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EBI is an Outstation of the European Molecular Biology Laboratory.
The EB-eye search engine
E-MeP (Feb. 22nd, 2008)
Mickael Goujon – External Services group
The EB-eye search engine22/02/20082
Summary
• Background• Description of the service• General users
• Web Interface: Demonstration of the functionalities
• Developer/Technical users• Web Services: User API Description
The EB-eye search engine22/02/20083
Project background
• 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
• Searching the data at the EBI• Diversity and heterogeneity of the data (format, size, content…)• Most of the data providers have their own search mechanism
• Heterogeneity of the search results (display, content, granularity…)
• Navigation between the different resources (references) not consistent
The EB-eye search engine22/02/20084
Ligand
Data at the EBI
Array
ExpressInterpro
<XML>. . .</XML>
<XML>. . .</XML>
<XML>. . .</XML>
<XML>. . .</XML>
<XML>. . .</XML>
<XML>. . .</XML>
<XML>. . .</XML>
ID : .. PARENT ID : ..RANK : .....
ID ...AC ...DT ...
ID ...AC ...DT ...
ID ...AC ...DT ...
The EB-eye search engine22/02/20085
EB-eye solution
• Global search mechanism• Searches most of the EBI resources in one go• Not specific to any resource
• Unified searches of the EBI resources• Free-text search (unified semantic)• Basic results display (Google-like)• Simple cross reference navigation
• Available on all the EBI web pages
The EB-eye search engine22/02/20086
Ligand
Data coverage
Array
ExpressInterpro
> 30 domains (databases)
>170M entries
> 550 GB of data
The EB-eye search engine22/02/20087
Functionalities (Demo)
• Basic search• Query refinement• Clusters of information• Navigation between cross-references• Advanced search
The EB-eye search engine22/02/20088
Please, try it!
• Available everywhere on the EBI websitehttp://www.ebi.ac.uk
• We need your feedback!http://www.ebi.ac.uk/support/
• Comments• Defect reports• New ideas
The EB-eye search engine22/02/20089
EB-eye Web Services
• SOAP Web Services for a programmatic access to the EB-eye functionalities
• Simple experimental API for basic operations• Basic metadata information• Basic queries (Full-text and entries)• Limited cross-references navigation
• Depending on the usage, we may implement a more complex API and more functionalities
The EB-eye search engine22/02/200810
Web services – Listing the domains
> listDomains()…astd…ensemblemblcdsembldeletedemblnew_ann_conemblnew_conemblnew_standard emblnew_wgsemblrelease_ann_con emblrelease_conemblrelease_standard emblrelease_wgsensembl
…
List available domains(list only the leaves)
String[] listDomains()
The EB-eye search engine22/02/200811
Web services – Number of results
> getNumberOfResults(‘medline’, 'immunolog* nutrition')
6954
Get number of results for a simple query
int getNumberOfResults(String domain, String query)
The EB-eye search engine22/02/200812
Web services – Get results ids
> getResultsIds(‘uniprot’, ‘polymerase’, 0, 5)
A2VB99_9VIRUQ86777_9CALIQ779J8_9VIRUQ8I944_9STICQ8I945_9STIC
List result IDs for a simple queryString[] getResultsIds(String domain, String query)String[] getResultsIds(String domain, String query, int start, int size)
The EB-eye search engine22/02/200813
Web services – Get referenced domains
> getDomainsReferencedInEntry(‘ensembl’, ‘cg2102’)
embldeletedemblnew_ann_conemblnew_conemblnew_standardemblnew_wgsemblrelease_ann_conemblrelease_conemblrelease_standardemblrelease_wgsgotaxonomyuniprot
Get referenced domains in a domain or an entry
String[] getDomainsReferencedInEntry(String domain, String entryId)String[] getDomainsReferencedInDomain(String domain)
The EB-eye search engine22/02/200814
Web services – Get referenced entries
getReferencedEntries(‘ensembl’, ‘cg2102’, ‘go’)
GO:0005634 GO:0046872 GO:0008270 GO:0016319 GO:0003676 GO:0003677 GO:0045892 GO:0006350 GO:0006355 GO:0007275 GO:0007399 GO:0007402 GO:0007417 GO:0007419 GO:0003700 GO:0009791 GO:0030154
Get referenced entries for a domain in a particular entryString[] getReferencedEntries(String domain, String entryId, String referencedDomain)
The EB-eye search engine22/02/200815
Web services – External cross-references
listAdditionalReferenceFields(‘msdpdb’)
CATHPFAMSCOP
List non EB-eye domains referenced in a domain
String[] listAdditionalReferenceFields(String domain)
The EB-eye search engine22/02/200816
Web services – The fields
Db
ID AF030562; SV 1; linear; genomic DNA; STS; FUN; 852 BP.AC AF030562;DT 04-DEC-1997 (Rel. 53, Created)DT 03-MAR-2000 (Rel. 62, Last updated, Version 2)XXDE Fusarium venenatum clone VEN-A RAPD band generated using Operon primerDE OPW-03, sequence tagged site.. . .
Flat files
<MedlineCitationSet><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID>10997935</PMID><DateCreated><Year>2000</Year><Month>10</Month><Day>04</Day></DateCreated>…
XML files
<database> <name>IntAct.Experiment</name> <description>Experimental procedures that allowed to…</description> <release>1.0</release> <release_date>2007-Feb-16</release_date> <entry_count>5697</entry_count> <entries> <entry id="EBI-77680">…
Dump file (XML)
<MedlineCitationSet> <MedlineCitation Owner="NLM" Status="MEDLINE"> <PMID>14216186</PMID> <DateCreated> <Year>1965</Year> <Month>02</Month> <Day>01</Day> </DateCreated> <DateCompleted> <Year>1996</Year> <Month>12</Month> <Day>01</Day> </DateCompleted> <DateRevised> <Year>2007</Year> <Month>03</Month> <Day>01</Day> </DateRevised> <Article PubModel="Print"> <Journal> <ISSN IssnType="Print">0009-8981</ISSN> <JournalIssue CitedMedium="Print"> <Volume>10</Volume> <PubDate> <Year>1964</Year> <Month>Jul</Month> </PubDate> </JournalIssue> <Title>Clinica chimica acta; international journal of clinical chemistry</Title> <ISOAbbreviation>Clin. Chim. Acta</ISOAbbreviation> </Journal> . . .. . .
id (value stored)
creation_date (value non stored)
last_modification_date (value non stored)
issn (value non stored)
volume (value stored)
name (value non stored)
ID AF030562; SV 1; linear; genomic DNA; STS; FUN; 852 BP.XXAC AF030562;XXDT 04-DEC-1997 (Rel. 53, Created)DT 03-MAR-2000 (Rel. 62, Last updated, Version 2)XXDE Fusarium venenatum clone VEN-A RAPD band generated using Operon primerDE OPW-03, sequence tagged site.XXKW STS.XXOS Fusarium venenatumOC Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes;OC Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium.XXRN [1]RP 1-852RA Yoder W.T., Christianson L.M.;RT "Species-specific primers resolve members of the section Fusarium.RT Taxonomic status of the edible 'Quorn' fungus re-evaluated";RL Fungal Genet. Biol. 0:0-0(1997).XXRN [2]RP 1-852RA Yoder W.T., Christianson L.M.;RT ;RL Submitted (21-OCT-1997) to the EMBL/GenBank/DDBJ databases.RL Microbiology, Novo Nordisk Biotech, Inc., 1445 Drew Ave., Davis, CA 95616,RL USAXXFH Key Location/QualifiersFHFT source 1..852FT /organism="Fusarium venenatum"FT /strain="ATCC20334". . .
id (value stored)
acc (value stored)
creation_date /last_modificationdate (values non stored)
description (value stored)
organism_species (value non stored)organism_classification (value non stored)
references (non stored)
The EB-eye search engine22/02/200817
Web services – The fields
listFields(‘uniprot’)
acc_numberdescriptionidname
List available (stored) fields in a domain
String[] listFields(String domain)
The EB-eye search engine22/02/200818
Web services – Get results with fields
>getResults(‘uniprot’, ‘polymerase’, [‘acc’, ‘id’, ‘description’], 0, 5)
acc description id-------------------------------------------------------------------A2VB99 Polymerase. A2VB99_9VIRU Q86777 RNA polymerase (Fragment). Q86777_9CALI Q779J8Q0E5A0 DNA polymerase (EC 2.7.7.7). Q779J8_9VIRU Q8I944 DNA polymerase (EC 2.7.7.7). Q8I944_9STIC
List result fields values for a simple query
String[][] getResults(String domain, String query, String[] fields, int start, int size)
The EB-eye search engine22/02/200819
Web services – Get result fields values for entries
>getEntry(‘medline’, ‘7605758’, [‘description’, ‘publication_date’ , ‘authors’])
description :BACKGROUND AND OBJECTIVES: Intraspinally administered alpha 2-adrenergic agonists produce analgesia in part by causing spinal acetylcholine and nitric oxide (NO) release. Clonidine-induced analgesia is enhanced by subarachnoid neostigmine and inhibited by N-methyl-L-arginine (NMLA), a blocker of NO synthesis. The authors tested whether dexmedetomidine, an alpha [...]
publication_date :1995 Mar-Apr
authors :Bouaziz H.Hewitt C.Eisenach J.C.
Get result fields values for one or several entries
String[] getEntry(String domain, String entryId, String[] fields)String[][] getEntries(String domain, String[] entryIds, String[] fields)
The EB-eye search engine22/02/200820
Web services – Get the urls
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-+[UNIPROT:Q9QUZ9_9MURI]+-newId
getEntryFieldUrls(‘uniprot’, ‘Q9QUZ9_9MURI’, [‘id’])
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[UNIPROT:Q9QUZ9_9MURI]+-newId
returns the urls configured for a field of an entry
String[] getEntryFieldUrls(String domain, String entry, String[] fields)String[][] getEntriesFieldUrls(String domain, String[]entries, String[]fields)
The EB-eye search engine22/02/200821
Web services – Referenced entries from a domain
>getReferencedEntriesSet(‘ensembl’, [‘AAEL005345’, ‘CG2102’], ‘go’, [‘id’, ‘name’])
‘AAEL005345’->[GO:0016319, ‘mushroom body development’],[GO:0045892, ‘negative regulation of transcription,DNA-dependent’],[GO:0007417, ‘central nervous system development’], [GO:0009791, ‘post-embryonic development’]
‘CG2102’->[GO:0005634, ‘nucleus’],[GO:0046872, ‘metal ion binding’], [GO:0008270, ‘zinc ion binding’],[GO:0016319, ‘mushroom body development’],][GO:0003676, ‘nucleic acid binding’],[GO:0003677, ‘DNA binding, ...
List of referenced entries from a domain referenced in a set of entries
String[][] getReferencedEntriesFlatSet(String domain, String[] entries, String referencedDomain, String[] fields)dict(String[][]) getReferencedEntriesSet(String domain, String[] entries, String referencedDomain, String[] fields)
The EB-eye search engine22/02/200822
Web services – Links
• WSDL: http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl
• Documentation: http://www.ebi.ac.uk/Tools/webservices/services/eb-eye
• Feedback! http://www.ebi.ac.uk/support/