<p>Typically you want to use a <code>ComponentDefinition</code> when an sub-structure is something you might want to pull out and re-use in another genetic design, and a <code>SequenceAnnotation</code> whenever it is not.</p>

<p>For example:</p>

<ul>
<li>Promoters, terminators, and protein coding sequences are typically best represented with their own <code>ComponentDefinition</code>, since these are often pulled out and re-combined in new genetic designs.  Representing such an element with a <code>ComponentDefinition</code> makes it easy to find the commonalities between designs.</li>
<li>Assembly scars, binding sites, and cut sites are typically best represented with a <code>SequenceAnnotation</code> because they are typically not very interesting except in the context of their surrounding genetic context. Representing such an element with a <code>SequenceAnnotation</code> helps keep them associated tightly with that context.</li>
</ul>

<p>Not every case is cut and dried, however.  For example, ribosome entry sites are often treated as separable components, but their performance is very tightly tied to the specifics of the coding sequence that they modulate.  Thus, in some cases it may make more sense to represent them separately as a <code>ComponentDefinition</code> and in others to represent them as a <code>SequenceAnnotation</code> on a joint RES/CDS <code>ComponentDefinition</code>.</p>

CC BY-SA 4.0
2021-03-16T21:55:13.623Z
Note that this answer was written for SBOL 2.  For SBOL 3, change `ComponentDefinition` to `Component` and `SequenceAnnotation` to `SequenceFeature`. There are also shortcuts in SBOL 3 for representing things in other databases like UniProt and ChEBI
jakebeal
CC BY-SA 4.0
2019-07-25T00:15:54.680Z
2019-07-29T10:29:45.007Z
2019-07-29T10:29:45.007Z
jakebeal
<p>When representing a DNA sequence in SBOL as a <code>ComponentDefinition</code>, you can mark things like promoters and coding sequences in two different ways:</p>

<ul>
<li>either as a <code>SequenceAnnotation</code> in the <code>ComponentDefinition</code>, or </li>
<li>as a <code>Component</code> linking to a <code>ComponentDefinition</code> for the sub-comoponent</li>
</ul>

<p>When should you choose one over the other?</p>

CC BY-SA 4.0
2019-07-26T13:55:36.453Z
@James McLaughlin. If there is some error on the question and answers about the class I think it would be better if you provide a comment it could be a misunderstanding (unless it has changed and you are updating the question which it would be nice to know in the edit summary)
llrs
CC BY-SA 4.0
2019-07-29T09:09:09.183Z
@jakebeal, there is a pending edit for both [your question](https://bioinformatics.stackexchange.com/review/suggested-edits/2527) and [your answer](https://bioinformatics.stackexchange.com/review/suggested-edits/2526) (you might not have access to those links, if you don't just click on the "edit" under each or the notification in your inbox) changing `SequenceFeature` to  `SequenceAnnotation`. Please confirm which of those is the correct class name.
terdon
CC BY-SA 4.0
2019-07-29T10:30:19.030Z
@terdon Ah, James was right --- I typo'ed the names.  Edit accepted.
jakebeal
<sequence-annotation><sbol>
In SBOL, when should I annotate a DNA sequence vs. making sub-components?
# In SBOL, when should I annotate a DNA sequence vs. making sub-components?

(Asked by: username_0 on 2019-07-24)

When representing a DNA sequence in SBOL as a `ComponentDefinition`, you can mark things like promoters and coding sequences in two different ways:

* either as a `SequenceAnnotation` in the `ComponentDefinition`, or
* as a `Component` linking to a `ComponentDefinition` for the sub-comoponent

When should you choose one over the other?

**Tags:** sequence-annotation, sbol
> **Comments:**
> **username_1**: @James McLaughlin. If there is some error on the question and answers about the class I think it would be better if you provide a comment it could be a misunderstanding (unless it has changed and you are updating the question which it would be nice to know in the edit summary)  
> **username_2**: @jakebeal, there is a pending edit for both [your question](https://bioinformatics.stackexchange.com/review/suggested-edits/2527) and [your answer](https://bioinformatics.stackexchange.com/review/suggested-edits/2526) (you might not have access to those links, if you don't just click on the "edit" under each or the notification in your inbox) changing `SequenceFeature` to  `SequenceAnnotation`. Please confirm which of those is the correct class name.  
> **username_0**: @terdon Ah, James was right --- I typo'ed the names.  Edit accepted.  

---

## 1 answers

### Answer by username_0 on 2019-07-25. Score: 4

Typically you want to use a `ComponentDefinition` when an sub-structure is something you might want to pull out and re-use in another genetic design, and a `SequenceAnnotation` whenever it is not.

For example:

* Promoters, terminators, and protein coding sequences are typically best represented with their own `ComponentDefinition`, since these are often pulled out and re-combined in new genetic designs. Representing such an element with a `ComponentDefinition` makes it easy to find the commonalities between designs.
* Assembly scars, binding sites, and cut sites are typically best represented with a `SequenceAnnotation` because they are typically not very interesting except in the context of their surrounding genetic context. Representing such an element with a `SequenceAnnotation` helps keep them associated tightly with that context.

Not every case is cut and dried, however. For example, ribosome entry sites are often treated as separable components, but their performance is very tightly tied to the specifics of the coding sequence that they modulate. Thus, in some cases it may make more sense to represent them separately as a `ComponentDefinition` and in others to represent them as a `SequenceAnnotation` on a joint RES/CDS `ComponentDefinition`.

> **Comments:**
> **username_0**: Note that this answer was written for SBOL 2.  For SBOL 3, change `ComponentDefinition` to `Component` and `SequenceAnnotation` to `SequenceFeature`. There are also shortcuts in SBOL 3 for representing things in other databases like UniProt and ChEBI  

---

