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Literature Resources at the EBI
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  1. Literature Resources at the EBI Information Workshop on European Bioinformatics Resources Vienna, 3rd-4th September 2009

  2. What is the scientific literature? Abstracts Full text research articles Patents Grey literature Books

  3. Accessing the literature: search and browse PubMed, PubMed Central Google, Google Scholar EPO, USPO Scopus, WoS, Journal websites Databases, Websites, blogs, Wikis Hard copy publications CiteXplore

  4. Role for CiteXplore • Opportunity to provide content in the public domain from a number of sources • Unique position in EBI to add value through other public domain databases • Text mining capabilities to leverage content • Forge collaborative relationships to find solutions for different user groups

  5. Components of CiteXplore: Abstracts

  6. CiteXplore: Search Features • Simple search box • Query expansion • Ranking by relevance or publication date • Some advanced search features e.g. source, full text links • SOAP web service http://www.ebi.ac.uk/citexplore/

  7. Search the website: ADAMTS7 case study

  8. Added value: Anatomy of a CiteXplore record Full text links Database links Text mining Citation info

  9. Added value: Citation and full text links

  10. Added value: Citation and full text links

  11. Added value: database links

  12. Added value: Database Links Database        #links      CiteXplore records   DB records UniProtKB       5228552  225854           3801970 InterPro           40011      16730            12646 IntAct             10330       3920            10330

  13. Added value: Text mining

  14. Anatomy of a Patent Record

  15. Those are the facts Now for some fiction …. Improvements over the next ~ 6 months include • Full text searching • Addition of content to CiteXplore • Enhanced text mining functions • Leveraging of citation information • Facelift to highlight new features

  16. Full text search 1.5 million articles Search will be available from UKPMC 1.3 million patents Search will be available from EBI

  17. ~ 9 % the size of PubMed

  18. Addition of content to CiteXplore ~ 0.5 million PubMed 19 million PubMed Central 1.8 million PMC will be a true subset at CiteXplore and UKPMC

  19. Enhanced text mining functions • Article summaries • Semantic types: • genes/proteins • GO terms • organisms • diseases • drugs • chemicals • Leveraging semantic indexing • Web service for results, where possible

  20. Text mining for Patents

  21. Leveraging Citations Published research articles Counts Citation sort order Social networking CiteULike Connotea Web hits, downloads (cf PLoS One)

  22. CiteXplore USPs • Search patent abstracts, agricola, other • Search all PubMed and UKPMC abstracts • Text mining: highlighting for abstracts • Text mining: e.g. article summaries for Open Access, Patents • Most complete citation information in the public domain • Full text patent search

  23. Credits Core EBI Staff Peter Stoehr Sharmila Pilia Alan Horne Mark Rijnbeek Content Providers PubMed Agricola EPO Chinese Biological Abstracts Collaborators Dietrich Rebholz-Schuhmann (EBI text mining) NacTeM, MIMAS, British Library (UKPMC) European Patent Office http://www.ebi.ac.uk/citexplore/