Difference between revisions of "BIN-Databases"

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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%;">
 
Bioinformatics Databases
 
Bioinformatics Databases
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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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(Database principles for bioinformatics)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Database principles for bioinformatics
 
 
</div>
 
</div>
  
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{{Smallvspace}}
  
  
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__TOC__
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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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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/BIN-Databases.components.wtxt", section: "abstract" -->
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Large, scalable, multi-user database systems require a fair amount of technology underneath the hood. In particular, they need to fulfill the ACID requirements that ensure database integrity. This unit introduces the principles, and then moves onto an overview of current bioinformatics databases, and Web services.
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...
 
 
<section end=abstract />
 
<section end=abstract />
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<!-- ============================  -->
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<hr>
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<table>
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<tr>
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<td style="padding:10px;">
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<b>Objectives:</b><br />
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This unit will ...
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* ... describes construction principles for database systems;
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* ... mentions some general aspects of dtabase use in bioinformatics;
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* ... explores the current NAR database and Web service issues.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... can define the four ACID requirements for tranactional integrity of databases;
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* ... are familar with a spectrum of database and Web service offerings in bioinformatics.
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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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This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-Storing_data|BIN-Storing_data (Storing Data)]]
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<section end=prerequisites />
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<!-- ============================  -->
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== This unit ... ==
 
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=== Prerequisites ===
 
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<!-- included from "../components/BIN-Databases.components.wtxt", section: "prerequisites" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-Storing_data]]
 
  
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=== Objectives ===
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__TOC__
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<!-- included from "../components/BIN-Databases.components.wtxt", section: "objectives" -->
 
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...
 
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=== Outcomes ===
 
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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]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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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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<!-- included from "../components/BIN-Databases.components.wtxt", section: "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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== Contents ==
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{{Vspace}}
 
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In this unit we develop the technical context of bioinformatics databases and get a perspective on the multitude of data offerings in the field. Data and service offerings have no clearly defined boundaries, and many sites offer a mix of both. Thus we explore current Web services as well to define the landscape.
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<div id="BIO">
 
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== Contents ==
 
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<!-- included from "../components/BIN-Databases.components.wtxt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
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*Read the introductory notes on {{ABC-PDF|BIN-Databases| database concepts for bioinformatics}}.
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*Read the introductory notes on {{ABC-PDF|BIN-Databases| construction principles for large, multi-user, scalable database systems}}.
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}}
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* Visit the current [https://academic.oup.com/nar/issue/48/D1 '''Database Issue of NAR'''] and browse the titles.
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* Read the editorial article in this issue:
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{{#pmid: 31906604}}
  
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* Visit the current [https://academic.oup.com/nar/issue/48/W1 '''Web Service Issue of NAR'''] and browse the titles.
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* Read the editorial article in this issue:
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{{#pmid: 32589733}}
  
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* For both issues: find one article that you find particularly interesting, intruguing, or surprising, cite it in your journal, and comment on it.
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== Further reading, links and resources ==
 
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== Notes ==
 
== Notes ==
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SKIP
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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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:2020-09-20
 
<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 Annual update ... and a task
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*1.0 First live version.
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 09:26, 25 September 2020

Bioinformatics Databases

(Database principles for bioinformatics)


 


Abstract:

Large, scalable, multi-user database systems require a fair amount of technology underneath the hood. In particular, they need to fulfill the ACID requirements that ensure database integrity. This unit introduces the principles, and then moves onto an overview of current bioinformatics databases, and Web services.

Objectives:
This unit will ...

  • ... describes construction principles for database systems;
  • ... mentions some general aspects of dtabase use in bioinformatics;
  • ... explores the current NAR database and Web service issues.

Outcomes:
After working through this unit you ...

  • ... can define the four ACID requirements for tranactional integrity of databases;
  • ... are familar with a spectrum of database and Web service offerings in bioinformatics.

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


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    In this unit we develop the technical context of bioinformatics databases and get a perspective on the multitude of data offerings in the field. Data and service offerings have no clearly defined boundaries, and many sites offer a mix of both. Thus we explore current Web services as well to define the landscape.

    Task:

    Rigden & Fernández (2020) The 27th annual Nucleic Acids Research database issue and molecular biology database collection. Nucleic Acids Res 48:D1-D8. (pmid: 31906604)

    [ PubMed ] [ DOI ]

    (2020) Editorial: the 18th annual Nucleic Acids Research web server issue 2020. Nucleic Acids Res 48:W1-W4. (pmid: 32589733)

    [ PubMed ] [ DOI ]

    • For both issues: find one article that you find particularly interesting, intruguing, or surprising, cite it in your journal, and comment on it.

    Notes

    SKIP


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-20

    Version:

    1.1

    Version history:

    • 1.1 Annual update ... and a task
    • 1.0 First live version.
    • 0.1 First stub

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