Table of Contents
Introduction
Relational Database Fundamentals
Introduction
Tables, Rows, and Columns
External and Internal Representations of Data
Advantages over Spreadsheets
Relationships among Tables
Entity Relationship Diagrams
Uniqueness
Sequences
Keys
Constraints
Indexes
Joining Tables
Normal Forms
Structured Query Language (SQL)
Introduction
Databases, Schemas, Tables, Rows and Columns
Create
Insert
Select
Update and Delete
SQL Functions
Domains, Triggers, and Views
Unions, Intersections, and Differences
Relational Database Management Systems (RDBMS)
Introduction
Standard SQL
A Sampling of Differences
Server and Client
Compatibility
Client and Web Applications
Introduction
Command Line Programs
Web-Based Applications
Client Applications
SQL Interfaces in Various Languages
Data Storage, Searching, and Manipulation
Introduction
General Schema Design Decisions
Sample Schema for Tracking Chemical Samples
Schemas for PubChem Data
Data Constraints and Data Integrity
Developing Complex SQL
Sub-Select Statements
Views
Computer Representations of Molecular Structures
Introduction
SMILES Representation of Molecular Structure
Extensions to SQL for Chemical Structures
SMARTS Representation of Molecular Searches
SMILES and SMARTS Quirks
SMILES and Inorganic Structures
Other SMILES Extensions
Input and Output of Molecular Structures
Useful SQL Extensions
SMILES as a SQL Data Type
Summary
Molecular Fragments and Fingerprints
Introduction
Fragments
Fingerprints
Similarity Measures
Computing Fragment-Based Properties
Reactions and Transformations
Introduction
Reaction SMILES
Transformations
Canonical Reaction SMILES
PostgreSQL Extensions
Introduction
Composite Data Types
Composite Data Type for Experimental Values
Array Data Types for Two- and Three-Dimensional Coordinates
Functions in Other Languages
Object RDBMS
Three-Dimensional Molecular Structure Tables
Introduction
Using Tables Instead of Files
Molfile and Other Common File Formats
Processing SDF Files
Using Tables Instead of Files in Client Programs
File Import, Export, and Conversions
Functions Using Three-Dimensional Atomic Coordinates
Conformations
Other Representations of Three-Dimensional Molecular Structure
More on Client and Web Interfaces to RDBMS
Introduction
Store All Possible Data in the RDBMS
Advanced SQL Techniques
R Programs
Applications
Introduction
Compound Registration
Experimental Chemical and Biological Data Integration
Data from External Sources
Utilities
Appendix
Introduction
Symbols and Bonds from SMILES
Normalizing Data
SQL Functions
Tables Used in Functions
Core Function Implementation for PostgreSQL
C Language PostgreSQL Functions
Database Utilities Dbutils
Loading Files into Simple Tables
Index
References appear at the end of each chapter.
