XML for Bioinformatics

By: Ethan Cerami

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Hardcover | 11 April 2005

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Hardcover
324 Pages

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23.5 x 18.42 x 1.91

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Introduction The goal of this book is to introduce XML to a bioinformatics audience. It does so by introducing the fundamentals of XML, Document Type De?nitions (DTDs), XML Namespaces, XML Schema, and XML parsing, and illustrating these concepts with speci?c bioinformatics case studies. The book does not assume any previous knowledge of XML and is geared toward those who want a solid introduction to fundamental XML concepts. The book is divided into nine chapters: Chapter 1: Introduction to XML for Bioinformatics. This chapter provides an introduction to XML and describes the use of XML in biological data exchange. A bird's-eye view of our ?rst case study, the Distributed Annotation System (DAS), is provided and we examine a sample DAS XML document. The chapter concludes with a discussion of the pros and cons of using XML in bioinformatic applications. Chapter 2: Fundamentals of XML and BSML. This chapter introduces the fundamental concepts of XML and the Bioinformatic Sequence Markup Language (BSML). We explore the origins of XML, de?ne basic rules for XML document structure, and introduce XML Na- spaces. We also explore several sample BSML documents and visualize these documents in the TM Rescentris Genomic Workspace Viewer.

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Introduction to XML for Bioinformatics	p. 1
Introduction to XML	p. 2
XML Defined	p. 2
Origins of XML	p. 4
The XML Family of Specifications	p. 5
Web Services Defined	p. 6
Using XML for Biological Data Exchange	p. 7
Case Study: The Distributed Annotation System	p. 8
XML Formats for Bioinformatics	p. 11
Evaluating XML Usage in Bioinformatics	p. 12
Advantages of XML	p. 12
Disadvantages of XML	p. 13
Useful Resources	p. 14
Articles	p. 14
Web Site and Web Resources	p. 15
Fundamentals of XML and BSML	p. 17
Getting Started with BSML	p. 17
Using Genomic Workspace	p. 20
Fundamentals of XML	p. 22
Working with Elements	p. 22
Working with Attributes	p. 23
The XML Prolog	p. 24
Comments	p. 24
Processing Instructions	p. 24
Character Encoding	p. 25
CDATA Sections	p. 26
Creating Well-Formed XML Documents	p. 27
Creating Valid XML Documents	p. 28
Working with XML Parsers	p. 30
Fundamentals of XML Namespaces	p. 31
Why We Need XML Namespaces	p. 31
Declaring and Using XML Namespaces	p. 33
Declaring a Default Namespace	p. 34
Fundamentals of BSML	p. 35
BSML File Formats	p. 36
BSML Document Structure	p. 36
Representing Sequences	p. 38
Representing Sequence Features	p. 39
Retrieving Live BSML Data via XEMBL	p. 45
Useful Resources	p. 47
DTDs for Bioinformatics	p. 49
Introduction to DTDs	p. 49
A Bird's-Eye View: Protein DTD	p. 50
Validating XML Documents	p. 52
Document Type Declarations	p. 55
Declaring Elements	p. 57
EMPTY	p. 57
ANY	p. 58
#PCDATA	p. 58
Child Elements	p. 59
Mixed Content	p. 60
Declaring Attributes	p. 61
Attribute Types	p. 62
Attribute Behaviors	p. 65
Working with Entities	p. 66
General Entities	p. 66
Parameter Entities	p. 69
Entity Summary	p. 70
Conditional DTD Sections	p. 70
Case Study: NCBI TinySeq	p. 72
NCBI and XML	p. 72
The TinySeq DTD	p. 73
XML Schemas for Bioinformatics	p. 81
Introduction to XML Schemas	p. 81
XML Schemas for Bioinformatics	p. 82
Essential Concepts: Representing Protein Data	p. 82
The [left angle bracket]schema[right angle bracket] element	p. 84
Schema Documentation	p. 86
Simple Types vs. Complex Types	p. 86
Global Elements vs. Local Elements	p. 86
Creating Instance Documents	p. 87
Validating Instance Documents	p. 88
Working with Simple Types	p. 89
Built-in Schema Types	p. 89
Working with Facets	p. 91
Working with Complex Types	p. 94
Introduction to Complex Types	p. 94
Declaring Empty Element Types	p. 96
Declaring Mixed Element Types	p. 97
Occurrence Constraints	p. 98
Declaring Default Values	p. 99
Compositors: Sequence and Choice	p. 100
Defining Named Complex Types	p. 102
All Together Now!	p. 103
Basic Namespace Issues	p. 103
Case Study: The HUPO PSI Molecular Interaction Format	p. 107
PSI-MI Schema Overview	p. 108
A Sample PSI-MI Instance Document	p. 109
Working with the PSI-MI Controlled Vocabulary	p. 113
Parsing NCBI XML in Perl	p. 115
Introduction to XML Parsing in Perl	p. 115
Tree-Based vs. Event-Based XML Parsers	p. 116
Installing Modules via CPAN	p. 117
The Simple API for XML (SAX)	p. 118
Introduction to SAX	p. 118
SAX and Bioinformatics Applications	p. 118
SAX 2.0	p. 119
Introduction to XML::SAX	p. 119
Using NCBI EFetch and XML::SAX	p. 125
The Document Object Model (DOM)	p. 129
DOM Traversal with XML::LibXML	p. 129
Validating XML Documents with XML::LibXML	p. 132
Creating New Documents with XML::LibXML	p. 132
Using NCBI EFetch and XML::LibXML	p. 132
The Distributed Annotation System (DAS)	p. 137
Genome Annotation	p. 137
Introduction to DAS	p. 140
The WormBase DAS Viewer	p. 141
DAS Protocol Overview	p. 141
Getting Started	p. 144
DAS Requests	p. 145
DAS Responses	p. 146
X-DAS-Capabilities Header	p. 148
DAS Command Reference	p. 149
Retrieving Data Sources	p. 149
Retrieving Entry Points	p. 151
Retrieving Sequence Data	p. 153
Retrieving Annotations	p. 155
Working with Reference Maps	p. 168
Traversing the Ensembl Reference Map	p. 169
Working with Evolving Reference Maps	p. 171
The Future of DAS	p. 172
Parsing DAS Data with SAX	p. 175
Introduction to SAX	p. 175
A First Example	p. 175
The XMLReader Interface	p. 179
The ContentHandler Interface	p. 182
Extending the DefaultHandler	p. 184
Using InputSource Objects	p. 186
Validating XML Documents	p. 188
Checking for Well-Formedness	p. 188
Validating XML Documents: Overview	p. 190
Activating the SAX Validation Feature	p. 191
The ErrorHandler Interface	p. 191
Validating against XML Schemas	p. 196
Elements, Attributes, and Namespaces	p. 197
Working with Elements and Namespaces	p. 197
Working with Attributes	p. 202
Building Custom Data Structures with SAX	p. 204
Parsing DAS Feature Data	p. 204
Integrating with BioJava	p. 208
Parsing DAS Data with JDOM	p. 215
JDOM Basics	p. 215
JDOM Package Overview	p. 215
Parsing XML Documents with JDOM	p. 216
Parsing DAS Documents with JDOM	p. 221
Introduction to the JDOM Element API	p. 221
Traversing DAS Documents	p. 224
Parsing DAS dsn Documents	p. 229
Creating DAS Documents with JDOM	p. 233
Creating New Documents	p. 233
Creating New Elements	p. 234
A Complete Example	p. 235
Building the JDAS Library	p. 238
Using JDAS	p. 238
The JDAS Source Code	p. 243
Web Services for Bioinformatics	p. 247
Introduction to Web Services	p. 247
Web Services Defined	p. 247
Architectural Options	p. 250
Case Study: Introduction to the NCI caBIO Project	p. 251
Background: Connecting to caBIO via the Java RMI Interface	p. 253
Introduction to REST-Based Web Services	p. 257
Introduction to REST	p. 257
Connecting to the caBIO REST Interface	p. 258
Example Application: Command Line caBIO Browser	p. 262
Introduction to SOAP	p. 267
SOAP Overview	p. 268
Constructing SOAP Messages	p. 270
Transporting SOAP via HTTP	p. 273
Introduction to Apache Axis	p. 275
Building a Web Service with Axis	p. 276
Connecting to caBIO with Axis	p. 281
Appendix	p. 283
Nucleotide Base Codes	p. 283
Amino Acid Codes	p. 283
Bibliography	p. 285
Index	p. 291
Table of Contents provided by Ingram. All Rights Reserved.

XML for Bioinformatics

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