EB-eye

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

• EB-eye help

Web services registry entries:

• BioCatalogue
• EMBRACE Registry
• Health 2.0 API
• seekda!

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 lib-1.4.zip.
	Executable jar: EBeye_JAXWS.jar; Source: EBeyeClient.java	JAX-WS; Various dependencies including Commons-CLI, are available in lib-1.4.zip.
Perl	ebeye_soaplite.pl	SOAP::Lite
	ebeye_xmlcompile.pl	XML::Compile::SOAP
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.

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

• 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 (see EB-eye query syntax & Apache Lucene query syntax)

• 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 (see EB-eye query syntax & Apache Lucene query syntax)
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 (see EB-eye query syntax & Apache Lucene query syntax)

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 (see EB-eye query syntax & Apache Lucene query syntax)
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 (see EB-eye query syntax & Apache Lucene query syntax)
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)

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 EBI Support.