XML for Bioinformatics
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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application ATTLIST attribute base pairs bioinformatics BioJava BRCA2 browser BSML caBIO CDATA REQUIRED chapter characters child elements chromosome client complete complex type contain create DASDNA data sources data types database declaration default defined Distributed Annotation System DOCTYPE Document Type Definitions encoding encoding="UTF-8 Ensembl error example GBSeq GenBank gene genome annotation handler header identifier implementation import import import includes indicates instance document interaction interface Java JDOM LibXML Listing Markup Language method Namespace URI NCBI options parsing Perl protein protocol provides PSI-MI public void qName raw sequence data request retrieve root element SAXBuilder SEGMENT SOAP message specified String syntax System.out.println throws SAXException TinySeq type="xs:string UCSC validation web service WormBase XLinks XML document XML format XML Namespaces XML parser XML Schema XMLReader XPath xs:annotation xs:complexType xs:element xs:sequence XSLT