EBI is an Outstation of the European Molecular Biology Laboratory.

EB-eye - The EMBL-EBI search engine

ISMB 2008 - Tuesday, July 22

Franck ValentinEMBL-EBI

2

Summary

• Why the EB-eye?• Web interface• Advanced searches

• Web services• Future

3

The reasons behind the EB-eye

• New EBI web site (launched in Dec. 2006)

• Focus: Improving the user experience• Consistency in the pages• Easier and quicker navigation• Easier to search EBI data resources

• Challenge of searching the data at the EBI• Diversity and heterogeneity of the data (format, size, content…)• Most of the data providers had their own search mechanism• Heterogeneity of the search results (display, content, granularity…)• Navigation between the different resources (cross-references)

4

EB-eye

• Global search mechanism• Searches most of the EBI resources in one go• Generic, not specific to any resource

• Unified searches of the EBI resources• Free-text search (Google-like)• Basic results display (Google-like)• Simple cross reference navigation

• Available on all the EBI web pages

5

EB-eye results summary page

• Organized into categories called “domains”

• Number of results per domain• Refine your search• Expand/Collapse for more

details

6

EB-eye domain result page

• Results for all the resources in a domain• A domain can contain several resources• First 3 entries displayed for each resource• View more entries for a particular resource

• Hierarchy of domains• Forward search (smaller set of resources)• Backward search (wider set of resources)

• Refine your search• Navigate the results pages

7

EB-eye domain result page (one resource)

• Basic information: ID, name, description…• Link to the main resource web site• Additional links• EB-eye internal references

8

EB-eye cross-references navigation

• Navigate inside the EB-eye• References context• Navigation…

• Using resources explicit references• Using resources implicit references

9

EB-eye Advanced Search

• Accessible from all the pages• Simple search criteria• Domain specific search

• Domain selection• Fields selection• References

10

Web services for the EB-eye

• Simple experimental API for basic operations• Basic metadata information• Queries (Full-text and entries)• Cross-references navigation

• Depending on the usage, we may implement a more complex API and more functionalities

11

Web services – Listing the domains

> l i s t Domai ns ( )…

as t d

…

e n s e mb l

e mb l c d s

e mb l d e l e t e d

e mb l n e w_ an n _ c o n

e mb l n e w_ c o n

e mb l n e w_ s t an d ar d

e mb l n e w_ wgs

e mb l r e l e as e _ an n _ c o n

e mb l r e l e as e _ c o n

e mb l r e l e as e _ s t an d ar d

e mb l r e l e as e _ wgs

e n s e mb l

…

List available domains(list only the leaves)

St r i ng[ ] l i s t Domai ns ( )

12

Web services – Number of results

> getNumberOfResults(‘medline’, 'immunolog* nutrition')

6954

Get number of results for a simple query

int getNumberOfResults(String domain, String query)

13

Web services – Get results ids

> ge t Re s u l t s I d s ( ‘ u n i p r o t ’ , ‘ p o l yme r as e ’ , 0, 5 )

A2VB99_ 9VI RU

Q86777_ 9CALI

Q779J8_ 9VI RU

Q8I 944_ 9STI C

Q8I 945_ 9STI C

List result IDs for a simple querySt r i ng[ ] get Res ul t s I ds ( St r i ng domai n, St r i ng quer y)St r i ng[ ] get Res ul t s I ds ( St r i ng domai n, St r i ng quer y, i nt s t ar t , i nt s i z e)

14

Web services – Get referenced domains

> ge t Do mai n s Re f e r e n c e d I n En t r y( ‘ e n s e mb l ’ , ‘ c g2 1 02 ’ )

e mb l d e l e t e d

e mb l n e w_ an n _ c o n

e mb l n e w_ c o n

e mb l n e w_ s t an d ar d

e mb l n e w_ wgs

e mb l r e l e as e _ an n _ c o n

e mb l r e l e as e _ c o n

e mb l r e l e as e _ s t an d ar d

e mb l r e l e as e _ wgs

go

t ax o n o my

u n i p r o t

Get referenced domains in a domain or an entry

St r i ng[ ] get Domai ns Ref er enc edI nEnt r y( St r i ng domai n, St r i ng ent r yI d)St r i ng[ ] get Domai ns Ref er enc edI nDomai n( St r i ng domai n)

15

Web services – Get referenced entries

ge t Re f e r e n c e d En t r i e s ( ‘ e n s e mb l ’ , ‘ c g2 1 02 ’ , ‘ go ’ )

GO: 0005634 GO: 0046872 GO: 0008270 GO: 001 631 9 GO: 0003676 GO: 0003677

GO: 0045892 GO: 0006350 GO: 0006355 GO: 0007275 GO: 0007399 GO: 0007402

GO: 000741 7 GO: 000741 9 GO: 0003700 GO: 0009791 GO: 00301 54

Get referenced entries for a domain in a particular entrySt r i n g[ ] ge t Re f e r e n c e d En t r i e s ( St r i n g d o mai n , St r i n g e n t r yI d ,

S t r i n g r e f e r e n c e d Do mai n )

16

Web services – External cross-references

l i s t Ad d i t i o n al Re f e r e n c e F i e l d s ( ‘ ms d p d b ’ )

CATH

PFAM

SCOP

List non EB-eye domains referenced in a domain

St r i ng[ ] l i s t Addi t i onal Ref er enc eFi el ds ( St r i ng domai n)

17

Future

• Interoperability with analytical tools (e.g. alignments, similarity searches, text-mining tools, etc.)

• Export results of searches in various formats (e.g. flat lists, Excel sheets, XML, etc.)

• Addition of third party databases

• Links to external data resources

18

Try it!

• Available everywhere on the EBI website http://www.ebi.ac.uk

• Web services http://www.ebi.ac.uk/Tools/webservices/services/eb-eye

• We need your feedback! http://www.ebi.ac.uk/support/ support@ebi.ac.uk

• Comments

• Defect reports

• New ideas