Toc: Contents......Page 91. Introduction to XML for Bioinformatics......Page 141.1.1 XML Defined......Page 151.1.2 Origins of XML......Page 171.1.3 The XML Family of Specifications......Page 181.1.4 Web Services Defined......Page 191.2 Using XML for Biological Data Exchange......Page 201.2.1 Case Study: The Distributed Annotation System......Page 211.2.2 XML Formats for Bioinformatics......Page 241.3.1 Advantages of XML......Page 251.3.2 Disadvantages of XML......Page 261.4.1 Articles......Page 271.4.2 Web Site and Web Resources......Page 282.1 Getting Started with BSML......Page 292.1.1 Using Genomic Workspace™......Page 322.2.1 Working with Elements......Page 342.2.2 Working with Attributes......Page 352.2.5 Processing Instructions......Page 362.2.6 Character Encoding......Page 372.2.7 CDATA Sections......Page 382.2.8 Creating Well-Formed XML Documents......Page 392.2.9 Creating Valid XML Documents......Page 402.2.10 Working with XML Parsers......Page 422.3.1 Why We Need XML Namespaces......Page 432.3.2 Declaring and Using XML Namespaces......Page 452.3.3 Declaring a Default Namespace......Page 462.4 Fundamentals of BSML......Page 472.4.2 BSML Document Structure......Page 482.4.3 Representing Sequences......Page 502.4.4 Representing Sequence Features......Page 512.4.5 Retrieving Live BSML Data via XEMBL......Page 572.5 Useful Resources......Page 593.1 Introduction to DTDs......Page 613.1.1 A Bird's-Eye View: Protein DTD......Page 623.1.2 Validating XML Documents......Page 643.2 Document Type Declarations......Page 673.3.1 EMPTY......Page 693.3.3 #PCDATA......Page 703.3.4 Child Elements......Page 713.3.5 Mixed Content......Page 723.4 Declaring Attributes......Page 733.4.1 Attribute Types......Page 743.4.2 Attribute Behaviors......Page 773.5.1 General Entities......Page 783.5.2 Parameter Entities......Page 813.5.4 Conditional DTD Sections......Page 823.6.1 NCBI and XML......Page 843.6.2 The TinySeq DTD......Page 854.1 Introduction to XML Schemas......Page 924.2 Essential Concepts: Representing Protein Data......Page 934.2.1 The <schema> element......Page 954.2.4 Global Elements vs. Local Elements......Page 974.2.5 Creating Instance Documents......Page 984.2.6 Validating Instance Documents......Page 994.3.1 Built-in Schema Types......Page 1004.3.2 Working with Facets......Page 1024.4.1 Introduction to Complex Types