The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute (EBI).[1]
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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 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 databases 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.
The global search is available at the top of all EBI web pages. 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. The user can expand or contract the visualization of the query results for each or all the databases by clicking the relevant '+' or '-' signs in the page. When expanded, each data set is shown along with the number of entries found.
Insulin receptor = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=insulin+receptor P53 = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=p53 External Services group = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=external+services Bos taurus (cow) data on the EB-eye = http://www.ebi.ac.uk/ebisearch/entryreferencesearch.ebi?db=allebi&relateddb=taxonomy&relatedid=9913 escherichia NOT coli = http://www.ebi.ac.uk/ebisearch/search.ebi?query=escherichia+%21coli&db=allebi C2H2 zinc finger family = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=C2H2+zinc+finger+family+&FormsButton3=Go DNA binding = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=DNA+binding
This kind of search is available from the 'Advanced Search' page. It first 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 'domain-specific search' 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. When multiple data resources are available in a 'domain' the user can select all of them or just one. After the selection of databases and fields has been completed the user can type the query terms of interest. See also Advanced Search Examples section.
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.
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.
Further pages describing the syntax for quering using this search engine are available at the EBI's web site.
EB-eye is also accessible using web services technologies from the EBI. Please see the main Web Services pages at the EBI. A WSDL (Web Services Description Language) document is available here
Lucene has been around for a while now. Many bioinformatic 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.