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Literature Informatics

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.

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Literature Informatics

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  1. Literature Informatics Beyond PubMed: Next Generation Literature Searching Carrie Iwema, PhD, MLS 24th August 2011

  2. Growth of PubMed citations from 1986 to 2010 Lu, Database 2011 HSLS, U.Pitt

  3. Information Overload? HSLS, U.Pitt

  4. 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 Statistics! • 4 filter categories: • What • Who • Where • When • Related search engines: • Go3R • GoGene • GoWeb Developed by Transinsight GmbH HSLS, U.Pitt

  5. http://www.gopubmed.org GoPubMed HSLS, U.Pitt

  6. 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

  7. Pubget: “Find papers fast.” • The search results ARE the papers—PDFs! • Synched w/home institutionjournal 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

  8. http://pubget.com Pubget HSLS, U.Pitt

  9. eTBLAST: text similarity-based search engine Uses natural language processing, keywordweighting, 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

  10. http://etest.vbi.vt.edu/etblast3/ eTBLAST HSLS, U.Pitt

  11. 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

  12. http://dejavu.vbi.vt.edu/dejavu Deja Vu HSLS, U.Pitt

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

  14. Lu Z Database 2011 http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search / HSLS, U.Pitt

  15. Lu Z Database 2011

  16. 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

  17. Thanks for your attention. Good luck searching! Carrie Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh iwema@pitt.edu

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