Difference between revisions of "BIN-Abstractions"

From "A B C"
Jump to navigation Jump to search
m
m
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
<div id="BIO">
+
<div id="ABC">
−
  <div class="b1">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Abstractions for Bioinformatics
 
Abstractions for Bioinformatics
−
  </div>
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
−
 
+
(Introduction to nature of abstractions; examples; abstractions for biology; structuring abstractions: controlled vocabularies and ontologies.)
−
  {{Vspace}}
+
</div>
−
 
 
−
<div class="keywords">
 
−
<b>Keywords:</b>&nbsp;
 
−
Elements of abstractions for biology
 
 
</div>
 
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
__TOC__
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
−
 
+
<div style="font-size:118%;">
−
{{Vspace}}
+
<b>Abstract:</b><br />
−
 
 
−
 
 
−
{{DEV}}
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
−
== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "abstract" -->
+
This unit comprises introductory notes on the nature of abstractions with an example from the art of tying ties. We review typical abstractions for biology and discuss options for structuring labels and relationships.
−
...
 
 
<section end=abstract />
 
<section end=abstract />
−
 
+
</div>
−
{{Vspace}}
+
<!-- ============================  -->
−
 
+
<hr>
−
 
+
<table>
−
== This unit ... ==
+
<tr>
−
=== Prerequisites ===
+
<td style="padding:10px;">
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "prerequisites" -->
+
<b>Objectives:</b><br />
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
+
This unit will ...
−
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
+
* ... introduce the concept of an "abstraction", as applied to making concepts about biology computable;
−
<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
+
* ... illustrate with examples;
 +
* ... discuss principles of how to address issues of uniqueness and structuring of abstractions.
 +
</td>
 +
<td style="padding:10px;">
 +
<b>Outcomes:</b><br />
 +
After working through this unit you ...
 +
* ... can describe what the purpose of an abstraction is;
 +
* ... have encountered common abstractions for bioinformatics;
 +
* ... are able to come up with examples for "numerically controlled vocabularies" and "synonym constrained vocabularies";
 +
* ... have thought about an abstraction for a complex biological situation;
 +
* ... are able to contrast your solution to the canonical approach.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================ -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<ul>
 +
<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
 +
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
</ul>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:<br />
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
+
This unit builds on material covered in the following prerequisite units:<br />
−
You need to complete the following units before beginning this one:
 
 
*[[ABC-BIN-Preparation|ABC-BIN-Preparation (Bioinformatics Course Preparation)]]
 
*[[ABC-BIN-Preparation|ABC-BIN-Preparation (Bioinformatics Course Preparation)]]
 +
*[[BIN-MYSPE|BIN-MYSPE (MYSPE (My Species))]]
 +
*[[FND-Cell_cycle|FND-Cell_cycle (The Yeast Cell Cycle)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
−
 
 
  
−
=== Objectives ===
 
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "objectives" -->
 
−
...
 
  
−
{{Vspace}}
 
  
 +
{{Smallvspace}}
  
−
=== Outcomes ===
 
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "outcomes" -->
 
−
...
 
  
−
{{Vspace}}
+
__TOC__
−
 
 
−
 
 
−
=== Deliverables ===
 
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "deliverables" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
−
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
Line 76: Line 76:
  
 
=== Evaluation ===
 
=== Evaluation ===
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "evaluation" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
−
:This unit is not evaluated for course marks.
+
<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-Abstractions|"Abstractions" for Bioinformatics}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-Abstractions|"Abstractions" for Bioinformatics}}.
−
}}
+
* It is common for transcription factors to stimulate or repress the expression of other transcription factors, which in turn act on the expression of more proteins. In addition, proteins that catalyze post-translational modifications can play an important role in such regulation. Assume you would like to store facts about this situation. What abstraction could you design?
 +
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 +
More ...
 +
<div class="mw-collapsible-content">
 +
Think about the actors and their roles in this process. Then define what is essential.
  
 +
The common abstraction for this is a [[FND-MAT-Graphs_and_networks{{!}}'''graph''']]. In this graph the nodes are gene labels and the edges define a relationship of influence -  activating or repressing. The individual facts are represented as the existence of nodes and edges, and as attributes to nodes and edges. This is called a "'''gene regulatory network'''". Now ask yourself: can this abstraction represent all types of facts?
  
−
{{Vspace}}
+
Is this abstraction what you came up with? Is your idea different? Better?
−
 
 
−
 
 
−
== Further reading, links and resources ==
 
−
*{{WP|Database normalization}}
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
== Notes ==
 
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "notes" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
−
<references />
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
−
== Self-evaluation ==
 
−
<!-- included from "../components/BIN-Abstractions.components.wtxt", section: "self-evaluation" -->
 
−
<!--
 
−
=== Question 1===
 
−
 
 
−
Question ...
 
−
 
 
−
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
−
Answer ...
 
−
<div class="mw-collapsible-content">
 
−
Answer ...
 
  
 
</div>
 
</div>
 
   </div>
 
   </div>
  
−
  {{Vspace}}
+
}}
−
 
 
−
-->
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_ask" -->
 
  
−
----
 
  
 
{{Vspace}}
 
{{Vspace}}
  
−
<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
−
 
−
----
 
−
 
−
{{Vspace}}
 
  
 
<div class="about">
 
<div class="about">
Line 159: Line 109:
 
:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
−
:2017-08-07
+
:2017-09-19
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:0.1
+
:1.0
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.0 Completed to first live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
−
[[Category:ABC-units]]
 
−
<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
 +
[[Category:ABC-units]]
 +
{{UNIT}}
 +
{{LIVE}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 09:25, 25 September 2020

Abstractions for Bioinformatics

(Introduction to nature of abstractions; examples; abstractions for biology; structuring abstractions: controlled vocabularies and ontologies.)


 


Abstract:

This unit comprises introductory notes on the nature of abstractions with an example from the art of tying ties. We review typical abstractions for biology and discuss options for structuring labels and relationships.

Objectives:
This unit will ...

  • ... introduce the concept of an "abstraction", as applied to making concepts about biology computable;
  • ... illustrate with examples;
  • ... discuss principles of how to address issues of uniqueness and structuring of abstractions.

Outcomes:
After working through this unit you ...

  • ... can describe what the purpose of an abstraction is;
  • ... have encountered common abstractions for bioinformatics;
  • ... are able to come up with examples for "numerically controlled vocabularies" and "synonym constrained vocabularies";
  • ... have thought about an abstraction for a complex biological situation;
  • ... are able to contrast your solution to the canonical approach.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Prerequisites:
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

  • Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.

This unit builds on material covered in the following prerequisite units:


 



 



 


Evaluation

Evaluation: NA

This unit is not evaluated for course marks.

Contents

Task:

  • Read the introductory notes on "Abstractions" for Bioinformatics.
  • It is common for transcription factors to stimulate or repress the expression of other transcription factors, which in turn act on the expression of more proteins. In addition, proteins that catalyze post-translational modifications can play an important role in such regulation. Assume you would like to store facts about this situation. What abstraction could you design?

More ...

Think about the actors and their roles in this process. Then define what is essential.

The common abstraction for this is a graph. In this graph the nodes are gene labels and the edges define a relationship of influence - activating or repressing. The individual facts are represented as the existence of nodes and edges, and as attributes to nodes and edges. This is called a "gene regulatory network". Now ask yourself: can this abstraction represent all types of facts?

Is this abstraction what you came up with? Is your idea different? Better?


 


About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-09-19

Version:

1.0

Version history:

  • 1.0 Completed to first live version
  • 0.1 First stub

CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-Abstractions&oldid=11670"