designing databases for biological research

21
Designing Databases for Biological Research Brian R. Mitchell Fall 2006

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Designing Databases for Biological Research. Brian R. Mitchell Fall 2006. Introduction. Participants Syllabus Website: http://www.uvm.edu/~bmitchel/databases.html Database options at UVM. What is a Database?. Definition Keys Structured Query Language (SQL) Relationships. - PowerPoint PPT Presentation

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Page 1: Designing Databases for Biological Research

Designing Databases for Biological Research

Brian R. Mitchell

Fall 2006

Page 2: Designing Databases for Biological Research

Introduction

• Participants

• Syllabus• Website:

http://www.uvm.edu/~bmitchel/databases.html

• Database options at UVM

Page 3: Designing Databases for Biological Research

What is a Database?

• Definition

• Keys

• Structured Query Language (SQL)

• Relationships

Page 4: Designing Databases for Biological Research

Relationships

• One-to-one

Technicians Contact_Info

Amy Amy’s address

Joe Joe’s Address

Fred Fred’s Address

Page 5: Designing Databases for Biological Research

Relationships

• One-to-many

Site Count_Data

286 (+ site fields) 286 (species 1)

286 (species 2)

286 (species 3)

Page 6: Designing Databases for Biological Research

Relationships

• Many-to-many

Students Classes

Ralph BIO 165

Susan NR 385?

Page 7: Designing Databases for Biological Research

Relationships

• Many-to-many

Students Classes

Ralph BIO 165

Susan NR 385

Schedule

Student & Class

Page 8: Designing Databases for Biological Research

Why Use a Database?

Page 9: Designing Databases for Biological Research
Page 10: Designing Databases for Biological Research

Naming Conventions

• Keep it short

• Make it meaningful

• No spaces – use underscores “_”

• Avoid @#%$*& special characters

• Be consistent

Page 11: Designing Databases for Biological Research

Naming Fields

• Be specific

• One piece of information per field

• No calculated fields

• Identify your keys

Page 12: Designing Databases for Biological Research

Naming Objects

• Conventional abbreviations for objects:• Tables

– tbl = data table– tlu = lookup table– xref = linking table

• Queries = qry• Forms

– frm = form– frm_sub or fsub = subform

• Reports– rpt = report– rpt_sub or rsub = subreport

• Pages = pag (not widely used)• Macros = mac (not widely used)• Modules = mod

Page 13: Designing Databases for Biological Research

Avoid Reserved Words

avg key propertycount max sectioncurrency memo setdate min sumdesc name time exists number typegroup order valueindex percent year

Page 14: Designing Databases for Biological Research

Data Types

• AutoNumber• Currency• Date/Time• Hyperlink• Memo• Number• OLE• Text• Yes/No

Page 15: Designing Databases for Biological Research

Database Design

• Single Database or Front End / Back End?

• Normalization

Page 16: Designing Databases for Biological Research

Database Design

• Non-normalized

Spreadsheet-style

Site Date Observer Bird24 7/1/04 BRM BTBW24 7/1/04 BRM OVEN24 7/1/04 BRM YBSA

Page 17: Designing Databases for Biological Research

Database Design

• First Normal Form (1NF)

Each field contains one value

NO YES

Coordinates UTM_E & UTM_N

Birds seen Separate table

Page 18: Designing Databases for Biological Research

Database Design

• Second Normal Form (2NF)

If you have a composite key, no data relates to one of the keys

Example from Northwind database

Page 19: Designing Databases for Biological Research

Database Design

• Third Normal Form (3NF)

Information in the table must not be related to a non-key field

Example from Northwind database

Page 20: Designing Databases for Biological Research

Database Design

• Plan your database– Why bother?– Iterative process– Tables– Relationships– Fields– Rules

Page 21: Designing Databases for Biological Research

Exercise

Tables FieldsSpecies Species_ID, Common, SciLocation Habitat, CoordinateVisit Time, Weather, DateSurvey Minute, species, vis/aud

Multiple visits to each location10 minute count during each visit: listens for each individual

of each species that can see or hear, records species, minute during count, visual/auditory