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EBI is an Outstation of the European Molecular Biology Laboratory. The EB-eye search engine E-MeP (Feb. 22 nd, 2008) Mickael Goujon – External Services.

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Presentation on theme: "EBI is an Outstation of the European Molecular Biology Laboratory. The EB-eye search engine E-MeP (Feb. 22 nd, 2008) Mickael Goujon – External Services."— Presentation transcript:

1 EBI is an Outstation of the European Molecular Biology Laboratory. The EB-eye search engine E-MeP (Feb. 22 nd, 2008) Mickael Goujon – External Services group

2 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

3 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

4 The EB-eye search engine22/02/20084 Ligand Data at the EBI Array Express Interpro..................... ID :.. PARENT ID :.. RANK :..... ID... AC... DT... ID... AC... DT... ID... AC... DT...

5 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

6 The EB-eye search engine22/02/20086 Ligand Data coverage Array Express Interpro > 30 domains (databases) >170M entries > 550 GB of data

7 The EB-eye search engine22/02/20087 Functionalities (Demo) Basic search Query refinement Clusters of information Navigation between cross-references Advanced search

8 The EB-eye search engine22/02/20088 Please, try it! Available everywhere on the EBI website  http://www.ebi.ac.uk http://www.ebi.ac.uk We need your feedback!  http://www.ebi.ac.uk/support/ http://www.ebi.ac.uk/support/ Comments Defect reports New ideas

9 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

10 The EB-eye search engine22/02/200810 Web services – Listing the domains > listDomains() … astd … ensembl emblcds embldeleted emblnew_ann_con emblnew_con emblnew_standard emblnew_wgs emblrelease_ann_con emblrelease_con emblrelease_standard emblrelease_wgs ensembl … List available domains (list only the leaves) String[] listDomains()

11 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)

12 The EB-eye search engine22/02/200812 Web services – Get results ids > getResultsIds(‘uniprot’, ‘polymerase’, 0, 5) A2VB99_9VIRU Q86777_9CALI Q779J8_9VIRU Q8I944_9STIC Q8I945_9STIC List result IDs for a simple query String[] getResultsIds(String domain, String query) String[] getResultsIds(String domain, String query, int start, int size)

13 The EB-eye search engine22/02/200813 Web services – Get referenced domains > getDomainsReferencedInEntry(‘ensembl’, ‘cg2102’) embldeleted emblnew_ann_con emblnew_con emblnew_standard emblnew_wgs emblrelease_ann_con emblrelease_con emblrelease_standard emblrelease_wgs go taxonomy uniprot Get referenced domains in a domain or an entry String[] getDomainsReferencedInEntry(String domain, String entryId) String[] getDomainsReferencedInDomain(String domain)

14 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 entry String[] getReferencedEntries(String domain, String entryId, String referencedDomain)

15 The EB-eye search engine22/02/200815 Web services – External cross-references  listAdditionalReferenceFields(‘msdpdb’) CATH PFAM SCOP List non EB-eye domains referenced in a domain String[] listAdditionalReferenceFields(String domain)

16 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) XX DE Fusarium venenatum clone VEN-A RAPD band generated using Operon primer DE OPW-03, sequence tagged site.... Flat files 10997935 2000 10 04 … XML files IntAct.Experiment Experimental procedures that allowed to… 1.0 2007-Feb-16 5697 … Dump file (XML) 14216186 1965 02 01 1996 12 01 2007 03 01 0009-8981 10 1964 Jul Clinica chimica acta; international journal of clinical chemistry Clin. Chim. Acta... 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. XX AC AF030562; XX DT 04-DEC-1997 (Rel. 53, Created) DT 03-MAR-2000 (Rel. 62, Last updated, Version 2) XX DE Fusarium venenatum clone VEN-A RAPD band generated using Operon primer DE OPW-03, sequence tagged site. XX KW STS. XX OS Fusarium venenatum OC Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; OC Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium. XX RN [1] RP 1-852 RA 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). XX RN [2] RP 1-852 RA 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 USA XX FH Key Location/Qualifiers FH FT source 1..852 FT /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)

17 The EB-eye search engine22/02/200817 Web services – The fields  listFields(‘uniprot’) acc_number description id name List available (stored) fields in a domain String[] listFields(String domain)

18 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 Q779J8 Q0E5A0 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)

19 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)

20 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)

21 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)

22 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/


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