Today, biological databases comprise large collections of data that are relatively difficult to maintain outside the centres and institutions that produce them. These resources are mainly accessed using browser-based web interfaces, but when you need to retrieve and analyse large amounts of data, or perform complex analyses that involve several nested searches spanning a range of different data resources, you need a more powerful, automated approach.
It is possible to create a local bioinformatics work environment by downloading and installing the relevant database content and services (such as retrieval and analysis programmes) and writing scripts to automate your analysis. However, as the data explosion continues apace, few researchers have the resources to make this a viable option.
What are web services?
Web services (www.ebi.ac.uk/Tools/webservices ) allow you to access the EMBL-EBI’s data and analysis applications as if they were installed on your laboratory computers. They provide an easy and flexible way to deal with repetitive tasks such as bulk submission with minimal intervention from the user. They also allow programmers to build complex applications without having to install and maintain the databases and analysis tools 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.
How do I run the EMBL-EBI’s web services?
To use the EMBL-EBI’s web services, all you need is a lightweight programme (a client) that communicates with the servers running at the EMBL-EBI. You can create your own clients and we provide perl-based and java-based examples for each of our web services. Instructions on how to build your own clients in a variety of programming languages can be found in the tutorials at www.ebi.ac.uk/Tools/webservices/tutorial.html. You can then access any of the EBI’s web services as though they were on your own machine. A full list of services is available at www.ebi.ac.uk/Tools/webservices/services. html .
Web Services clients allow programmers and service providers to build and integrate complex analysis workflows using existing EBI services. For example, Figure 1 shows a simple workflow that is designed to predict protein function from genomic sequence. This workflow fetches sequences using WSDbfetch, uses WSEmboss tools to extract the coding sequences, searches for homologous sequences using WSWUBlast, retrieves the sequences for the hits, and constructs an alignment using WSClustalW. It also searches the InterProScan database for domain families, and retrieves annotation from the scientific literature and ontologies. Instead of going through several different web pages, saving the results, converting formats, etc., you can create a simple script that calls upon different web services to go through the whole process and deliver the results to you. You can use graphical workflow tools such as Taverna (taverna.sourceforge.net) or Triana (www.trianacode.org ) to create your workflows if you prefer.