Literature Informatics Beyond PubMed: Next Generation Literature Searching Carrie Iwema, PhD, MLS 24 th 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

GoPubMed 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

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 Developed by Pubget HSLS, U.Pitt

Pubget HSLS, U.Pitt

eTBLAST: text similarity-based search engine 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 Uses natural language processing, keyword weighting, and sentence alignment to search MEDLINE (and more) for query-similar text. HSLS, U.Pitt

eTBLAST 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

Deja Vu HSLS, U.Pitt

Why They’re Cool… GoPubMed—Statistics! LigetCat— Word Clouds! Pubget— PDFs! eTBLAST— Text Similarity! Deja Vu— Plagiarism Buster! HSLS, U.Pitt

SystemsYearMajor features Ranking search results RefMed 2010Featuring multi-level relevance feedback for ranking Quertle 2009Allowing searches with concept categories MedlineRanker 2009Finding relevant documents through classification MiSearch 2009Using implicit feedback for improving ranking Hakia 2008Powered by Hakia’s proprietary semantic search technology SemanticMEDLINE 2008Powered by cognition’s proprietary search technology MScanner 2008Finding relevant documents through classification eTBLAST 2007Finding documents similar to input text PubFocus 2006Sorting by impact factor and citation volume Twease 2005Query expansion with relevance ranking technique Clustering results into topics Anne O’Tate 2008Clustering by important words, topics, journals, authors, etc. McSyBi 2007Clustering by MeSH or UMLS concepts GoPubMed 2005Clustering by MeSH or GO terms ClusterMed 2004Clustering by MeSH, title/abstract, author, affiliation, or date XplorMed 2001Clustering by extracted keywords from abstracts Extracting and displaying semantics and relations MedEvi 2008Providing textual evidence of semantic relations in output EBIMed 2007Displaying proteins, GO annotations, drugs and species CiteXplore 2006EBI’s tool for integrating biomedical literature and data MEDIE 2006Extracting text fragments matching queried semantics PubNet 2005Visualizing literature-derived network of bio-entities Improving search interface and retrieval experience iPubMed 2010Allow fuzzy search and approximate match PubGet 2007Retrieving results in PDFs BabelMeSH 2006Multi-language search interface HubMed 2006Export data in multiple format; visualization; etc askMEDLINE 2005Converting questions into formulated search as PICO SLIM 2005Slider interface for PubMed searches PICO 2004Search with patient, intervention, comparison, outcome PubCrawler 1999Alerting users with new articles based on saved searches Lu Z Database 2011 HSLS, U.Pitt /

Lu Z Database 2011

Video Tutorials Searching using MESH terms: Pubmed Clinical Queries: GoPubmed : 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