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Title:
XML for Bioinformatics |
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Division: Genetics / Springer / 英文版 |
Author/Editor: Ethan Cerami Star:  |
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ISBN: 0387230289 |
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Introduce Date: 2006年08月19日20:54 , Release Date: 2006年08月19日22:25 |
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Introducer: kinginsun , Rate: 3/215 |
| Format: pdf(editorial) Download |
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| Description: |
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 assumes no background in XML, and take readers from basic to intermediate XML concepts. Core topics include: fundamentals of XML, creating XML grammars, web services via SOAP, and parsing XML documents in Perl and Java.
Table of Contents
Chapter 1: Introduction to XML for Bioinformatics
Chapter 2: Fundamentals of XML and BSML
Chapter 3: DTDs for Bioinformatics
Chapter 4: XML Schemas for Bioinformatics
Chapter 5: Parsing NCBI XML in Perl
Chapter 6: The Distributed Annotation System (DAS)
Chapter 7: Parsing DAS Data with SAX
Chapter 8: Parsing DAS Data with JDOM
Chapter 9: Web Services for Bioinformatics
Chapter 1: Introduction to XML for Bioinformatics
Examples:
Listing 1: A Nucleotide Sequence Record, encoded in HTML.
Listing 2: A Nucleotide Sequence Record, encoded in XML.
Select Resources:
Interoperable Informatics Infrastructure Consortium
Biodas.org: Home of the Distributed Annotation System (DAS)
The Annotated XML Specification. (Author: Tim Bray)
XML.com Bioinformatics Resources
Creating a bioinformatics nation (Author: Lincoln Stein.) Nature 417, 119–120 (9 May 2002)
Creating a bioinformatics nation (Author: Lincoln Stein.) PPT Slides from O'Reilly 2002 Bioinformatics Technology Conference.
Chapter 2: Fundamentals of XML and BSML
Examples:
Listing 1: The SARS virus, encoded in BSML.
Listing 2: The SARS Virus, Take 2. This example is identical to Listing 1, except that we have now added additional attributes.
Listing 3: The SARS Virus, Take 3. The record now includes a single non-positional feature, describing the direct submission to GenBank.
Listing 4: SARS Virus, Take 4. The record now includes a single positional feature.
Select Resources:
BSML Web Site: Bioinformatic Sequence Markup Language.
Rescentris Web Site
Rescentris Genomic Workspace™ Viewer
XEMBL Home Page @EMBL/EBI
The XML FAQ (Editor: Peter Flynn).
Extensible Markup Language (XML) 1.0 (Third Edition) (W3C Recommendation 04 February 2004).
Namespaces in XML (W3C Recommendation 14 January 1999).
Chapter 3: DTDs for Bioinformatics
Examples:
Listing 1: Sample DTD for representing protein data.
Listing 2: Sample instance document adhering to the protein DTD.
Listing 3: NCBI_TSeq.dtd
Listing 4: NCBI_Entity.mod
Listing 5: NCBI_TSeq.mod
Listing 6: Sample instance document adhering to the TinySeq DTD.
Select Resources:
A List of XML Editors from xmlsoftware.com
oXygen XML Editor
Altova XML Spy Software
Elcel Command Line XML Validator
Brown University Online XML Validator
NCBI Data in XML National Center for Biotechnology Information (NCBI).
Directory of all DTDs hosted at NCBI
Chapter 4: XML Schemas for Bioinformatics
Examples*:
Listing 1: protein.xsd
Listing 2: Sample protein instance document.
Listing 3: Illustrates basic use of XML Schema Facets.
Listing 4: Illustrates how to declare and reference a named simple type.
Listing 5: Using the pattern facet, first example.
Listing 6: Using the pattern facet, second example.
Listing 7: Using the enumeration facet.
Listing 8: An example of a complex type with simple content.
Listing 9: An example of a complex type with complex content.
Listing 10: An example of the abbreviated complexType syntax.
Listing 11: Declaring an Empty Element.
Listing 12: Declaring an Element with Mixed Content.
Listing 13: Using Occurrence Constraints.
Listing 14: Declaring a Default Value.
Listing 15: Declaring a Fixed Value.
Listing 16: Using the sequence compositor.
Listing 17: Using the choice compositor.
Listing 18: Combining Compositors.
Listing 19: Our final complex type example.
Listing 20: Using a Target Namespace.
Listing 21: Using the schemaLocation attribute.
Listing 22: Using the schemaLocation attribute with a default namespace.
Listing 23: Sample PSI-MI Instance Document.
Listing 24: PSI-MI XML Schema (complete).
Select Resources:
Sun Multi-Schema XML Validator
Proteomics Standards Initiative Web Site
Open Biological Ontologies (OBO) Web Site
Chapter 5: Parsing NCBI XML in Perl
Examples:
Listing 1: Excerpt of a Sample GBSeq Document from NCBI.
Listing 2: First XML::SAX Application.
Listing 3: ContentReporter.pm
Listing 4: Parsing NCBI EFetch Data via the SAX API.
Listing 5: NcbiHandler.pm
Listing 6: First DOM Example.
Listing 7: Creating a TinySeq XML Document via the DOM API.
Listing 8: Parsing NCBI EFetch Data via the DOM API.
Select Resources:
Perl-XML FAQ (Editor: Grant McLean).
Perl CPAN Documentation
SAX Web Site
NCBI E-Fetch Help Page
LibXML Perl Module
Chapter 6: The Distributed Annotation System (DAS)
Examples:
Listing 1: DAS Response from TIGR. Note that the complete DAS response includes a total of 13 FEATURE elements. For brevity, only the first three FEATURE elements are included here.
Select Resources:
Biodas.org: Home of the Distributed Annotation System (DAS)
Ensembl Genome Browser
Wormbase.org Genome Browser
TIGR DAS Viewers
BioJava DAS Client
OmniGene: Standardizing Biological Data Interchange Through Web Services Technology
List of Public DAS Servers (Maintained at TIGR).
GFF (General Feature Format) Specifications Document
Sequence Ontology Project
Chapter 7: Parsing DAS Data with SAX
Examples:
Listing 1: ensembl_dna.xml
Listing 2: SAXBasic.java
Listing 3: SAXDefaultHandler.java
Listing 4: ensembl_dna_error.xml. The second end tag has been removed, and the document is therefore no longer well-formed.
Listing 5: SAXValidator.java
Listing 6: ensembl_dna_invalid.xml. The id attributes have been removed and the document is therefore no longer valid.
Listing 7: SAXElementNamespace.java
Listing 8: Sample SPTr-XML File. For brevity, we have only included a small excerpt of the file.
Listing 9: Feature.java
Listing 10: DASHandler.java
Listing 11: FeatureViewer.java
Listing 12: DASProcessor.java
Select Resources:
Xerces 2 Java Parser
Piccolo XML Parser for Java
SAX Project Web Site
SAX 2.0 Javadoc
BioJava.org Web Site
Chapter 8: Parsing DAS Data with JDOM
Examples:
Listing 1: JDOMBasic.java
Listing 2: JDOMValidator.java
Listing 3: DASWalker.java
Listing 4: DAS DSN Response from Wormbase.org
Listing 5: DAS_DSNProcessor.java
Listing 6: DASCreator.java
Listing 7: SampleDsnRequest.java
Listing 8: DsnResponse.java
Select Resources:
JDOM Web Site
JDOM API
Jaxen XPath Engine
JDAS
Chapter 9: Web Services for Bioinformatics
Examples:
Listing 1: caBioBrowser.java. Command Line caBIO Browser.
Listing 2: A Sample SOAP Request.
Listing 3: A Sample SOAP Response.
Listing 4: BioService1.java. A Simple Bioinformatics Web Service.
Listing 5: A Web Services Deployment Descriptor (WSDD) File. Deploys the BioService.
Listing 6: A Web Services Deployment Descriptor (WSDD) File. Undeploys the BioService.
Listing 7: BioClient1.java.
Listing 8: GeneSoap.java.
Select Resources:
Cancer Bioinformatics Infrastructure Objects (caBIO): National Cancer Institute, U.S. National Institutes of Health.
BioBrowser: Author: Jonny Wray.
XEMBL Web Service: European Bioinformatics Institute (EBI).
DNA Database of Japan SOAP Project
Apache Axis: The Apache Software Foundation.
Apache Axis User Guide: The Apache Software Foundation.
* Some of these XML Document / XML Schema fragments may not render in Internet Explorer. Try right clicking, and select "Save Target As...".
Product Details
Hardcover: 304 pages
Publisher: Springer; 1 edition (March 15, 2005)
Language: English
ISBN: 0387230289
Product Dimensions: 9.4 x 7.3 x 0.8 inches
Shipping Weight: 1.43 pounds (View shipping rates and policies)
Average Customer Review: based on 1 review. (Write a review.)
Amazon.com Sales Rank: #634,479 in Books (See Top Sellers in Books)
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