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
 
 
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</div>
  
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__TOC__
 
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{{LIVE}}
 
  
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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.txt", section: "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.
 
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.
 
<section end=abstract />
 
<section end=abstract />
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<!-- ============================ -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "./components/BIN-Databases.components.txt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "./data/ABC-unit_components.txt", 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|BIN-Storing_data (Storing Data)]]
 
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{{Vspace}}
 
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=== Objectives ===
 
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<!-- included from "./components/BIN-Databases.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... describes construction principles for database systems;
 
* ... describes construction principles for database systems;
 
* ... mentions some general aspects of dtabase use in bioinformatics;
 
* ... mentions some general aspects of dtabase use in bioinformatics;
 
* ... explores the current NAR database and Web service issues.
 
* ... 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 />
 +
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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</div>
  
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=== Outcomes ===
 
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<!-- included from "./components/BIN-Databases.components.txt", section: "outcomes" -->
 
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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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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Deliverables ===
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__TOC__
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<!-- included from "./components/BIN-Databases.components.txt", section: "deliverables" -->
 
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<!-- included from "./data/ABC-unit_components.txt", 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 "./data/ABC-unit_components.txt", 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 "./data/ABC-unit_components.txt", 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 ===
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<div id="BIO">
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
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<!-- included from "./components/BIN-Databases.components.txt", section: "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.
 
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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{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-Databases| construction principles for large, multi-user, scalable database systems}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-Databases| construction principles for large, multi-user, scalable database systems}}.
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* Visit the current [https://academic.oup.com/nar/issue/45/D1 '''Database Issue of NAR'''] and browse the titles.
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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.
 
* Read the editorial article in this issue:
 
* Read the editorial article in this issue:
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{{#pmid: 28053160}}
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{{#pmid: 32589733}}
  
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* Visit the current [https://academic.oup.com/nar/issue/45/W1 '''Web Service Issue of NAR'''] and browse the titles.
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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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* Read the [https://academic.oup.com/nar/article/45/W1/W1/3896331/Editorial-the-15th-annual-Nucleic-Acids-Research '''editorial article on this issue'''].
 
  
 
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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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
 
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<b>Version:</b><br />
 
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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
 
*1.0 First live version.
 
*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 ] The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid-liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

    (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

    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-Databases&oldid=11678"