Xml For Bioinformatics

by Cerami, Ethan

• ISBN13: 9780387230283
• ISBN10: 0387230289
• Format: Hardcover
• Copyright: 2005-03-30
• Publisher: Springer-Verlag New York Inc

Summary

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.

Author Biography

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	1	(16)
Introduction to XML	2	(5)
XML Defined	2	(2)
Origins of XML	4	(1)
The XML Family of Specifications	5	(1)
Web Services Defined	6	(1)
Using XML for Biological Data Exchange	7	(5)
Case Study: The Distributed Annotation System	8	(3)
XML Formats for Bioinformatics	11	(1)
Evaluating XML Usage in Bioinformatics	12	(2)
Advantages of XML	12	(1)
Disadvantages of XML	13	(1)
Useful Resources	14	(3)
Articles	14	(1)
Web Site and Web Resources	15	(2)
Fundamentals of XML and BSML	17	(32)
Getting Started with BSML	17	(5)
Using Genomic Workspace™	20	(2)
Fundamentals of XML	22	(9)
Working with Elements	22	(1)
Working with Attributes	23	(1)
The XML Prolog	24	(1)
Comments	24	(1)
Processing Instructions	24	(1)
Character Encoding	25	(1)
CDATA Sections	26	(1)
Creating Well-Formed XML Documents	27	(1)
Creating Valid XML Documents	28	(2)
Working with XML Parsers	30	(1)
Fundamentals of XML Namespaces	31	(4)
Why We Need XML Namespaces	31	(2)
Declaring and Using XML Namespaces	33	(1)
Declaring a Default Namespace	34	(1)
Fundamentals of BSML	35	(12)
BSML File Formats	36	(1)
BSML Document Structure	36	(2)
Representing Sequences	38	(1)
Representing Sequence Features	39	(6)
Retrieving Live BSML Data via XEMBL	45	(2)
Useful Resources	47	(2)
DTDs for Bioinformatics	49	(32)
Introduction to DTDs	49	(6)
A Bird's-Eye View: Protein DTD	50	(2)
Validating XML Documents	52	(3)
Document Type Declarations	55	(2)
Declaring Elements	57	(4)
EMPTY	57	(1)
ANY	58	(1)
#PCDATA	58	(1)
Child Elements	59	(1)
Mixed Content	60	(1)
Declaring Attributes	61	(5)
Attribute Types	62	(3)
Attribute Behaviors	65	(1)
Working with Entities	66	(6)
General Entities	66	(3)
Parameter Entities	69	(1)
Entity Summary	70	(1)
Conditional DTD Sections	70	(2)
Case Study: NCBI TinySeq	72	(9)
NCBI and XML	72	(1)
The TinySeq DTD	73	(8)
XML Schemas for Bioinformatics	81	(34)
Introduction to XML Schemas	81	(1)
XML Schemas for Bioinformatics	82	(1)
Essential Concepts: Representing Protein Data	82	(7)
The <schema> element	84	(2)
Schema Documentation	86	(1)
Simple Types vs. Complex Types	86	(1)
Global Elements vs. Local Elements	86	(1)
Creating Instance Documents	87	(1)
Validating Instance Documents	88	(1)
Working with Simple Types	89	(5)
Built-in Schema Types	89	(2)
Working with Facets	91	(3)
Working with Complex Types	94	(9)
Introduction to Complex Types	94	(2)
Declaring Empty Element Types	96	(1)
Declaring Mixed Element Types	97	(1)
Occurrence Constraints	98	(1)
Declaring Default Values	99	(1)
Compositors: Sequence and Choice	100	(2)
Defining Named Complex Types	102	(1)
All Together Now!	103	(1)
Basic Namespace Issues	103	(4)
Case Study: The HUPO PSI Molecular Interaction Format	107	(8)
PSI-MI Schema Overview	108	(1)
A Sample PSI-MI Instance Document	109	(4)
Working with the PSI-MI Controlled Vocabulary	113	(2)
Parsing NCBI XML in Perl	115	(22)
Introduction to XML Parsing in Perl	115	(3)
Tree-Based vs. Event-Based XML Parsers	116	(1)
Installing Modules via CPAN	117	(1)
The Simple API for XML (SAX)	118	(11)
Introduction to SAX	118	(1)
SAX and Bioinformatics Applications	118	(1)
SAX 2.0	119	(1)
Introduction to XML::SAX	119	(6)
Using NCBI EFetch and XML::SAX	125	(4)
The Document Object Model (DOM)	129	(8)
DOM Traversal with XML::LibXML	129	(3)
Validating XML Documents with XML::LibXML	132	(1)
Creating New Documents with XML::LibXML	132	(1)
Using NCBI EFetch and XML::LibXML	132	(5)
The Distributed Annotation System (DAS)	137	(38)
Genome Annotation	137	(3)
Introduction to DAS	140	(1)
The WormBase DAS Viewer	141	(1)
DAS Protocol Overview	141	(8)
Getting Started	144	(1)
DAS Requests	145	(1)
DAS Responses	146	(2)
X-DAS-Capabilities Header	148	(1)
DAS Command Reference	149	(19)
Retrieving Data Sources	149	(2)
Retrieving Entry Points	151	(2)
Retrieving Sequence Data	153	(2)
Retrieving Annotations	155	(13)
Working with Reference Maps	168	(4)
Traversing the Ensembl Reference Map	169	(2)
Working with Evolving Reference Maps	171	(1)
The Future of DAS	172	(3)
Parsing DAS Data with SAX	175	(40)
Introduction to SAX	175	(13)
A First Example	175	(4)
The XMLReader Interface	179	(3)
The ContentHandler Interface	182	(2)
Extending the DefaultHandler	184	(2)
Using InputSource Objects	186	(2)
Validating XML Documents	188	(9)
Checking for Well-Formedness	188	(2)
Validating XML Documents: Overview	190	(1)
Activating the SAX Validation Feature	191	(1)
The ErrorHandler Interface	191	(5)
Validating against XML Schemas	196	(1)
Elements, Attributes, and Namespaces	197	(7)
Working with Elements and Namespaces	197	(5)
Working with Attributes	202	(2)
Building Custom Data Structures with SAX	204	(11)
Parsing DAS Feature Data	204	(4)
Integrating with BioJava	208	(7)
Parsing DAS Data with JDOM	215	(32)
JDOM Basics	215	(6)
JDOM Package Overview	215	(1)
Parsing XML Documents with JDOM	216	(5)
Parsing DAS Documents with JDOM	221	(12)
Introduction to the JDOM Element API	221	(3)
Traversing DAS Documents	224	(5)
Parsing DAS dsn Documents	229	(4)
Creating DAS Documents with JDOM	233	(5)
Creating New Documents	233	(1)
Creating New Elements	234	(1)
A Complete Example	235	(3)
Building the JDAS Library	238	(9)
Using JDAS	238	(5)
The JDAS Source Code	243	(4)
Web Services for Bioinformatics	247	(36)
Introduction to Web Services	247	(4)
Web Services Defined	247	(3)
Architectural Options	250	(1)
Case Study: Introduction to the NCI caBIO Project	251	(6)
Background: Connecting to caBIO via the Java RMI Interface	253	(4)
Introduction to REST-Based Web Services	257	(10)
Introduction to REST	257	(1)
Connecting to the caBIO REST Interface	258	(4)
Example Application: Command Line caBIO Browser	262	(5)
Introduction to SOAP	267	(8)
SOAP Overview	268	(2)
Constructing SOAP Messages	270	(3)
Transporting SOAP via HTTP	273	(2)
Introduction to Apache Axis	275	(8)
Building a Web Service with Axis	276	(5)
Connecting to caBIO with Axis	281	(2)
Appendix	283	(2)
1 Nucleotide Base Codes	283	(1)
2 Amino Acid Codes	283	(2)
Bibliography	285	(6)
Index	291