "flat" notion of "biological replicate" vs "technical replicate" often ends up obscuring these relationships.
Answers.UserDisplayName: jakebeal
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Answers.UserDisplayName: jakebeal
Body: <p>I have a library of biological implementations (i.e. plasmids) of genetic circuits and their experimental data associated. I want to implement an <em>in silico</em> version with SBOL, but to be consistent with what I have I'm my freezer, I need to identify not only the genetic circuit but also the biological replicate (i.e. the different colonies picked), as they have their own associated experimental data.</p>
  
Tags: <sbol>
Title: In SBOL, is there a way to distinguish biological replicates?
ThreadText: # In SBOL, is there a way to distinguish biological replicates?
  
  (Asked by: username_0 on 2021-03-16)
  
  I have a library of biological implementations (i.e. plasmids) of genetic circuits and their experimental data associated. I want to implement an *in silico* version with SBOL, but to be consistent with what I have I'm my freezer, I need to identify not only the genetic circuit but also the biological replicate (i.e. the different colonies picked), as they have their own associated experimental data.
  
  **Tags:** sbol
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-03-16. Score: 6 | Accepted answer
  
  Support for distinguishing replicates was added in SBOL 2.2, along with other support for linking data throughout the experiment cycle. I will explain this in terms of SBOL 3, which is simpler, then give the SBOL 2 translation at the end.
  
  For SBOL 3, all designs, including those for a plasmid, a strain, etc, are specified in terms of the `Component` class. This is just a "paper" design, however, and may or may not actually exist. When you have a real physical aliquot that you want to talk about, this is represented by an `Implementation` object: this is your biological replicate.
  
  The `Implementation` doesn't really have any content of its own; its nature is defined by linking back to the intended design with a `prov:wasDerivedFrom` link. If you've verified that what you got is what you intended, you can supplement that with a `built` link as well.
  
  One additional note, however: when you're representing a colony, you're probably not actually representing just a plasmid, but rather are representing a particular strain that has been transformed by a plasmid. The actual data you have may then be one level further removed, since the data has been gathered from a sample under particular growth conditions. SBOL can represent that as well, by describing the sample as a mixture of particular media, inducers, etc., with a transformed strain, which is itself a cell type containing your plasmid.
  
  Here is an example diagram showing just this sort of relationship, of data associated with three replicates of a sample.
  
  [![SBOL representation of three replicates of a sample](https://i.sstatic.net/ajATx.png)](https://i.sstatic.net/ajATx.png)
  
  You can find this example in [the SBOL3 tutorial from COMBINE 2020](https://github.com/SynBioDex/Community-Media/tree/master/2020/COMBINE20).
  
  Finally, in SBOL 2, this works exactly the same way, except that instead of a `Component` your implementation points to a `ComponentDefinition` or a `ModuleDefinition`, depending on the nature of the design you're representing. I won't go into that distinction, because it was a bad idea and there's a reason we got rid of it for SBOL 3.
  
  > **Comments:**
  > **username_0**: Indeed, as @username_1 says, the "colony" is a strain transformed with a plasmid, and then this `Implementation` can be used in experiments with different media and inducers.  
  > **username_1**: Exactly, @username_0: you can end up with trees of replicate derivation. I personally value that quite a bit, because the "flat" notion of "biological replicate" vs "technical replicate" often ends up obscuring these relationships.  
  
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