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EBIEMBL-EBI Web Servicesserviceseb-eye
Table of Contents

EB-eye

Description

EB-eye 1) 2) is a high-performance, full-featured text search engine using Apache Lucene technology to index EMBL-EBI databases in various formats (e.g. flat-files, XML dumps, OBO format, etc.) and provides very fast access to the EMBL-EBI's data resources. The system allows the user to search globally across all EMBL-EBI databases.

The Web Services API offers programmatic access to most of the functionality available in the EB-eye search engine.

For more information see:

Web services registry entries:

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: EBeyeCliClient.exe; Source: EBeyeClient.cs, EBeyeCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: EBeye_Axis1.jar; Source: EBeyeClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in ebiws-lib.zip.
Executable jar: EBeye_JAXWS.jar; Source: EBeyeClient.java JAX-WS; Various dependencies including Commons-CLI, are available in ebiws-lib.zip.
Perl ebeye_soaplite.pl SOAP::Lite
ebeye_xmlcompile.pl XML::Compile::SOAP
Python ebeye_suds.py suds
VB.NET Source: EBeyeClient.vb, EBeyeCliClient.vb A .NET runtime with development tools to build from source, see the .NET tutorial for details. For a .NET executable see the C# client above.

Workflows

In addition to these sample clients users have submitted workflows using this service to the myExperiment workflow repository. See workflows using the EB-eye Web Service for a list.

WSDL

The WSDL for the EB-eye SOAP service: http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl

Methods documentation

  • listDomains()

Returns a list of all the domains identifiers which can be used in a query.

  • getNumberOfResults(domain, query)

Executes a query and returns the number of results found.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
query string the terms to look for


  • getResultsIds(domain, query, start, size)

Executes a query and returns the list of identifiers for the entries found.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
query string the terms to look for
start int the index of the first entry in the results list to be returned
size int the number of entries to be returned (limit: 100)


  • getAllResultsIds(domain, query)

Executes a query and returns the list of all the identifiers for the entries found.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
query string the terms to look for

Warning: This method can fail if the number of entries is really huge. The method getResultsIds is a lot safer.

  • listFields(domain)

Returns the list of fields that can be retrieved for a particular domain.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)


  • getResults(domain, query, fields, start, size)

Executes a query and returns a list of results. Each result contains the values for each field specified in the “fields” argument in the same order as they appear in the “fields” list.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
query string the terms to look for
fields array of string a list of fields which data will be included in the results
start int the index of the first entry in the results list to be returned
size int the number of entries to be returned (limit: 100)


  • getEntry(domain, entry, fields)

Search for a particular entry in a domain and returns the values for some of the fields of this entry. The result contains the values for each field specified in the “fields” argument in the same order as they appear in the “fields” list.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
entry string the entry identifier
fields array of string a list of fields which data will be included in the results


  • getEntries(domain, entries, fields)

Search for entries in a domain and returns the values for some of the fields of these entries. The result contains the values for each field specified in the “fields” argument in the same order as they appear in the “fields” list.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
entries array of string the list of entry identifiers
fields array of string a list of fields which data will be included in the results


  • getEntryFieldUrls(domain, entry, fields)

Search for a particular entry in a domain and returns the urls configured for some of the fields of this entry. The result contains the urls for each field specified in the “fields” argument in the same order as they appear in the “fields” list.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
entry string the entry identifier
fields array of string a list of fields which corresponding urls will be included in the results


  • getEntriesFieldUrls(domain, entries, fields)

Search for a list of entries in a domain and returns the urls configured for some of the fields of these entries. Each result contains the url for each field specified in the “fields” argument in the same order as they appear in the “fields” list.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
entries array of string the list of entry identifiers
fields array of string a list of fields which corresponding urls will be included in the results


  • getDomainsReferencedInDomain(domain)

Returns the list of domains with entries referenced in a particular domain. These domains are indexed in the EB-eye.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)


  • getDomainsReferencedInEntry(domain, entry)

Returns the list of domains with entries referenced in a particular domain entry. These domains are indexed in the EB-eye.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)
entry string the entry identifier


  • listAdditionalReferenceFields(domain)

Returns the list of fields corresponding to databases referenced in the domain but not included as a domain in the EB-eye.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)


  • getReferencedEntries(domain, entry, referencedDomain)

Returns the list of referenced entry identifiers from a domain referenced in a particular domain entry.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)
entry string the entry identifier
referencedDomain string the identifier for the domain referenced in the entry (must be one of the domains returned by the getDomainsReferencedInEntry(domain, entry) method)


  • getReferencedEntriesSet(domain, entries, referencedDomain, fields)

Returns the list of referenced entries from a domain referenced in a set of entries. The result will be returned as a list of objects, each representing an entry reference.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)
entries array of string the entry identifiers
referencedDomain string the identifier for the domain referenced in the entry (must be one of the domains returned by the getDomainsReferencedInEntry(domain, entry) method)
fields array of string a list of fields which data will be included in the results


  • getReferencedEntriesFlatSet(domain, entries, referencedDomain, fields)

Returns the list of referenced entries from a domain referenced in a set of entries. The result will be returned as a flat table corresponding to the list of results where, for each result, the first value is the original entry identifier and the other values correspond to the fields values.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)
entries array of string the entry identifiers
referencedDomain string the identifier for the domain referenced in the entry (must be one of the domains returned by the getDomainsReferencedInEntry(domain, entry) method)
fields array of string a list of fields which data will be included in the results


  • getDomainsHierarchy()

Returns the hierarchy of the domains available.

  • getDetailledNumberOfResults(domain, query, flat)

Executes a query and returns the number of results found per domain

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the getDomainsHierarchy() method)
query string the terms to look for
flat boolean defines whether the results have to be flatten or not. I.E. Only the searchable domains (leaves of the tree) or the complete domain hierarchy


  • listFieldsInformation(domain)

Returns the list of fields that can be retrieved and/or searched for a particular domain.

Parameters Type Description
domain string the domain identifier (must be one of the domains returned by the listDomains() method)


  • getFacets(domain, query)

Executes a query and returns the list of facets available on the entries that match the given query.
For each facet found, along with the indication of the field on which the given facet is defined, a list of facet values and labels with their relative hit numbers is detailed in the response.

Parameters Type Description
domain string the id of the domain to search into (must be one of the domains returned by the listDomains() method)
query string the terms to look for

Warning: At the moment this API method is experimental and might be subject to change in the future.

Note: currently the number of facet values returned per facet field is limited to a maximum of 1000 values.

Query syntax

For more information about the syntax that can be used in the API query parameters see:

Contact

If you have any questions or comments, or you plan to use this service as part of a course or for a high number of submissions, please contact us EMBL-EBI Support.

1) Valentin F., Squizzato S., Goujon M., McWilliam H., Paern J. and Lopez R. (2010)
Fast and efficient searching of biological data resources–using EB-eye.
Brief. Bioinformatics 11(4):375-84
PubMed: 20150321
DOI: 10.1093/bib/bbp065
2) Goujon M., Valentin F., Miyar T., McWilliam H. and Lopez, R. (2008)
The EB-eye
EMBnet.news 13.4:18-21 December 2007
http://journal.embnet.org/index.php/embnetnews/article/view/88/99
 
services/eb-eye.txt · Last modified: 2013/07/10 09:39 by hpm
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