Difference between revisions of "BIN-FUNC-Concepts"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Biomolecular Function Concepts
 
Biomolecular Function Concepts
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(The concept of function, representation of function, annotation, and prediction.)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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The concept of function, function abstraction; function ontology
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
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{{DEV}}
 
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{{Vspace}}
 
  
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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<section begin=abstract />
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Function is a ''concept'', not an observation and it is not trivial how we categorize and arrange observed activities to "functions". Once defined, functions need to be represented in the computer, associated with biomolecules through annotation, and used in prediction to complement experimentation.
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<section end=abstract />
 
</div>
 
</div>
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<div id="ABC-unit-framework">
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<!-- ============================  -->
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== Abstract ==
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<hr>
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<!-- included from "../components/BIN-FUNC-Concepts.components.wtxt", section: "abstract" -->
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<table>
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...
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<tr>
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<td style="padding:10px;">
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{{Vspace}}
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<b>Objectives:</b><br />
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This unit will ...
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* Introduce the meaning of "function" and issues that arise from it being a concept, not an observable;
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== This unit ... ==
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* Introduce principles of representation, annotation and prediction of biomolecular function.
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=== Prerequisites ===
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</td>
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<!-- included from "../components/BIN-FUNC-Concepts.components.wtxt", section: "prerequisites" -->
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<td style="padding:10px;">
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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<b>Outcomes:</b><br />
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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:
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After working through this unit you ...
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<!-- included from "FND-prerequisites.wtxt", section: "bch" -->
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* understand how observed activities are conceptualized as "functions" on various levels;
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<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
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* know about three common resources for function representation: E.C. codes, pathway collections, and above all, the Gene Ontology project;
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* can name the three fundamental strategies for function prediction and give one example for each.
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</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<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>
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<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>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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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.
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<!-- included from "FND-prerequisites.wtxt", section: "metabolism" -->
 
 
*<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
 
*<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
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<!-- included from "FND-prerequisites.wtxt", section: "cellular_components" -->
 
 
*<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix.
 
*<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix.
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:<br />
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You need to complete the following units before beginning this one:
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*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]]
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*[[BIN-Abstractions]]
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<section end=prerequisites />
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<!-- ============================  -->
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</div>
  
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=== Objectives ===
 
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...
 
  
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=== Outcomes ===
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__TOC__
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...
 
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=== Deliverables ===
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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{{Task|1=
 
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== Further reading, links and resources ==
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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<references />
 
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== Self-evaluation ==
 
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<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.
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
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:2020-09-23
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 2020 Maintenance
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*1.0 First final version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 08:51, 24 September 2020

Biomolecular Function Concepts

(The concept of function, representation of function, annotation, and prediction.)


 


Abstract:

Function is a concept, not an observation and it is not trivial how we categorize and arrange observed activities to "functions". Once defined, functions need to be represented in the computer, associated with biomolecules through annotation, and used in prediction to complement experimentation.

Objectives:
This unit will ...

  • Introduce the meaning of "function" and issues that arise from it being a concept, not an observable;
  • Introduce principles of representation, annotation and prediction of biomolecular function.

Outcomes:
After working through this unit you ...

  • understand how observed activities are conceptualized as "functions" on various levels;
  • know about three common resources for function representation: E.C. codes, pathway collections, and above all, the Gene Ontology project;
  • can name the three fundamental strategies for function prediction and give one example for each.

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.
    • Metabolism: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
    • Organelles: Compartmentalization, organelles and structures of the cell; the extracellular matrix.

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


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:



     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-23

    Version:

    1.1

    Version history:

    • 1.1 2020 Maintenance
    • 1.0 First final 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-FUNC-Concepts&oldid=11627"