EB-eye EBI's Search Engine
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The 'EB-eye' - EBI's Search Engine for biological databases
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 all facets of 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 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.
Access to the EB-eye
- From the top of any page on the EBI web portal.
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.
Global Search Examples
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.
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
- Searching for "Influenza A Virus" strain H1N1 from "April 2009" in EMBL-Bank Updates: http://www.ebi.ac.uk/ebisearch/search.ebi?db=emblnew_standard&t=creation_date%3A(2%3F-apr-2009)+description%3A(influenza+virus)
- Searching for "Search for description:(azurin) in UniProt KB": Uniprot description=azurin http://www.ebi.ac.uk/ebisearch/search.ebi?query=description%3A%28azurin%29&db=uniprot Uniprot description=azurin
- Searching Paired box protein in all databases at the EBI AllEBI Paired Box Protein BUT NOT fragment OR paxillin = http://www.ebi.ac.uk/ebisearch/search.ebi?query=paired+box+protein+%21fragment++%21paxillin&db=allebi
- description:(paired box protein) INTERPRO:(IPR001523) in UniProt KB UniProt (description:paired box protein) with cross references to InterPro:IPR001523 = http://www.ebi.ac.uk/ebisearch/search.ebi?query=description%3A%28paired+box+protein%29++INTERPRO%3A%28IPR001523%29&db=uniprot
- Finding environmental samples in All EBI (bacterium OR organism) AND (unidentified OR uncultured) = http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=%28bacterium+OR+organism%29+AND+%28unidentified+OR+uncultured%29
- Ca(2+) oscillation models Calcium oscillation = http://www.ebi.ac.uk/ebisearch/search.ebi?db=biomodels&query=Ca+oscillation
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 & FAQ on EB-eye
Further pages describing the syntax for quering using this search engine are available at the EBI's web site.
Programmatic access to the EB-eye
Other Lucene-based search engine in biology/bioinformatics
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 [ http://www.uniprot.org 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.
- "EMBnet.News (Volume 14, Nr. 1, December 2007)". EMBnetNews. December 2007. http://www.embnet.org/files/shared/EMBnetNews/embnet_news13_4-low.pdf. Retrieved 2009-04-01.