Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [ABC-BIN]
Preparation 		  [BIN]
MYSPE 		  [FND]
Cell_cycle 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Introduction to nature of abstractions; examples; abstractions for biology; structuring abstractions: controlled vocabularies and ontologies
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.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

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.

Task…

  • Read the introductory notes on “Abstractions” for BioinformaticsPDF.
  • Think about a particular abstraction for biology. Transcription factors are proteins that regulate which genes are expressed at what time. In this regulation, it is common that transcription factors stimulate or repress the expression of other transcription factors, which in turn act on the expression of more proteins. In addition, enzymes1 that catalyze post-translational modifications can play an important role in such regulation since these modifications can activate or repress their target proteins. Thus there are many, many levels of feedback and regulation: at the level of gene transcription, at the level of mRNA translation, at the level of protein activity, and many more. Assume you would like to store facts about this situation. What abstraction could you design?

  • Think about the actors and their roles in this process. Then define what is essential.
  • The common abstraction for this is a graph(W). In a graph that can represent our abstraction, the nodes could be gene labels and the edges define a relationship: here it is an influence - activation or repression. 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?

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-Abstractions

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-21
Version:
1.0.1
Version History:
–  1.0.1 2022 Maintenance
–  1.0 Completed to first live version
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides

 

[END]

  1. Enzymes are a special type of protein.↩︎