Literature Informatics Beyond PubMed: Next Generation Literature Searching Carrie Iwema, PhD, MLS 24 th August 2011
Dec 19, 2015
Literature Informatics
Beyond PubMed: Next Generation
Literature Searching
Carrie Iwema, PhD, MLS24th August 2011
Growth of PubMed citations from 1986 to 2010
Lu, Database 2011
HSLS, U.Pitt
Information Overload?
HSLS, U.Pitt
Ontology-based literature searching
– Medical Subject Headings (MeSH)• Hierarchical vocabulary for biomedical and health-
related topics– Gene Ontology (GO)
• Controlled vocabulary for molecular biology topics
GoPubMed: “searching is now sorted”
Developed by Transinsight GmbH
4 filter categories:
• What• Who• Where• When
Related search engines:
• Go3R• GoGene• GoWeb
Statistics!
HSLS, U.Pitt
LigerCat: “Literature & Genomics Resource Catalog”
Developed by the Biology of Aging project at MBLWHOI Library
• Search articles/journals/genes• Explore tag clouds• Craft queries to PubMed• View Publication History
HSLS, U.Pitt
http://ligercat.ubio.org/
Pubget: “Find papers fast.”
• The search results ARE the papers—PDFs!• Synched w/home institution journal
subscriptions• Customizable “latest issues” journal list• Easily browse your favorite journals
PaperPlanehttp://pubget.com/site/help/paper_plane
Developed by Pubget
HSLS, U.Pitt
eTBLAST: text similarity-based search engine
Uses:– Find an expert– Find a journal– View publication history– Identify implicit
keywordsDeveloped by UT Southwestern Computational Biology
Group, serviced by Virginia Bioinformatics Institute eTBLAST team
Uses natural language processing, keyword weighting, and sentence alignment to search MEDLINE (and
more) for query-similar text.
HSLS, U.Pitt
Deja Vu: database of highly similar & duplicate citations
Classifications:– Distinct– Duplicate– Erratum
– Sanctioned
– No abstract
– Unverified
• Offshoot of eTBLAST• Identifies articles from Medline
exhibiting similar if not identical text
• Plagiarism buster!
Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute
eTBLAST team
HSLS, U.Pitt
Why They’re Cool…
• GoPubMed— Statistics!
• LigetCat— Word Clouds!
• Pubget— PDFs!
• eTBLAST— Text Similarity!
• Deja Vu— Plagiarism Buster!
HSLS, U.Pitt
Systems Year Major featuresRanking search results
RefMed 2010 Featuring multi-level relevance feedback for ranking Quertle 2009 Allowing searches with concept categories MedlineRanker 2009 Finding relevant documents through classification MiSearch 2009 Using implicit feedback for improving ranking Hakia 2008 Powered by Hakia’s proprietary semantic search technology SemanticMEDLINE 2008 Powered by cognition’s proprietary search technology MScanner 2008 Finding relevant documents through classification eTBLAST 2007 Finding documents similar to input text PubFocus 2006 Sorting by impact factor and citation volume Twease 2005 Query expansion with relevance ranking technique
Clustering results into topics Anne O’Tate 2008 Clustering by important words, topics, journals, authors, etc. McSyBi 2007 Clustering by MeSH or UMLS concepts GoPubMed 2005 Clustering by MeSH or GO terms
ClusterMed 2004 Clustering by MeSH, title/abstract, author, affiliation, or date
XplorMed 2001 Clustering by extracted keywords from abstractsExtracting and displaying semantics and relations
MedEvi 2008 Providing textual evidence of semantic relations in output EBIMed 2007 Displaying proteins, GO annotations, drugs and species CiteXplore 2006 EBI’s tool for integrating biomedical literature and data MEDIE 2006 Extracting text fragments matching queried semantics PubNet 2005 Visualizing literature-derived network of bio-entities
Improving search interface and retrieval experience iPubMed 2010 Allow fuzzy search and approximate match PubGet 2007 Retrieving results in PDFs BabelMeSH 2006 Multi-language search interface HubMed 2006 Export data in multiple format; visualization; etc askMEDLINE 2005 Converting questions into formulated search as PICO SLIM 2005 Slider interface for PubMed searches PICO 2004 Search with patient, intervention, comparison, outcome PubCrawler 1999 Alerting users with new articles based on saved searches
Lu
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2011
HSLS, U.Pitt
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search /
Lu Z Database 2011
Video Tutorials
• Searching using MESH terms: http://media.hsls.pitt.edu/media/clres2705/mesh.swf
• Pubmed Clinical Queries: http://media.hsls.pitt.edu/media/clres2705/scz.swf
• GoPubmed: http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf
HSLS, U.Pitt
Thanks for your attention.
Good luck searching!Carrie Iwema, PhD, MLS
Information Specialist in Molecular Biology
Health Sciences Library SystemUniversity of Pittsburgh