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E-raamat: Design and Use of Relational Databases in Chemistry

(President, gNova Inc., San Diego, California, USA)
  • Formaat: PDF+DRM
  • Ilmumisaeg: 05-Dec-2008
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420064438
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Design and Use of Relational Databases in ChemistrySuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 05-Dec-2008
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420064438
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O'Donnell (an independent consultant in the field of computational chemistry) aims to convince the reader that most everyday work with chemical information, whether storage, search, or operation can benefit greatly from the organization, data integrity, and extensibility inherent in a relational database. Thirteen chapters discuss how to design and use tables to store and search numerical or text data; provide an introduction to SQL (structured query language) and relational database management systems (RDBMS) such as Oracle, MySQL, and PostgreSQL; discuss how client programs are used to connect to the database server; examine ways in which RDBMS are used to handle chemical structural information using chemical computer language representations; show ways in which molecular fragments can be used to speed up searches for chemical structures; discuss chemical reactions and transformations within the database; describe how to extend a relational database; give advice on the ways in which client programs can interface with the database; and provide sample applications that can be developed to produce a registry of compounds for use within a company or project. Annotation ©2009 Book News, Inc., Portland, OR (booknews.com)
Preface xi
Acknowledgments xiii
Biography xv
Chapter 1 Introduction 1
Chapter 2 Relational Database Fundamentals 5
2.1 Introduction
5
2.2 Tables, Rows, and Columns
5
2.3 External and Internal Representations of Data
7
2.4 Advantages over Spreadsheets
8
2.4.1 Size and Speed
8
2.4.2 Multiple Users
8
2.5 Relationships among Tables
9
2.5.1 One-to-Many Relationships
9
2.5.2 One-to-One Relationships
11
2.5.3 Many-to-Many Relationships
12
2.6 Entity Relationship Diagrams
12
2.7 Uniqueness
14
2.8 Sequences
14
2.9 Keys
15
2.9.1 Primary Keys
15
2.9.2 Foreign Keys
15
2.10 Constraints
16
2.11 Indexes
16
2.12 Joining Tables
16
2.13 Normal Forms
17
2.13.1 First Normal Form
17
2.13.2 Second Normal Form
18
2.13.3 Third Normal Form
19
2.13.4 Summary of Normal Forms
20
References
20
Chapter 3 Structured Query Language (SQL) 21
3.1 Introduction
21
3.2 Databases, Schemas, Tables, Rows, and Columns
21
3.3 Create
22
3.4 Insert
23
3.5 Select
24
3.6 Update and Delete
25
3.7 SQL Functions
26
3.7.1 Regular Functions
26
3.7.2 Aggregate Functions
27
3.8 Domains, Triggers, and Views
28
3.9 Unions, Intersections, and Differences
29
References
30
Chapter 4 Relational Database Management Systems 31
4.1 Introduction
31
4.2 Standard SQL
32
4.3 A Sampling of Differences
32
4.4 Server and Client
33
4.5 Compatibility
35
References
35
Chapter 5 Client and Web Applications 37
5.1 Introduction
37
5.2 Command Line Programs
37
5.3 Web-Based Applications
38
5.4 Client Applications
39
5.5 SQL Interfaces in Various Languages
41
5.5.1 Perl
43
5.5.2 Python
44
5.5.3 PHP
44
5.5.4 Java
45
References
46
Chapter 6 Data Storage, Searching, and Manipulation 47
6.1 Introduction
47
6.2 General Schema Design Decisions
47
6.3 Sample Schema for Tracking Chemical Samples
49
6.4 Schemas for PubChem Data
53
6.4.1 BioAssay Data
54
6.4.2 Substances
56
6.4.3 Compounds
58
6.5 Data Constraints and Data Integrity
60
6.6 Developing Complex SQL
63
6.7 Subselect Statements
66
6.8 Views
67
References
70
Chapter 7 Computer Representations of Molecular Structures 71
7.1 Introduction
71
7.2 SMILES Representation of Molecular Structure
72
7.3 Extensions to SQL for Chemical Structures
72
7.4 SMARTS Representation of Molecular Searches
74
7.5 SMILES and SMARTS Quirks
76
7.5.1 Hydrogen Atoms
76
7.5.2 Aromaticity
77
7.5.3 Tautomers
77
7.5.4 Valence
80
7.5.5 Chirality
80
7.5.6 Isotopes
81
7.5.7 Salts and Mixtures
81
7.5.8 InChI and Canonical SMILES
82
7.6 SMILES and Inorganic Structures
82
7.7 Other SMILES Extensions
82
7.8 Input and Output of Molecular Structures
83
7.9 Useful SQL Extensions
85
7.10 SMILES as an SQL Data Type
86
7.10.1 Domains
86
7.10.2 Triggers
87
7.11 Summary
88
References
88
Chapter 8 Molecular Fragments and Fingerprints 91
8.1 Introduction
91
8.2 Fragments
91
8.2.1 Fragment Keys
92
8.2.2 MACCS Keys and Other Fragment Keys
95
8.3 Fingerprints
95
8.4 Similarity Measures
96
8.5 Computing Fragment-Based Properties
96
References
98
Chapter 9 Reactions and Transformations 99
9.1 Introduction
99
9.2 Reaction SMILES
99
9.3 Transformations
100
9.3.1 Unimolecular Transformations
101
9.3.2 Multi-Component Transformations
104
9.4 Canonical Reaction SMILES
106
References
107
Chapter 10 PostgreSQL Extensions 109
10.1 Introduction
109
10.2 Composite Data Types
109
10.3 Composite Data Type for Experimental Values
111
10.4 Array Data Types for Two- and Three-Dimensional Coordinates
115
10.5 Functions in Other Languages
117
10.5.1 Plpgsql
117
10.5.2 Plperl, Plpython, Pltcl
118
10.5.3 Core Chemical Functions
119
10.5.4 C Language Functions
120
10.6 Object RDBMS
121
References
121
Chapter 11 Three-Dimensional Molecular Structure Tables 123
11.1 Introduction
123
11.2 Using Tables Instead of Files
123
11.3 Molfile and Other Common File Formats
124
11.4 Processing SDF Files
125
11.5 Using Tables Instead of Files in Client Programs
131
11.6 File Import, Export, and Conversions
132
11.7 Functions Using Three-Dimensional Atomic Coordinates
133
11.8 Conformations
135
11.9 Other Representations of Three-Dimensional Molecular Structure
136
References
136
Chapter 12 More on Client and Web Interfaces to RDBMS 137
12.1 Introduction
137
12.2 Store All Possible Data in the RDBMS
139
12.3 Advanced SQL Techniques
140
12.3.1 Placeholders in SQL Statements
141
12.3.2 Bind Values in SQL Statements
142
12.4 Web Applications
143
12.5 R Programs
147
12.5.1 Hierarchical Clustering
147
12.5.2 Linear Models
148
References
153
Chapter 13 Applications 155
13.1 Introduction
155
13.2 Compound Registration
155
13.3 Experimental Chemical and Biological Data Integration
162
13.4 Data from External Sources
164
13.5 Utilities
167
13.5.1 molgrep
168
13.5.2 molcat
168
13.5.3 molview
169
13.5.4 molarb
170
13.5.5 molrandom
170
13.5.6 molnear
171
13.5.7 molsame
171
References
172
Appendix 173
A.1 Introduction
173
A.2 Symbols and Bonds from Simplified Molecular Input Line Entry System (SMILES)
173
A.3 Normalizing Data
175
A.4 SQL Functions
176
A.4.1 Public166keys
176
A.4.2 Orsum
176
A.4.3 Tanimoto
176
A.4.4 Euclid
177
A.4.5 Hamming
177
A.4.6 Nbits_set
177
A.4.7 Amw
177
A.4.8 Tpsa
181
A.5 Tables Used in Functions
182
A.5.1 Amw
183
A.5.2 Tpsa
183
A.5.3 Public166keys
183
A.6 Core Function Implementation for PostgreSQL
188
A.6.1 PerlMol/plperlu
188
A.6.2 FROWNS/plpythonu
191
A.6.3 OpenBabel/python
197
A.7 C Language PostgreSQL Functions
203
A.8 Database Utilities Dbutils
205
A.9 Loading Files into Simple Tables
206
A.9.1 Smiloader
207
A.9.2 Sdfloader
208
References
210
Index 211
TJ O'Donnell
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