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Open Access Software

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

Dariusz Mrozek123*, Bożena Małysiak-Mrozek13 and Artur Siążnik1

Author Affiliations

1 Institute of Informatics, Silesian University of Technology, Akademicka 16, Gliwice, 44-100, Poland

2 Biotechnology Center, Silesian University of Technology, Akademicka 2A, Gliwice, 44-100, Poland

3 IBM Competence Center, Silesian University of Technology, Akademicka 16, Gliwice, 44-100, Poland

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BMC Bioinformatics 2013, 14:73  doi:10.1186/1471-2105-14-73

Published: 1 March 2013

Abstract

Background

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing.

Results

We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases.

Conclusions

search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/ webcite.

Keywords:
NCBI entrez; Entrez databases; Entrez search engine; Entrez programming utilities; Data exploration; Data searching; Data querying; Web services; Orchestration; Choreography