EB-eye Technology Track (ISMB 2008)


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The EB-eye is an Apache Lucene-based search engine aimed at providing unified access to the EBI databases. The system generates indices using a condensed but meaningful subset of the original data and returns summary information and links to the original data as well as all EBI specific database cross-references

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EB-eye Technology Track (ISMB 2008)

  1. 1. EB-eye - The EMBL-EBI search engine ISMB 2008 - Tuesday, July 22 Franck Valentin EMBL-EBI
  2. 2. Summary <ul><li>Why the EB-eye? </li></ul><ul><li>Web interface </li></ul><ul><li>Advanced searches </li></ul><ul><li>Web services </li></ul><ul><li>Future </li></ul>
  3. 3. The reasons behind the EB-eye <ul><li>New EBI web site (launched in Dec. 2006) </li></ul><ul><li>Focus: Improving the user experience </li></ul><ul><ul><li>Consistency in the pages </li></ul></ul><ul><ul><li>Easier and quicker navigation </li></ul></ul><ul><ul><li>Easier to search EBI data resources </li></ul></ul><ul><li>Challenge of searching the data at the EBI </li></ul><ul><ul><li>Diversity and heterogeneity of the data (format, size, content…) </li></ul></ul><ul><ul><li>Most of the data providers had their own search mechanism </li></ul></ul><ul><ul><li>Heterogeneity of the search results (display, content, granularity…) </li></ul></ul><ul><ul><li>Navigation between the different resources (cross-references) </li></ul></ul>
  4. 4. EB-eye <ul><li>Global search mechanism </li></ul><ul><ul><li>Searches most of the EBI resources in one go </li></ul></ul><ul><ul><li>Generic, not specific to any resource </li></ul></ul><ul><li>Unified searches of the EBI resources </li></ul><ul><ul><li>Free-text search (Google-like) </li></ul></ul><ul><ul><li>Basic results display (Google-like) </li></ul></ul><ul><ul><li>Simple cross reference navigation </li></ul></ul><ul><li>Available on all the EBI web pages </li></ul>
  5. 5. EB-eye results summary page <ul><li>Organized into categories called “domains” </li></ul><ul><li>Number of results per domain </li></ul><ul><li>Refine your search </li></ul><ul><li>Expand/Collapse for more details </li></ul>
  6. 6. EB-eye domain result page <ul><li>Results for all the resources in a domain </li></ul><ul><ul><li>A domain can contain several resources </li></ul></ul><ul><ul><li>First 3 entries displayed for each resource </li></ul></ul><ul><ul><li>View more entries for a particular resource </li></ul></ul><ul><li>Hierarchy of domains </li></ul><ul><ul><li>Forward search (smaller set of resources) </li></ul></ul><ul><ul><li>Backward search (wider set of resources) </li></ul></ul><ul><li>Refine your search </li></ul><ul><li>Navigate the results pages </li></ul>
  7. 7. EB-eye domain result page (one resource) <ul><li>Basic information: ID, name, description… </li></ul><ul><li>Link to the main resource web site </li></ul><ul><li>Additional links </li></ul><ul><li>EB-eye internal references </li></ul>
  8. 8. EB-eye cross-references navigation <ul><li>Navigate inside the EB-eye </li></ul><ul><li>References context </li></ul><ul><li>Navigation… </li></ul><ul><ul><li>Using resources explicit references </li></ul></ul><ul><ul><li>Using resources implicit references </li></ul></ul>
  9. 9. EB-eye Advanced Search <ul><li>Accessible from all the pages </li></ul><ul><li>Simple search criteria </li></ul><ul><li>Domain specific search </li></ul><ul><ul><li>Domain selection </li></ul></ul><ul><ul><li>Fields selection </li></ul></ul><ul><ul><li>References </li></ul></ul>
  10. 10. Web services for the EB-eye <ul><li>Simple experimental API for basic operations </li></ul><ul><ul><li>Basic metadata information </li></ul></ul><ul><ul><li>Queries (Full-text and entries) </li></ul></ul><ul><ul><li>Cross-references navigation </li></ul></ul><ul><li>Depending on the usage, we may implement a more complex API and more functionalities </li></ul>
  11. 11. 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()
  12. 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. 13. 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)
  14. 14. 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)
  15. 15. Web services – Get referenced entries <ul><li>getReferencedEntries(‘ensembl’, ‘cg2102’, ‘go’) </li></ul><ul><li>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 </li></ul>Get referenced entries for a domain in a particular entry String[] getReferencedEntries(String domain, String entryId, String referencedDomain)
  16. 16. Web services – External cross-references <ul><li>listAdditionalReferenceFields(‘msdpdb’) </li></ul><ul><li>CATH </li></ul><ul><li>PFAM </li></ul><ul><li>SCOP </li></ul>List non EB-eye domains referenced in a domain String[] listAdditionalReferenceFields(String domain)
  17. 17. Future <ul><li>Interoperability with analytical tools (e.g. alignments, similarity searches, text-mining tools, etc.) </li></ul><ul><li>Export results of searches in various formats (e.g. flat lists, Excel sheets, XML, etc.) </li></ul><ul><li>Addition of third party databases </li></ul><ul><li>Links to external data resources </li></ul>
  18. 18. Try it! <ul><li>Available everywhere on the EBI website </li></ul><ul><ul><li>http://www.ebi.ac.uk </li></ul></ul><ul><li>Web services </li></ul><ul><ul><li>http:// www.ebi.ac.uk/Tools/webservices/services/eb -eye </li></ul></ul><ul><li>We need your feedback! </li></ul><ul><ul><li>http://www.ebi.ac.uk/support/ </li></ul></ul><ul><ul><li>[email_address] </li></ul></ul><ul><ul><ul><li>Comments </li></ul></ul></ul><ul><ul><ul><li>Defect reports </li></ul></ul></ul><ul><ul><ul><li>New ideas </li></ul></ul></ul>