XML for Bioinformatics

Front Cover
Springer Science & Business Media, Jun 2, 2006 - Computers - 304 pages
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.
 

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Contents

I
1
II
2
III
7
IV
12
V
14
VI
17
VIII
22
IX
31
XXIX
129
XXX
137
XXXII
140
XXXIII
141
XXXIV
149
XXXV
168
XXXVI
172
XXXVII
175

X
35
XI
47
XII
49
XIV
55
XV
57
XVI
61
XVII
66
XVIII
72
XIX
81
XXI
82
XXII
89
XXIII
94
XXIV
103
XXV
107
XXVI
115
XXVIII
118
XXXIX
188
XL
197
XLI
204
XLII
215
XLIV
221
XLV
233
XLVI
238
XLVII
247
XLIX
251
L
257
LI
267
LII
275
LIII
283
LIV
285
LV
291
Copyright

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About the author (2006)

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.