Design and Use of Relational Databases in Chemistry

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Optimize Your Chemical Database

Design and Use of Relational Databases in Chemistry helps programmers and users improve their ability to search and manipulate chemical structures and information, especially when using chemical database "cartridges". It illustrates how the organizational, data integrity, and extensibility properties of relational databases are best utilized when working with chemical information.

The author facilitates an understanding of existing relational database schemas and shows how to design new schemas that contain tables of data and chemical structures. By using database extension cartridges, he provides methods to properly store and search chemical structures. He explains how to download and install a fully functioning database using free, open-source chemical extension cartridges within PostgreSQL. The author also discusses how to access a database on a computer network using both new and existing applications.

Through examples of good database design, this book shows you that relational databases are the best way to store, search, and operate on chemical information.

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Product Details

  • ISBN-13: 9781420064421
  • Publisher: Taylor & Francis
  • Publication date: 12/1/2008
  • Pages: 224
  • Product dimensions: 6.30 (w) x 9.30 (h) x 0.80 (d)

Table of Contents


Relational Database Fundamentals


Tables, Rows, and Columns

External and Internal Representations of Data

Advantages over Spreadsheets

Relationships among Tables

Entity Relationship Diagrams






Joining Tables

Normal Forms

Structured Query Language (SQL)


Databases, Schemas, Tables, Rows and Columns




Update and Delete

SQL Functions

Domains, Triggers, and Views

Unions, Intersections, and Differences

Relational Database Management Systems (RDBMS)


Standard SQL

A Sampling of Differences

Server and Client


Client and Web Applications


Command Line Programs

Web-Based Applications

Client Applications

SQL Interfaces in Various Languages

Data Storage, Searching, and Manipulation


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


Computer Representations of Molecular Structures


SMILES Representation of Molecular Structure

Extensions to SQL for Chemical Structures

SMARTS Representation of Molecular Searches


SMILES and Inorganic Structures

Other SMILES Extensions

Input and Output of Molecular Structures

Useful SQL Extensions

SMILES as a SQL Data Type


Molecular Fragments and Fingerprints




Similarity Measures

Computing Fragment-Based Properties

Reactions and Transformations


Reaction SMILES


Canonical Reaction SMILES

PostgreSQL Extensions


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


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


Other Representations of Three-Dimensional Molecular Structure

More on Client and Web Interfaces to RDBMS


Store All Possible Data in the RDBMS

Advanced SQL Techniques

R Programs



Compound Registration

Experimental Chemical and Biological Data Integration

Data from External Sources




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


References appear at the end of each chapter.

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