ebi is an outstation of the european molecular biology laboratory. the eb-eye search engine e-mep...

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


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


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 ...


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


Ligand

Data coverage

Array

ExpressInterpro

> 30 domains (databases)

>170M entries

> 550 GB of data


Functionalities (Demo)

• Basic search• Query refinement• Clusters of information• Navigation between cross-references• Advanced search


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


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


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()


Web services – Number of results

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

6954

Get number of results for a simple query

int getNumberOfResults(String domain, String query)


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)


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)


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)


Web services – External cross-references

listAdditionalReferenceFields(‘msdpdb’)

CATHPFAMSCOP

List non EB-eye domains referenced in a domain

String[] listAdditionalReferenceFields(String domain)


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)


Web services – The fields

listFields(‘uniprot’)

acc_numberdescriptionidname

List available (stored) fields in a domain

String[] listFields(String domain)


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)


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)


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)


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)


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/

ebi is an outstation of the european molecular biology laboratory. the eb-eye search engine e-mep...

Documents

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string query slide

ebeye search engine

string referenceddomain

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search mechanism heterogeneity