Permalink
Browse files

update text to include plasmid comparison UML

  • Loading branch information...
graik committed Dec 3, 2017
1 parent fde5c25 commit 7686fd7ec93e3b4f117b2fa729992d12dffcb48c
Showing with 12 additions and 4 deletions.
  1. +12 −4 sep_020.md
View
@@ -61,6 +61,7 @@ Table of Contents
* Allow to attach experimental results to clones/batches
This proposal is mostly identical and complementary to SEP 19 but differs in the following aspects (see also [Discussion](#differences)):
* Reduce complexity compared to SEP 19 -- the single `design` field proposed here will, in the most common scenarios, replace a complex prov-O construction that entails the rather staggering number of: 6 prov-O fields, two prov-O classes, and one newly minted sbol term;
* Allow tools to parse and generate `Implementation` records without having to deal with detailed workflow information or the prov-O ontology
* Workflow & provenance information form an *additional layer* of meta information rather than being required
* Ensure that the link from Experimental data through clone/batch to (intended) design is as direct and unambiguous as possible and does not require iterations over chains of events / activities (with the associated risk of missing links)
@@ -159,15 +160,22 @@ SEP 19 prescribes a host of additional validation rules related to prov-O usage.
The first example covers the, presumably, most common use case of transmitting information about one particular plasmid which may be shipped between labs or obtained from the iGEM registry or AddGene:
![Batch of plasmid DNA](images/sep_020_plasmid.png "Representation of one particular batch of plasmid DNA")
![Batch of plasmid DNA](images/sep_020_plasmid.png "Representation of one particular batch of plasmid DNA.")
**Example 1a:** This example covers the, presumably, most common use case of transmitting information about one particular plasmid which may be shipped between labs or obtained from the iGEM registry or AddGene.
**Example 1a:** This example covers the, presumably, most common use case of transmitting information about one particular plasmid which may be shipped between labs or obtained from the iGEM registry or AddGene. Two scenarios are shown. Above the, by far, most common use case where the plasmid corresponds exactly to the given design. Below, a scenario as it may, for example, happen in intermediate stages of assembly processes, where a plasmid is tracked and found to not exactly correspond to its design.
The same plasmid may be transformed into an E. coli expression strain for protein production. A cell stock of the single colony picked for the expression culture will be kept for future reference. Let's assume we later discover that there was a genomic mutation in this particular clone:
It is instructive to compare the above example to exactly the same information expressed according to SEP 19. Most UML diagrams in SEP 19 are highly simplified. So here is the same example with everything spelled out according to SEP 19 and the current prov-O documentation:
![SEP 19 plasmid DNA](images/sep_019_plasmid.png "Representation of one particular batch of plasmid DNA **according to SEP 19**.")
**SEP 19 Example**: The exact same data as in Example 1a shown in the notation suggested by SEP 19. Note that the same information expressed by a single `design` field in SEP 20, requires, in SEP 19, 6 prov-O fields, 2 prov-O class instances, and one novel sbol:"design" term.
Returning to SEP 20, the above (correct) plasmid may be transformed into an E. coli expression strain for protein production. A cell stock of the single colony picked for the expression culture will be kept for future reference. Let's again assume something went wrong and we later discover that there was a genomic mutation in this particular clone. In other words, the cell stock faithfully implements the core of the design (the expression plasmid) but its genome deviates from the original design (and from its sister clones). It may still be used in subsequent experiments and the deviation is documented using the `built` link:
![Bacterial clone](images/sep_020_plasmid_in_cell.png "Representation of a bacterial clone containing an engineered plasmid")
**Example 1b:** A clone of a bacterial strain harboring the same expression plasmid.
**Example 1b:** A clone of a bacterial strain harboring the same expression plasmid but with a novel genomic mutation.
Note: SBOL currently has no clear rule for the identification of organisms. Presumably, a plasmid within a cell will be represented by a `ComponentDefinition` for the plasmid, contained within a `ModuleDefinition` somehow representing the cell. The given scheme is thus merely a suggestion.

0 comments on commit 7686fd7

Please sign in to comment.