XML for bioinformatics [electronic book] / Ethan Cerami.

By: Cerami, Ethan [author.].

Material type: materialTypeLabel

BookPublisher: New York : Springer, [2005]Copyright date: ©2005Description: online resource (xv, 304 pages) : illustrations.Content type: text Media type: computer Carrier type: online resourceISBN: 9780387230283 (hardback); 0387230289 (hardback); 9780387274782 (e-book) .Subject(s): XML (Document markup language)

| Bioinformatics

DDC classification: 572.80285674 Online resources: E-book

List(s) this item appears in: E-BOOK LIST

Holdings
Item type	Current library	Call number	Status	Notes	Date due	Barcode	Item holds
e-BOOK	MTU Bishopstown Library eBook	572.80285674 (Browse shelf(Opens below))	Not for loan	MTU Module SOFT 9019 - Recommended reading.

Total holds: 0

Enhanced descriptions from Syndetics:

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.

Includes bibliographical references and index.

MTU Module SOFT 9019 - Recommended reading.

CIT Module SOFT 9019 - Core reading.

Electronic reproduction.: Dawson. Model of access: World Wide Web.

Electronic reproduction.: ProQuest LibCentral. Model of access: World Wide Web.

Table of contents provided by Syndetics

1 Introduction to XML for Bioinformatics (p. 1)
1.1 Introduction to XML (p. 2)
1.1.1 XML Defined (p. 2)
1.1.2 Origins of XML (p. 4)
1.1.3 The XML Family of Specifications (p. 5)
1.1.4 Web Services Defined (p. 6)
1.2 Using XML for Biological Data Exchange (p. 7)
1.2.1 Case Study: The Distributed Annotation System (p. 8)
1.2.2 XML Formats for Bioinformatics (p. 11)
1.3 Evaluating XML Usage in Bioinformatics (p. 12)
1.3.1 Advantages of XML (p. 12)
1.3.2 Disadvantages of XML (p. 13)
1.4 Useful Resources (p. 14)
1.4.1 Articles (p. 14)
1.4.2 Web Site and Web Resources (p. 15)
2 Fundamentals of XML and BSML (p. 17)
2.1 Getting Started with BSML (p. 17)
2.1.1 Using Genomic Workspace (p. 20)
2.2 Fundamentals of XML (p. 22)
2.2.1 Working with Elements (p. 22)
2.2.2 Working with Attributes (p. 23)
2.2.3 The XML Prolog (p. 24)
2.2.4 Comments (p. 24)
2.2.5 Processing Instructions (p. 24)
2.2.6 Character Encoding (p. 25)
2.2.7 CDATA Sections (p. 26)
2.2.8 Creating Well-Formed XML Documents (p. 27)
2.2.9 Creating Valid XML Documents (p. 28)
2.2.10 Working with XML Parsers (p. 30)
2.3 Fundamentals of XML Namespaces (p. 31)
2.3.1 Why We Need XML Namespaces (p. 31)
2.3.2 Declaring and Using XML Namespaces (p. 33)
2.3.3 Declaring a Default Namespace (p. 34)
2.4 Fundamentals of BSML (p. 35)
2.4.1 BSML File Formats (p. 36)
2.4.2 BSML Document Structure (p. 36)
2.4.3 Representing Sequences (p. 38)
2.4.4 Representing Sequence Features (p. 39)
2.4.5 Retrieving Live BSML Data via XEMBL (p. 45)
2.5 Useful Resources (p. 47)
3 DTDs for Bioinformatics (p. 49)
3.1 Introduction to DTDs (p. 49)
3.1.1 A Bird's-Eye View: Protein DTD (p. 50)
3.1.2 Validating XML Documents (p. 52)
3.2 Document Type Declarations (p. 55)
3.3 Declaring Elements (p. 57)
3.3.1 EMPTY (p. 57)
3.3.2 ANY (p. 58)
3.3.3 #PCDATA (p. 58)
3.3.4 Child Elements (p. 59)
3.3.5 Mixed Content (p. 60)
3.4 Declaring Attributes (p. 61)
3.4.1 Attribute Types (p. 62)
3.4.2 Attribute Behaviors (p. 65)
3.5 Working with Entities (p. 66)
3.5.1 General Entities (p. 66)
3.5.2 Parameter Entities (p. 69)
3.5.3 Entity Summary (p. 70)
3.5.4 Conditional DTD Sections (p. 70)
3.6 Case Study: NCBI TinySeq (p. 72)
3.6.1 NCBI and XML (p. 72)
3.6.2 The TinySeq DTD (p. 73)
4 XML Schemas for Bioinformatics (p. 81)
4.1 Introduction to XML Schemas (p. 81)
4.1.1 XML Schemas for Bioinformatics (p. 82)
4.2 Essential Concepts: Representing Protein Data (p. 82)
4.2.1 The [left angle bracket]schema[right angle bracket] element (p. 84)
4.2.2 Schema Documentation (p. 86)
4.2.3 Simple Types vs. Complex Types (p. 86)
4.2.4 Global Elements vs. Local Elements (p. 86)
4.2.5 Creating Instance Documents (p. 87)
4.2.6 Validating Instance Documents (p. 88)
4.3 Working with Simple Types (p. 89)
4.3.1 Built-in Schema Types (p. 89)
4.3.2 Working with Facets (p. 91)
4.4 Working with Complex Types (p. 94)
4.4.1 Introduction to Complex Types (p. 94)
4.4.2 Declaring Empty Element Types (p. 96)
4.4.3 Declaring Mixed Element Types (p. 97)
4.4.4 Occurrence Constraints (p. 98)
4.4.5 Declaring Default Values (p. 99)
4.4.6 Compositors: Sequence and Choice (p. 100)
4.4.7 Defining Named Complex Types (p. 102)
4.4.8 All Together Now! (p. 103)
4.5 Basic Namespace Issues (p. 103)
4.6 Case Study: The HUPO PSI Molecular Interaction Format (p. 107)
4.6.1 PSI-MI Schema Overview (p. 108)
4.6.2 A Sample PSI-MI Instance Document (p. 109)
4.6.3 Working with the PSI-MI Controlled Vocabulary (p. 113)
5 Parsing NCBI XML in Perl (p. 115)
5.1 Introduction to XML Parsing in Perl (p. 115)
5.1.1 Tree-Based vs. Event-Based XML Parsers (p. 116)
5.1.2 Installing Modules via CPAN (p. 117)
5.2 The Simple API for XML (SAX) (p. 118)
5.2.1 Introduction to SAX (p. 118)
5.2.2 SAX and Bioinformatics Applications (p. 118)
5.2.3 SAX 2.0 (p. 119)
5.2.4 Introduction to XML::SAX (p. 119)
5.2.5 Using NCBI EFetch and XML::SAX (p. 125)
5.3 The Document Object Model (DOM) (p. 129)
5.3.1 DOM Traversal with XML::LibXML (p. 129)
5.3.2 Validating XML Documents with XML::LibXML (p. 132)
5.3.3 Creating New Documents with XML::LibXML (p. 132)
5.3.4 Using NCBI EFetch and XML::LibXML (p. 132)
6 The Distributed Annotation System (DAS) (p. 137)
6.1 Genome Annotation (p. 137)
6.2 Introduction to DAS (p. 140)
6.2.1 The WormBase DAS Viewer (p. 141)
6.3 DAS Protocol Overview (p. 141)
6.3.1 Getting Started (p. 144)
6.3.2 DAS Requests (p. 145)
6.3.3 DAS Responses (p. 146)
6.3.4 X-DAS-Capabilities Header (p. 148)
6.4 DAS Command Reference (p. 149)
6.4.1 Retrieving Data Sources (p. 149)
6.4.2 Retrieving Entry Points (p. 151)
6.4.3 Retrieving Sequence Data (p. 153)
6.4.4 Retrieving Annotations (p. 155)
6.5 Working with Reference Maps (p. 168)
6.5.1 Traversing the Ensembl Reference Map (p. 169)
6.5.2 Working with Evolving Reference Maps (p. 171)
6.6 The Future of DAS (p. 172)
7 Parsing DAS Data with SAX (p. 175)
7.1 Introduction to SAX (p. 175)
7.1.1 A First Example (p. 175)
7.1.2 The XMLReader Interface (p. 179)
7.1.3 The ContentHandler Interface (p. 182)
7.1.4 Extending the DefaultHandler (p. 184)
7.1.5 Using InputSource Objects (p. 186)
7.2 Validating XML Documents (p. 188)
7.2.1 Checking for Well-Formedness (p. 188)
7.2.2 Validating XML Documents: Overview (p. 190)
7.2.3 Activating the SAX Validation Feature (p. 191)
7.2.4 The ErrorHandler Interface (p. 191)
7.2.5 Validating against XML Schemas (p. 196)
7.3 Elements, Attributes, and Namespaces (p. 197)
7.3.1 Working with Elements and Namespaces (p. 197)
7.3.2 Working with Attributes (p. 202)
7.4 Building Custom Data Structures with SAX (p. 204)
7.4.1 Parsing DAS Feature Data (p. 204)
7.4.2 Integrating with BioJava (p. 208)
8 Parsing DAS Data with JDOM (p. 215)
8.1 JDOM Basics (p. 215)
8.1.1 JDOM Package Overview (p. 215)
8.1.2 Parsing XML Documents with JDOM (p. 216)
8.2 Parsing DAS Documents with JDOM (p. 221)
8.2.1 Introduction to the JDOM Element API (p. 221)
8.2.2 Traversing DAS Documents (p. 224)
8.2.3 Parsing DAS dsn Documents (p. 229)
8.3 Creating DAS Documents with JDOM (p. 233)
8.3.1 Creating New Documents (p. 233)
8.3.2 Creating New Elements (p. 234)
8.3.3 A Complete Example (p. 235)
8.4 Building the JDAS Library (p. 238)
8.4.1 Using JDAS (p. 238)
8.4.2 The JDAS Source Code (p. 243)
9 Web Services for Bioinformatics (p. 247)
9.1 Introduction to Web Services (p. 247)
9.1.1 Web Services Defined (p. 247)
9.1.2 Architectural Options (p. 250)
9.2 Case Study: Introduction to the NCI caBIO Project (p. 251)
9.2.1 Background: Connecting to caBIO via the Java RMI Interface (p. 253)
9.3 Introduction to REST-Based Web Services (p. 257)
9.3.1 Introduction to REST (p. 257)
9.3.2 Connecting to the caBIO REST Interface (p. 258)
9.3.3 Example Application: Command Line caBIO Browser (p. 262)
9.4 Introduction to SOAP (p. 267)
9.4.1 SOAP Overview (p. 268)
9.4.2 Constructing SOAP Messages (p. 270)
9.4.3 Transporting SOAP via HTTP (p. 273)
9.5 Introduction to Apache Axis (p. 275)
9.5.1 Building a Web Service with Axis (p. 276)
9.5.2 Connecting to caBIO with Axis (p. 281)
Appendix (p. 283)
1 Nucleotide Base Codes (p. 283)
2 Amino Acid Codes (p. 283)
Bibliography (p. 285)
Index (p. 291)

Author notes provided by Syndetics

Ethan Cerami is a Senior Software Engineer at the Computational Biology Center at Memorial Sloan-Kettering Cancer Center