Modeling Biology Using Relational Databases

Robert M. Peitzsch1

1 Pfizer Global Research and Development, Groton, Connecticut
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.3
DOI:  10.1002/0471250953.bi0903s00
Online Posting Date:  February, 2003
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

There are several different methodologies that can be used for designing a database schema; no one is the best for all occasions. This unit demonstrates two different techniques for designing relational tables and discusses when each should be used. These two techniques presented are (1) traditional Entity‐Relationship (E‐R) modeling and (2) a hybrid method that combines aspects of data warehousing and E‐R modeling. The method of choice depends on (1) how well the information and all its inherent relationships are understood, (2) what types of questions will be asked, (3) how many different types of data will be included, and (4) how much data exists.

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Basic Protocol 1: Using Entity‐Relationship Modeling to Design a Database
  • Alternate Protocol 1: Using the Hybrid Method to Design a Database
  • Commentary
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

Basic Protocol 1: Using Entity‐Relationship Modeling to Design a Database

  Necessary Resources
  • Hardware
  • Personal computers with the Microsoft Windows operating system
  • Software
  • There are several software packages for designing formal schemas, some examples are: Microsoft Access, Designer from Oracle, PowerDesigner from Sybase, and Visio also from Microsoft. Pencil and paper also work well, and are recommended for those who are just starting out.
  • Files
  • None

Alternate Protocol 1: Using the Hybrid Method to Design a Database

  Necessary Resources
  • Hardware
  • Personal computers with the Microsoft Windows operating system
  • Software
  • There are several software packages for designing databases, some examples are: Microsoft Access, Designer from Oracle, PowerDesigner from Sybase, and Visio also from Microsoft. Pencil and paper also work well, and are recommended for those who are just starting out.
  • Files
  • None
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410.
   Codd, E.F. 1990. The Relational Model for Database Management; Version 2. Addison‐Wesley Publishing, New York.
   Date, C.J. 1995. An Introduction to Database Systems, 6th ed. Addison‐Wesley Publishing, New York.
   Dodge, G. and Gorman, T. 1998. Oracle8 Data Warehousing. John Wiley & Sons, New York.
   The Gene Ontology Consortium. 2000. Gene ontology: Tool for the unification of biology. Nature Gen. 25:25‐29.
   Inmon, W.H., Imhoff, C., and Battas, G. 1995. Building the Operational Data Store. John Wiley & Sons, New York.
   Kimball, R. 1996. The Data Warehouse Toolkit. John Wiley & Sons, New York.
   Yarger, R.J., Reese, G., and King, T. 1999. MySQL & mSQL. O'Reilly & Associates, CA.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library