Objects

Objects define attributes (data) and Methods
Objects can be extended, and inherit the attributes and methods of their parent classes

Class: Waterfowl
Data: Bill(String), Webbed Feet, Neck(String)
Methods: Walk(String), Vocalization(String)

Class: Duck extends Waterfowl
Data: Bill ("wide"), Neck("short")
Methods: Walk ("waddle"), Vocalization("quack")

Class: Goose extends Waterfowl
Data: Bill ("long"), Neck("long")
Methods: Walk ("waddle"), Vocalization("honk")

XML - Extended Markup Language

XML is a language designed for objects. Languages such as Java, C++, Perl and Python, are designed to allow networked objects to communicate with one another. The nature of the data must be hard-coded into the programs, or into the database definition.

Another approach to data interchange between objects is XML. XML is a protocol for defining datafile formats. It is not a file format per se. Rather, XML standardizes how data files are defined.

Although XML is still an evolving set of protocols, several components are critical to XML:

Data Definition

DTD - Document Type Definition
Remember, XML is not so much a language as a standard for describing a data object. For each new type of data object it is necessary to write a DTD to specify how the object is structured. The names of all elements and their components are defined.

Sample DTD file for GenBank entries used by gb2xml by Phillipe Bouige [genbank.dtd.txt ].
Schema
The DTD is limited to the description of data elements with simple text fields. While this model is adequate for most text documents, the definition of more complex data elements requires a schema. A schema (written in XML) describes relationships between data objects, as in a database. Numeric elements can also be described, unlike DTDs, in which numbers are represented as text. Constraints can be placed on data elements (eg. nucleotide can take the value A,G,C,T,U or N; the number of strands may have the value 1 or 2). The specification of constraints in the schema makes it possible to automatically validate an XML file.

XML - an instance of data following the specifications of the DTD or schema
Usually, an application will check each XML file to make sure it conforms to the DTD. If valid, the XML file is read, and the corresponding data objects are created.
EXAMPLE: The XML file U11716.xml was created from GenBank entry U11716 was created by gb2xml using the DTD listed above.
XSL - XML stylesheet language
One of the most important uses for XML is as an alternative to HTML. HTML is limited to displaying text in a fairly simple fashion. XML allows the creation of rich data types. However, XML files, unlike HTML, don't specify how data are to be displayed in a browser. Therefore, XML stylesheets can be written for each type of XML file, providing a consistent structure to XML document presentation. Most of the major web browsers (Netscape, IE, Mozilla, Firefox) provide at least some XML support.

a -In this example, an application has been programmed to read a specific type of XML file. An object is created within the application based on the specifications in the XML file.

b - Conversely to a, an object in the application is translated to an XML representation, and written to a file.

c - This is a complex example. Data from a binary database is written to an XML file. At top, an client program, specialized for this particular XML data type, reads the XML and creates an object.

If a stylesheet exists for this XML data type, a browser can import the same XML file and render it as a Web page. In this case, a complex page, consisting of text, graphics, and a Java applet, is rendered.

XML is still evolving! Use with caution!
The standards for XML are still under development, particularly with regard to XSL stylesheets, XML schemas, and XML browsers. As well, in particular fields, numerous mutually incompatible DTDs may exist for the same type of data object! For example, an XML file for a DNA sequence or a protein, produced by one program, may be unreadable by another program, even though both programs can read XML.

Most of the widely-used languages (Java, C++, Python, Perl) have extensive libraries for reading, writing and manipulating XML objects.

For more information, see XML for Molecular Biology by Paul Gordon

http://www.visualgenomics.ca/gordonp/xml/

http://home.cc.umanitoba.ca/~frist/Seminars/iims07/iims07.html