EBI is an Outstation of the European Molecular Biology Laboratory. Literature Resources at the EBI Information Workshop on European Bioinformatics Resources.

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Presentation transcript:

EBI is an Outstation of the European Molecular Biology Laboratory. Literature Resources at the EBI Information Workshop on European Bioinformatics Resources Vienna, 3rd-4th September 2009

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

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

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

Components of CiteXplore: Abstracts

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

Search the website: ADAMTS7 case study

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

Added value: Citation and full text links

Added value: database links

Added value: Database Links Database #links CiteXplore records DB records UniProtKB InterPro IntAct

Added value: Text mining

Anatomy of a Patent Record

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

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

~ 9 % the size of PubMed

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

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

Text mining for Patents

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

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

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