EBI is an Outstation of the European Molecular Biology Laboratory. Literature Resources at the EBI...
-
Upload
stuart-cross -
Category
Documents
-
view
222 -
download
0
Transcript of EBI is an Outstation of the European Molecular Biology Laboratory. Literature Resources at the EBI...
EBI is an Outstation of the European Molecular Biology Laboratory.
Literature Resources at the EBIInformation 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
http://www.ebi.ac.uk/citexplore/
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: Citation and full text links
Added value: database links
Added value: Database Links
Database #links CiteXplore records DB records
UniProtKB 5228552 225854 3801970
InterPro 40011 16730 12646
IntAct 10330 3920 10330
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
PubMed19 million
~ 0.5 million
PubMed Central1.8 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 StaffPeter StoehrSharmila PiliaAlan HorneMark Rijnbeek
Content ProvidersPubMedAgricolaEPOChinese Biological Abstracts
CollaboratorsDietrich Rebholz-Schuhmann (EBI text mining)NacTeM, MIMAS, British Library (UKPMC)European Patent Office
http://www.ebi.ac.uk/citexplore/