XML for Bioinformatics

1. Front Matter

   Pages i-xv

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2. Introduction to XML for Bioinformatics

   Pages 1-15

3. Fundamentals of XML and BSML

   Pages 17-48

4. DTDs for Bioinformatics

   Pages 49-79

5. XML Schemas for Bioinformatics

   Pages 81-114

6. Parsing NCBI XML in Perl

   Pages 115-135

7. The Distributed Annotation System (DAS)

   Pages 137-173

8. Parsing DAS Data with SAX

   Pages 175-213

9. Parsing DAS Data with JDOM

   Pages 215-246

10. Web Services for Bioinformatics

    Pages 247-282

11. Back Matter

    Pages 283-304

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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.

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

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.