Toc: Contents......Page 9 1. Introduction to XML for Bioinformatics......Page 14 1.1.1 XML Defined......Page 15 1.1.2 Origins of XML......Page 17 1.1.3 The XML Family of Specifications......Page 18 1.1.4 Web Services Defined......Page 19 1.2 Using XML for Biological Data Exchange......Page 20 1.2.1 Case Study: The Distributed Annotation System......Page 21 1.2.2 XML Formats for Bioinformatics......Page 24 1.3.1 Advantages of XML......Page 25 1.3.2 Disadvantages of XML......Page 26 1.4.1 Articles......Page 27 1.4.2 Web Site and Web Resources......Page 28 2.1 Getting Started with BSML......Page 29 2.1.1 Using Genomic Workspace™......Page 32 2.2.1 Working with Elements......Page 34 2.2.2 Working with Attributes......Page 35 2.2.5 Processing Instructions......Page 36 2.2.6 Character Encoding......Page 37 2.2.7 CDATA Sections......Page 38 2.2.8 Creating Well-Formed XML Documents......Page 39 2.2.9 Creating Valid XML Documents......Page 40 2.2.10 Working with XML Parsers......Page 42 2.3.1 Why We Need XML Namespaces......Page 43 2.3.2 Declaring and Using XML Namespaces......Page 45 2.3.3 Declaring a Default Namespace......Page 46 2.4 Fundamentals of BSML......Page 47 2.4.2 BSML Document Structure......Page 48 2.4.3 Representing Sequences......Page 50 2.4.4 Representing Sequence Features......Page 51 2.4.5 Retrieving Live BSML Data via XEMBL......Page 57 2.5 Useful Resources......Page 59 3.1 Introduction to DTDs......Page 61 3.1.1 A Bird's-Eye View: Protein DTD......Page 62 3.1.2 Validating XML Documents......Page 64 3.2 Document Type Declarations......Page 67 3.3.1 EMPTY......Page 69 3.3.3 #PCDATA......Page 70 3.3.4 Child Elements......Page 71 3.3.5 Mixed Content......Page 72 3.4 Declaring Attributes......Page 73 3.4.1 Attribute Types......Page 74 3.4.2 Attribute Behaviors......Page 77 3.5.1 General Entities......Page 78 3.5.2 Parameter Entities......Page 81 3.5.4 Conditional DTD Sections......Page 82 3.6.1 NCBI and XML......Page 84 3.6.2 The TinySeq DTD......Page 85 4.1 Introduction to XML Schemas......Page 92 4.2 Essential Concepts: Representing Protein Data......Page 93 4.2.1 The <schema> element......Page 95 4.2.4 Global Elements vs. Local Elements......Page 97 4.2.5 Creating Instance Documents......Page 98 4.2.6 Validating Instance Documents......Page 99 4.3.1 Built-in Schema Types......Page 100 4.3.2 Working with Facets......Page 102 4.4.1 Introduction to Complex Types