Synopses & Reviews
XML, or Extensible Markup Language, is rapidly becoming a critical tool in bioinformatics and biological data exchange. XML is currently used to represent a diverse set of biological data, from nucleotide and protein sequences to protein-protein interactions and signal transduction pathways. XML is also used in a wide array of bioinformatics applications, including stand-alone applications, federated database systems, distributed applications, and web services. The goal of XML for Bioinformatics is to provide a solid introduction to the emerging use of XML in the field of bioinformatics. It assumes no prior knowledge of XML, and illustrates all core concepts with specific bioinformatics examples and case studies. Core XML concepts include: fundamentals of XML, Document Type Definitions (DTDs), XML Namespaces, XML Schema, XML parsing in Perl and Java, web services and SOAP. Examples and case studies are drawn from a wide range of bioinformatics applications, including the Bioinformatic Sequence Markup Language (BSML), NCBI E-Fetch, the Distributed Annotation System (DAS), and the National Cancer Institute Cancer Bioinformatics Infrastructure Objects (caBIO) project. A companion web site, available at: http://www.xmlbio.org/, provides complete access to all examples in the book.
XML for Bioinformatics aims to provide biologists, software engineers, and bioinformatics professionals with a comprehensive introduction to XML and current XML applications in bioinformatics. The book will assume no background in XML, and take readers from basic to intermediate XML concepts. Core topics will include: fundamentals of XML, creating XML grammars, web services via SOAP, and parsing XML documents in Perl and Java.
About the Author
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.
Table of Contents
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.