Design and Use of Relational Databases in Chemistry - TJ O'Donnell

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Design and Use of Relational Databases in Chemistry

By: TJ O'Donnell

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Hardcover | 5 January 2008 | Edition Number 1

At a Glance

Hardcover
248 Pages

Dimensions(cm)
23.4 x 15.6 x 1.91

Hardcover

$579.25

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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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Preface	p. xi
Acknowledgments	p. xiii
Biography	p. xv
Introduction	p. 1
Relational Database Fundamentals	p. 5
Introduction	p. 5
Tables, Rows, and Columns	p. 5
External and Internal Representations of Data	p. 7
Advantages over Spreadsheets	p. 8
Size and Speed	p. 8
Multiple Users	p. 8
Relationships among Tables	p. 9
One-to-Many Relationships	p. 9
One-to-One Relationships	p. 11
Many-to-Many Relationships	p. 12
Entity Relationship Diagrams	p. 12
Uniqueness	p. 14
Sequences	p. 14
Keys	p. 15
Primary Keys	p. 15
Foreign Keys	p. 15
Constraints	p. 16
Indexes	p. 16
Joining Tables	p. 16
Normal Forms	p. 17
First Normal Form	p. 17
Second Normal Form	p. 18
Third Normal Form	p. 19
Summary of Normal Forms	p. 20
References	p. 20
Structured Query Language (SQL)	p. 21
Introduction	p. 21
Databases, Schemas, Tables, Rows, and Columns	p. 21
Create	p. 22
Insert	p. 23
Select	p. 24
Update and Delete	p. 25
SQL Functions	p. 26
Regular Functions	p. 26
Aggregate Functions	p. 27
Domains, Triggers, and Views	p. 28
Unions, Intersections, and Differences	p. 29
References	p. 30
Relational Database Management Systems	p. 31
Introduction	p. 31
Standard SQL	p. 32
A Sampling of Differences	p. 32
Server and Client	p. 33
Compatibility	p. 35
References	p. 35
Client and Web Applications	p. 37
Introduction	p. 37
Command Line Programs	p. 37
Web-Based Applications	p. 38
Client Applications	p. 39
SQL Interfaces in Various Languages	p. 41
Perl	p. 43
Python	p. 44
PHP	p. 44
Java	p. 45
References	p. 46
Data Storage, Searching, and Manipulation	p. 47
Introduction	p. 47
General Schema Design Decisions	p. 47
Sample Schema for Tracking Chemical Samples	p. 49
Schemas for PubChem Data	p. 53
BioAssay Data	p. 54
Substances	p. 56
Compounds	p. 58
Data Constraints and Data Integrity	p. 60
Developing Complex SQL	p. 63
Subselect Statements	p. 66
Views	p. 67
References	p. 70
Computer Representations of Molecular Structures	p. 71
Introduction	p. 71
SMILES Representation of Molecular Structure	p. 72
Extensions to SQL for Chemical Structures	p. 72
SMARTS Representation of Molecular Searches	p. 74
SMILES and SMARTS Quirks	p. 76
Hydrogen Atoms	p. 76
Aromaticity	p. 77
Tautomers	p. 77
Valence	p. 80
Chirality	p. 80
Isotopes	p. 81
Salts and Mixtures	p. 81
InChI and Canonical SMILES	p. 82
SMILES and Inorganic Structures	p. 82
Other SMILES Extensions	p. 82
Input and Output of Molecular Structures	p. 83
Useful SQL Extensions	p. 85
SMILES as an SQL Data Type	p. 86
Domains	p. 86
Triggers	p. 87
Summary	p. 88
References	p. 88
Molecular Fragments and Fingerprints	p. 91
Introduction	p. 91
Fragments	p. 91
Fragment Keys	p. 92
MACCS Keys and Other Fragment Keys	p. 95
Fingerprints	p. 95
Similarity Measures	p. 96
Computing Fragment-Based Properties	p. 96
References	p. 98
Reactions and Transformations	p. 99
Introduction	p. 99
Reaction SMILES	p. 99
Transformations	p. 100
Unimolecular Transformations	p. 101
Multi-Component Transformations	p. 104
Canonical Reaction SMILES	p. 106
References	p. 107
PostgreSQL Extensions	p. 109
Introduction	p. 109
Composite Data Types	p. 109
Composite Data Type for Experimental Values	p. 111
Array Data Types for Two- and Three-Dimensional Coordinates	p. 115
Functions in Other Languages	p. 117
Plpgsql	p. 117
Plperl, Plpython, Pltcl	p. 118
Core Chemical Functions	p. 119
C Language Functions	p. 120
Object RDBMS	p. 121
References	p. 121
Three-Dimensional Molecular Structure Tables	p. 123
Introduction	p. 123
Using Tables Instead of Files	p. 123
Molfile and Other Common File Formats	p. 124
Processing SDF Files	p. 125
Using Tables Instead of Files in Client Programs	p. 131
File Import, Export, and Conversions	p. 132
Functions Using Three-Dimensional Atomic Coordinates	p. 133
Conformations	p. 135
Other Representations of Three-Dimensional Molecular Structure	p. 136
References	p. 136
More on Client and Web Interfaces to RDBMS	p. 137
Introduction	p. 137
Store All Possible Data in the RDBMS	p. 139
Advanced SQL Techniques	p. 140
Placeholders in SQL Statements	p. 141
Bind Values in SQL Statements	p. 142
Web Applications	p. 143
R Programs	p. 147
Hierarchical Clustering	p. 147
Linear Models	p. 148
References	p. 153
Applications	p. 155
Introduction	p. 155
Compound Registration	p. 155
Experimental Chemical and Biological Data Integration	p. 162
Data from External Sources	p. 164
Utilities	p. 167
molgrep	p. 168
molcat	p. 168
molview	p. 169
molarb	p. 170
molrandom	p. 170
molnear	p. 171
molsame	p. 171
References	p. 172
Appendix	p. 173
Introduction	p. 173
Symbols and Bonds from Simplified Molecular Input Line Entry System (SMILES)	p. 173
Normalizing Data	p. 175
SQL Functions	p. 176
Public166keys	p. 176
Orsum	p. 176
Tanimoto	p. 176
Euclid	p. 177
Hamming	p. 177
Nbits_set	p. 177
Amw	p. 177
Tpsa	p. 181
Tables Used in Functions	p. 182
Amw	p. 183
Tpsa	p. 183
Public166keys	p. 183
Core Function Implementation for PostgreSQL	p. 188
PerlMol/plperlu	p. 188
FROWNS/plpythonu	p. 191
OpenBabel/python	p. 197
C Language PostgreSQL Functions	p. 203
Database Utilities Dbutils	p. 205
Loading Files into Simple Tables	p. 206
Smiloader	p. 207
Sdfloader	p. 208
References	p. 210
Index	p. 211
Table of Contents provided by Ingram. All Rights Reserved.

Design and Use of Relational Databases in Chemistry

At a Glance

Hardcover

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