Abhishek Tiwari:SOAP/WSDL based webservices for Biological Databases

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Using SOAP/WSDL to access the Biological/Bioinformatics Databases


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.

Accessing the Biological Databases

Entrez Utilities Web Service http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html

The NCBI Web service is a web program that enables developers to access Entrez Utilities via the Simple Object Access Protocol (SOAP). Programmers may write software applications that access the E-Utilities using any SOAP development tool.Version 1.5 provides access to EGQuery, EFetch, EInfo, ELink, ESearch, ESpell, and ESummary utilities.

KEGG API http://www.genome.jp/kegg/soap/

KEGG is a suite of databases including GENES, SSDB, PATHWAY, LIGAND, LinkDB, etc. for genome research and related research areas in molecular and cellular biology. KEGG API provides valuable means for accessing the KEGG system, such as for searching and computing biochemical pathways in cellular processes or analyzing the universe of genes in the completely sequenced genomes. The users can access the KEGG API server by the SOAP technology over the HTTP protocol. The SOAP server also comes with the WSDL, which makes it easy to build a client library for a specific computer language. This enables the users to write their own programs for many different purposes and to automate the procedure of accessing the KEGG API server and retrieving the results.

Also see DDBJ-SOAP Project http://xml.nig.ac.jp/soapp.html

EBI Web Services http://www.ebi.ac.uk/Tools/webservices/

The European Bioinformatics Institute (EBI) is using SOAP based technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides.Current services by EBI Web Services

  • Data retrieval
  • Analysis tools
  • Homology searches
  • Multiple Alignment
  • Structural analysis
  • Literature and ontologies

BIND SOAP http://soap.bind.ca/

BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API). This means that users can access and compute on BIND interaction, molecular complex, and pathway data directly within thier application. Since the web service is based on SOAP, users are not limited in choice of platform or object oriented language used to develop their application.

Read More

  • Top Ten FAQs for Web Services[1]
  • Using WSDL in SOAP applications[3]
  • Bioinformatics Open Source Conference 2004[4]

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