Difference between revisions of "BIN-Abstractions"
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Think about the actors and their roles in this process. Then define what is essential. | 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? | + | 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? |
Is this abstraction what you came up with? Is your idea different? Better? | Is this abstraction what you came up with? Is your idea different? Better? | ||
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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.
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Objectives:
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Outcomes:
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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:
Contents
Evaluation
Evaluation: NA
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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
