Abhishek Tiwari:SOAP/WSDL based webservices for Biological Databases

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Using SOAP/WSDL to access the Biological Databases

Intoduction

SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/ws) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. When large amounts of data need to be retrieved and analysed, this often proves to be tedious and impractical. Today, biological databases are large collections of data that are relatively difficult to maintain outside the centres and institutions that produce them. These data are traditionally accessed using browser-based World Wide Web interfaces. When large amounts of data need to be retrieved and analysed, this often proves to be tedious and impractical. Web Services technology enables scientists to access these data and analysis applications as if they were installed on their laboratory computers. Similarly, it enables programmers to build complex applications without the need to install and maintain the databases and analysis tools (1) and without having to take on the financial overheads that accompany these. Moreover, Web Services provide easier integration and interoperability between bioinformatics applications and the data they require.

Web service

The W3C defines a Web service as a software system designed to support interoperable machine-to-machine interaction over a network. Web services are frequently just application programming interfaces (API) that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.he specifications that define Web services are intentionally modular, and as a result there is no one document that defines it. Instead, there are a few "core" specifications that are supplemented by others as the circumstances and choice of technology dictate. The most common are:

   * SOAP: An XML-based, extensible message envelope format, with "bindings" to underlying protocols (e.g., HTTP, SMTP and XMPP).
   * WSDL: An XML format that allows service interfaces to be described, along with the details of their bindings to specific protocols. Typically used to generate server and client code, and for configuration.
   * UDDI: A protocol for publishing and discovering metadata about Web services, to enable applications to find Web services, ei

SOAP (originally Simple Object Access Protocol) is a protocol for exchanging XML-based messages over computer network, normally using HTTP. Both SMTP and HTTP are valid application layer protocols for SOAP, but HTTP has gained wider acceptance as it works well with today's Internet infrastructure; specifically, SOAP works well with network firewalls. XML was chosen as the standard message format because of its widespread use by major corporations and open source development efforts. Additionally, a wide variety of freely available tools significantly ease the transition to a SOAP-based implementation.

WSDL is an XML-based service description on how to communicate using the web service; namely, the protocol bindings and message formats required to interact with the web services listed in its directory. The supported operations and messages are described abstractly, and then bound to a concrete network protocol and message format. This means that WSDL describes the public interface to the web service.WSDL is often used in combination with SOAP and XML Schema to provide web services over the Internet. A client program connecting to a web service can read the WSDL to determine what functions are available on the server. Any special datatypes used are embedded in the WSDL file in the form of XML Schema. The client can then use SOAP to actually call one of the functions listed in the WSDL.

Web Services uses SOAP (the Simple Object Access Protocol) over HTTP. It interacts with other systems using messages based on Xtensible Markup Language (XML) (http://www.w3.org/XML). A SOAP message can be transferred using almost any application or transport protocol. SOAP uses the Web Services Description Language (WSDL) (http://www.w3.org/TR/wsdl) to describe its interface. A SOAP client can read the WSDL at runtime and dynamically select the proper data-encoding scheme and network transfer protocol. SOAP implementations are available for many programming languages, including Perl and Java, which are popular languages among bioinformaticians.