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Literature Informatics Beyond PubMed: Next Generation Literature Searching Carrie Iwema, PhD, MLS 24th August 2011 Growth of PubMed citations from 1986 to 2010 Lu, Database 2011 HSLS, U.Pitt Information Overload? HSLS, U.Pitt GoPubMed: “searching is now sorted” 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 4 filter categories: •What •Who •Where •When Statistics! Related search engines: •Go3R •GoGene •GoWeb Developed by Transinsight GmbH HSLS, U.Pitt GoPubMed http://www.gopubmed.org HSLS, U.Pitt LigerCat: “Literature & Genomics Resource Catalog” •Search articles/journals/genes •Explore tag clouds •Craft queries to PubMed •View Publication History http://ligercat.ubio.org/ Developed by the Biology of Aging project at MBLWHOI Library HSLS, U.Pitt 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 PaperPlane http://pubget.com/site/help/paper_plane Developed by Pubget HSLS, U.Pitt Pubget http://pubget.com HSLS, U.Pitt eTBLAST: text similarity-based search engine Uses natural language processing, keyword weighting, and sentence alignment to search MEDLINE (and more) for query-similar text. Uses: – – – – Find an expert Find a journal View publication history Identify implicit keywords Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute eTBLAST team HSLS, U.Pitt eTBLAST http://etest.vbi.vt.edu/etblast3/ HSLS, U.Pitt Deja Vu: database of highly similar & duplicate citations • Offshoot of eTBLAST • Identifies articles from Medline exhibiting similar if not identical text • Plagiarism buster! Classifications: – Distinct – Duplicate – Erratum – Sanctioned – No abstract – Unverified Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute eTBLAST team HSLS, U.Pitt Deja Vu http://dejavu.vbi.vt.edu/dejavu 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 features RefMed Quertle MedlineRanker MiSearch Hakia SemanticMEDLINE MScanner eTBLAST PubFocus Twease Clustering results into topics Anne O’Tate McSyBi GoPubMed ClusterMed XplorMed Extracting and displaying semantics and relations MedEvi EBIMed CiteXplore MEDIE PubNet Improving search interface and retrieval experience iPubMed PubGet BabelMeSH HubMed askMEDLINE SLIM PICO PubCrawler 2010 2009 2009 2009 2008 2008 2008 2007 2006 2005 Featuring multi-level relevance feedback for ranking Allowing searches with concept categories Finding relevant documents through classification Using implicit feedback for improving ranking Powered by Hakia’s proprietary semantic search technology Powered by cognition’s proprietary search technology Finding relevant documents through classification Finding documents similar to input text Sorting by impact factor and citation volume Query expansion with relevance ranking technique 2008 2007 2005 2004 2001 Clustering by important words, topics, journals, authors, etc. Clustering by MeSH or UMLS concepts Clustering by MeSH or GO terms Clustering by MeSH, title/abstract, author, affiliation, or date Clustering by extracted keywords from abstracts 2008 2007 2006 2006 2005 Providing textual evidence of semantic relations in output Displaying proteins, GO annotations, drugs and species EBI’s tool for integrating biomedical literature and data Extracting text fragments matching queried semantics Visualizing literature-derived network of bio-entities 2010 2007 2006 2006 2005 2005 2004 1999 Allow fuzzy search and approximate match Retrieving results in PDFs Multi-language search interface Export data in multiple format; visualization; etc Converting questions into formulated search as PICO Slider interface for PubMed searches Search with patient, intervention, comparison, outcome Alerting users with new articles based on saved searches http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search / Lu Z Database 2011 Ranking search results HSLS, U.Pitt 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 System University of Pittsburgh [email protected]