pySBOL2 MapsTo object tutorial by GeneCodeSavvy · Pull Request #46 · SynBioDex/SBOL-Notebooks

GeneCodeSavvy · 2025-06-17T14:25:26Z

Solves #22

jakebeal · 2025-06-19T12:09:46Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "source": [
+    "# MapsTo in pySBOL2\n",
+    "\n",
+    "The `MapsTo` class in the Synthetic Biology Open Language (SBOL) is used to explicitly state that two `ComponentInstance` objects, often from different levels of design hierarchy, represent the same biological entity. It is most often used when `ModuleDefinition` and `ComponentDefinition` objects are composed using `Module` and `ComponentInstance` objects.\n",


Give an intuitive example of what this means - why would you want to do this, biologically?

For example, to design a genetic "toggle switch" ModuleDefinition we can compose two mutually repressing transcriptional units as its Modules. The transcriptional units ModuleDefinition might be one where its promoter is repressed by the cI transcription factor (TF) protein ComponentInstance and its CDS codes for the LacI TF protein ComponentInstance. And the the other where its prmoter is repressed by LacI and its CDS codes for cI.
In this context we would like to know that the proteins expressed by each transcriptional unit is the one repressing the other. To do this we "map" LacI and ci ComponentInstance from one ModuleDefinition to the other.

jakebeal · 2025-06-19T12:10:22Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "-   `remote`: Refers to the `ComponentInstance` in the lower-level design. The referenced instance must have `access=\"public\"`.\n",
+    "-   `refinement`: Specifies how to interpret the relationship between the local and remote instances using a URI. For example: `http://sbols.org/v2#useRemote`.\n",
+    "\n",
+    "This example demonstrates linking a `FunctionalComponent` in a high-level toggle switch module to one in a lower-level LacI inverter using a `MapsTo` object. We will:\n",


Again, we need to explain what this means biologically

We think the example will provide enought link between the biology and its representation.

jakebeal · 2025-06-19T12:10:44Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "id": "cell-004",
+   "metadata": {},
+   "source": [
+    "Creating a MapsTo Object"


Say what we're actually doing, biologically

@GeneCodeSavvy TBI

jakebeal · 2025-06-19T12:10:51Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "source": [
+    "# Create lower-level ModuleDefinition\n",
+    "inverter_md = sbol2.ModuleDefinition('laci_inverter')\n",
+    "tf_fc = inverter_md.functionalComponents.create('TF')\n",


What is TF?

now included in the example

jakebeal · 2025-06-19T12:11:06Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "tf_fc = inverter_md.functionalComponents.create('TF')\n",
+    "tf_fc.definition = tf_fc\n",
+    "tf_fc.access = sbol2.SBOL_ACCESS_PUBLIC\n",
+    "tf_fc.direction = sbol2.SBOL_DIRECTION_IN_OUT\n",


Why is this in/out?

@GeneCodeSavvy TBI give readable and explicit names

jakebeal · 2025-06-19T12:12:05Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "# Create lower-level ModuleDefinition\n",
+    "inverter_md = sbol2.ModuleDefinition('laci_inverter')\n",
+    "tf_fc = inverter_md.functionalComponents.create('TF')\n",
+    "tf_fc.definition = tf_fc\n",


This is incorrect, and it shouldn't be letting us get away with this. This should be pointing at a ComponentDefinition.

jakebeal · 2025-06-19T12:14:02Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "# Create higher-level ModuleDefinition\n",
+    "toggle_md = sbol2.ModuleDefinition('toggle_switch')\n",
+    "laci_fc = toggle_md.functionalComponents.create('LacI')\n",
+    "laci_fc.definition = laci_fc\n",


This is incorrect, and it shouldn't be letting us get away with this. This should be pointing at a ComponentDefinition.

@GeneCodeSavvy create a ComponentDefinition for each object that needs it, then create the functionalComponents pointing to them.

jakebeal · 2025-06-19T12:14:46Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "\n",
+    "# Create higher-level ModuleDefinition\n",
+    "toggle_md = sbol2.ModuleDefinition('toggle_switch')\n",
+    "laci_fc = toggle_md.functionalComponents.create('LacI')\n",


Explain what this is for, biologically: why do we need this here if it is private and not interacting with anything?

@GeneCodeSavvy TBI

jakebeal · 2025-06-19T12:15:06Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "mod = toggle_md.modules.create('laci_inverter_instance')\n",
+    "mod.definition = inverter_md.identity\n",
+    "\n",
+    "# Create the MapsTo\n",


Explain what this means, intuitively.

@GeneCodeSavvy TBI

jakebeal · 2025-06-19T12:16:27Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "outputs": [],
+   "source": [
+    "# Validate the document\n",
+    "report = doc.validate()\n",


Can you do something with the contents of the document to show it's correct and useful besides just validate it?

do you have any idea in how to do it? We can use it as input fora model (like iBioSim)?

I was thinking something like starting with LacI and tracing the Interactions to show that the linkages go around in a circle.

@GeneCodeSavvy please implement this idea so we can review it in the 1o1

GeneCodeSavvy · 2025-06-26T18:31:27Z

I have considered all the comments and added more biological context overall, with the help of @Gonza10V explanation.

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

jakebeal · 2025-06-26T20:25:29Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+    "gene_out = laci_inverter_md.functionalComponents.create('output_gene')\n",
+    "gene_out.definition = cI_cds.identity\n",
+    "gene_out.access = sbol2.SBOL_ACCESS_PUBLIC\n",
+    "gene_out.direction = sbol2.SBOL_DIRECTION_OUT\n",


This ModuleDefinition is incomplete without the Interaction objects that link the Promoter to the TF to the output gene.
As such, you should either add the two Interaction objects (my preference) or should add a comment saying that they have been omitted for simplicity.
Same for the other inverter ModuleDefinition

Okay I will include it.

jakebeal · 2025-06-26T20:37:44Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "source": [
+    "# Map 1: LacI protein is the input to the LacI inverter\n",
+    "map1 = laci_inverter_instance.mapsTos.create('map_laci_in')\n",
+    "map1.refinement = sbol2.SBOL_REFINEMENT_USE_REMOTE\n",


Shouldn't the others have their refinement values set as well?

Sorry, missed this.
Updated.

jakebeal · 2025-06-26T20:40:42Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "outputs": [],
+   "source": [
+    "# Validate the document\n",
+    "report = doc.validate()\n",


I was thinking something like starting with LacI and tracing the Interactions to show that the linkages go around in a circle.

Co-authored-by: Jacob Beal <jakebeal@gmail.com>

Gonza10V · 2025-06-30T15:39:36Z

examples/sbol2/CreatingSBOL2Objects/MapsTo.ipynb

+   "outputs": [],
+   "source": [
+    "# Validate the document\n",
+    "report = doc.validate()\n",


@GeneCodeSavvy please implement this idea so we can review it in the 1o1

pySBOL2 MapsTo object tutorial

30342d6

GeneCodeSavvy requested a review from Gonza10V June 17, 2025 14:25

jakebeal requested changes Jun 19, 2025

View reviewed changes

Adding more biological context

4cc1c0c

GeneCodeSavvy requested a review from jakebeal June 26, 2025 18:28

jakebeal approved these changes Jun 26, 2025

View reviewed changes

remove .identity for definition property

7a2f6ad

Co-authored-by: Jacob Beal <jakebeal@gmail.com>

Gonza10V requested changes Jun 30, 2025

View reviewed changes

GeneCodeSavvy force-pushed the pysbol2-mapsto branch from 007e0c8 to 7a2f6ad Compare July 3, 2025 08:13

GeneCodeSavvy and others added 6 commits July 3, 2025 22:16

added interaction objects to mapsTo.ipynb

35f8867

mix mapsto validation

b0ddb30

replace with correct refinement property

26f07d3

interaction objects

7a9925d

updated MapsTo

5e11528

added interaction objects to sbol2 mapto notebook

2523b19

GeneCodeSavvy force-pushed the pysbol2-mapsto branch from 5ab2589 to 2523b19 Compare July 4, 2025 18:15

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GeneCodeSavvy commented Jun 17, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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GeneCodeSavvy commented Jun 26, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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GeneCodeSavvy commented Jun 17, 2025 •

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GeneCodeSavvy commented Jun 26, 2025 •

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