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.

Annotation
Document Object Model (DOM)
Extensible Markup Language (XML)
Java
Perl
SOAP
Service Oriented Architecture (SOA)
bioinformatics

• Front Matter
• Introduction to XML for Bioinformatics
• Fundamentals of XML and BSML
• DTDs for Bioinformatics
• XML Schemas for Bioinformatics
• Parsing NCBI XML in Perl
• The Distributed Annotation System (DAS)
• Parsing DAS Data with SAX
• Parsing DAS Data with JDOM
• Web Services for Bioinformatics
• Back Matter

Ethan Cerami is Senior Software Engineer at the Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY. Since 1997 he has also been a member of the Adjunct Faculty in Computer Science at New York University.

Book Title
XML for Bioinformatics

Authors
Ethan Cerami

DOI
https://doi.org/10.1007/0-387-27478-2

Hardcover ISBN
978-0-387-23028-3
Published: 15 March 2005

Softcover ISBN
978-1-4419-1998-4
Published: 24 December 2010

eBook ISBN
978-0-387-27478-2
Published: 02 June 2006

Edition Number
1

Number of Pages
XVI, 304

Number of Illustrations
59 b/w illustrations

Topics
Programming Languages, Compilers, Interpreters, Special Purpose and Application-Based Systems, Computer Systems Organization and Communication Networks, Coding and Information Theory, Bioinformatics