- 1 The EB-eye – the EBI Search engine for biological data
- 1.1 The Mission of the EBI
- 1.2 What is the EB-eye ?
- 1.3 Access to the EB-eye
- 2 References
- 3 External links
The EB-eye – the EBI Search engine for biological data
The European Bioinformatics Institute is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
The Mission of the EBI
- To provide freely available data and bioinformatics services to the scientific community in ways that promote scientific progress.
- To contribute to the advancement of biology through basic investigator-driven research in bioinformatics.
- To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators.
- To help disseminate cutting-edge technologies to industry.
What is the EB-eye ?
The EB-eye is a fast and efficient search engine that currently provides easy and uniform access to biological data resources hosted at the EBI. The project was started in August 2006 and is developed on top of the Apache Lucene technology. It is a Java framework that provides extremely powerful indexing and search capabilities. The EB-eye presents the hits of a search in a very simple way and acts as a gateway to access biological entries and related information in dedicated portals. One of the key features of EB-eye is the capability to coherently display the relationships that exist between diverse databases allowing the user to navigate this network of cross-references. The user can search globally across all EBI data resources through the “Global Search” box or even create more specific queries on targeted resources by using the EB-eye "Advanced search". EB-eye publicly exposes both a web and a web services interface.
Access to the EB-eye
The global search is available on the EBI web site. You can simply type some query terms into the text dialogue there and press GO (or press Enter). The system then displays a summary page with the name of the various data sets and the number of matches found in each of them.
Global Search examples
- Search for insulin receptor
- Search for p53
- Search for web production team
- Search for escherichia NOT coli
- Search for C2H2 zinc finger family
- Search for DNA binding
The Advanced Search page displays four text dialogues for each of the query types available in the system. By default the search is widened to the whole EBI data resources. Otherwise the 'particular data source' option in this page leads the user to a wizard where it is possible to select a given data resource specifying which fields to use in the query. See Advanced Search examples section.
What can the user Search for?
Many of the text fields of EBI data resources are indexed within the search engine, but some are not. The EB-eye can search only the information pertaining text fields that get indexed. This implies that other search engines operating on biological data might yield different results. As a rule of thumb, the EB-eye search engine index identifiers, names, descriptions, keywords and cross-references.
Advanced Search examples
- Search for description:azurin
- Search for paired box protein BUT NOT fragment OR paxillin
- Search for description:(paired box protein) INTERPRO:(IPR001523) in UniProtKB
- Search for (bacterium OR organism) AND (unidentified OR uncultured) (environmental samples)
- Search for Ca(2+) oscillation (Ca2++ oscillation models)
It is also possible to search using cross-references. In the same Advanced search select fields dialog it is possible to see which cross-references are indexed.
Help & documentation for EB-eye
Further information about how to use this search engine is available at the EB-eye help and documentation.
Programmatic access to the EB-eye
The EB-eye is also accessible using web services technologies from the EBI. Please see the main Web Services pages at the EBI. The EB-eye WSDL (Web Services Description Language document) is publicly available.
Other Lucene-based search engine in biology/bioinformatics
Lucene has been around for a while now. Many bioinformatics centres have been experimenting with its use with biological data and databases. A pioneering development in this field is headed by Dr. Don Gilbert at Indiana University, called LuceGene, a part of the GMOD (Generic Software Components for Model Organisms Databases) initiative. Another example is the search engine in the UniProt web site which is also based on Lucene and adds features such as sorting large data sets, subqueries across data sets and group-by queries. Lucene is also used in QuALM a question answering system for Wikipedia.
- Squizzato S., Park Y.M., Buso N., Gur T., Cowley A., Li W., Uludag M., Pundir S., Cham J.A., McWilliam H., Lopez R. (2015). "The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.". Nucleic Acids Res. doi:10.1093/nar/gkv316. PMID 25855807.
- Valentin F., Squizzato S., Goujon M., McWilliam H., Paern J., Lopez R. (2010). "Fast and efficient searching of biological data resources--using EB-eye.". Brief Bioinform 11 (4): 375–384. doi:10.1093/bib/bbp065. PMC 2905521. PMID 20150321.
- "EMBnet.News (Volume 14, Nr. 1, December 2007)". EMBnetNews. December 2007. Retrieved 2009-04-01.