XML for Bioinformatics

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Introduction to XML for Bioinformatics.- Fundamentals of XML and BSML.- Fundamentals of DTDs and the NCBI TinySeq DTD.- Fundamentals of XML Schemas and PSI-MI.- Parsing PSI-MI Data in Perl.- The Distributed Annotation System (DAS).- Parsing DAS Data via SAX.- Parsing DAS Data via JDOM.- Using SOAP to Integrate Biological Data.
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.
Autor: Ethan Cerami
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.

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Autor: Ethan Cerami
ISBN-13 :: 9781441919984
ISBN: 1441919988
Erscheinungsjahr: 24.12.2010
Verlag: Springer New York
Gewicht: 557g
Seiten: 320
Sprache: Englisch
Auflage Softcover reprint of hardcover 1st ed. 2005.
Sonstiges: Taschenbuch, 235x178x17 mm
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