Fast and efficient searching of biological data resources--using EB-eye

Abstract

The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.

Figure 1:

Modules available in the overall architecture for the search engine back-end.

Figure 2:

Summary overview page for the results of a search (expanded mode).

Figure 3:

The ‘Explore related information’ box in the domain specific results page displays the terms related to a given search query using Carrot2 clustering techniques.

Figure 4:

The Advanced Search page for a query allows for the use of boolean operators to write complex queries.

Figure 5:

Results of a Smith-Waterman search against UniProtKB/SwissProt showing the cross-reference information obtained for each hit using the EB-eye web service.