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Searching Bio Medical Literature

A Bioinformatics 800.6 Module A lecture given on February 5, 2008 on the topic of biomedical web-based literature searching tools

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Searching Bio Medical Literature

  1. 1. Searching BioMedical Literature Jean Song, MSI Health Sciences Libraries Informationist National Center for Integrative Biomedical Informatics Bioinformatics 800.6
  2. 2. Overview PubMed Search and manage citations MeSH, Services, PubMed Central NIH Public Access Policy Google Scholar ISI Web of Knowledge Cited Reference Searching Citation Analysis, Impact Factor Patent and Trademark Office
  3. 3. PubMed – What it is Web-based retrieval system developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. Component of Entrez Content MEDLINE OLDMEDLINE In-process Publisher supplied citations Links to Entrez molecular biology databases
  4. 4. PubMed – What it is not Hard Sciences Biosis Previews Engineering Index MathSciNet Search Tools Non-US/English Full-text PubMed Central vs PubMed@UM ool=umichlib
  5. 5. Searching PubMed Automatic Term Mapping Subject, Journal, Author Exploding No match – all fields Boolean operators – AND, OR, NOT Phrase Searching – “pressure point” Truncation – search* Spell check
  6. 6. Translated Search
  7. 7. Search Results Summary format Icons No abstract Abstract PMC Free full-text Display PMID Not Google Related Articles
  8. 8. Single Citation View
  9. 9. Displaying Results Action Bar Display format AbstractPlus Citation MEDLINE Show Sort By Send To
  10. 10. Citation View MeSH Headings Publication Types Substances Grant Support
  11. 11. MeSH – What it is Medical Subject Headings Controlled vocabulary Hierarchical Specific Descriptive Exploding Terms MeSH database
  12. 12. MeSH Details Manually indexed citations Up to 15 headings Major/Minor Subheadings Limitations Lengthy process – indexing and adding new terms Colloquial terms – “vending machines”
  13. 13. Killer Pop Machines
  14. 14. Related Articles Google-like Algorithm uses title, abstract, and MeSH
  15. 15. Refining the Search Limits Dates Language Humans Gender Age Subsets Full-text Article Type Tag Terms Preview/Index History Details
  16. 16. Tag Term Searching Address “Ann Arbor”[ad] OR 48109[ad] “Mich*”[ad] Grant da021519[gr] 8-character serial number consisting of a 2-letter NIH institute/center code and a 6-digit number Major “NF-kappa B”[majr]
  17. 17. Citation Management Send To Clipboard Text File Printer
  18. 18. Citation Management Bibliographic management software Endnote, Refworks… MEDLINE display RSS Feed Order vs Full-text
  19. 19. RSS Feeds Many readers CTools
  20. 20. My NCBI Login first Save searches Automatic updates Save citations Clipboard Send to my NCBI Collections Set filters User preferences
  21. 21. PubMed Services Journals Database MeSH Database Single Citation Matcher Clinical Queries
  22. 22. MeSH Database
  23. 23. PubMed Central Free digital archive of biomedical and life sciences journal literature Small percentage of the literature in PubMed Full-text through U of M /entrez?otool=umichlib
  24. 24. Full-Text
  25. 25. NIH Public Access Policy Newly Enacted The Policy implements Division G, Title II, Section 218 of PL 110-161 (Consolidated Appropriations Act, 2008) which states: The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.
  26. 26. Motive behind the Policy Ensure public access Publicly funded Advance science and improve human health Not open access - not immediate
  27. 27. Who does it apply to? Directly funded by an NIH grant or cooperative agreement active in Fiscal Year 2008 (October 1, 2007- September 30, 2008) or beyond Directly funded by a contract signed on or after April 7, 2008 Directly funded by the NIH Intramural Program If NIH pays your salary
  28. 28. Compliance Address copyright Author’s addendum Submit to NIH Yourself Your institution Your publisher Automatic publisher deposit Cite May 25, 2008 PubMed Central reference number (PMCID)
  29. 29. Implications Text mining, natural language processing Increased specificity Intelligent proximity indicators Approximately 65,000 articles now Estimated 80,000 articles per year from NIH funding
  30. 30. Google Scholar Broader scope of scholarly literature than PubMed “peer-reviewed papers, theses, books, abstracts and articles, from academic publishers, professional societies, preprint repositories, universities and other scholarly organizations” Ranking by citation, journal, full-text PubMed by reverse chronological order “importance” Likened to Scopus and ISI’s Web of Knowledge
  31. 31. Results Symbol Boolean operators Cited references Google search Related article search Authors related to search
  32. 32. Google Scholar @ UM
  33. 33. Limitations No controlled vocabulary No clear source listing No combining of searches Older citation bias Limited field search – title or entire article vs
  34. 34. Citation Analysis Research productivity measures Grant awards, grant dollars Publications, cited references Strengths vs weaknesses History, quantifiable, broad view Homographs (author disambiguation), cronyism, negative citations, lack of tools
  35. 35. ISI Web of Knowledge Institute for Scientific Information (ISI) is now Thomson Scientific Subject searches Cited reference searches Journal impact factor
  36. 36. Cited Reference Search Web of Science Science Citation Index Cited Ref Search
  37. 37. Journal Impact Factor Journal Citation Report Measure applies to journals only, not authors (h-index) or individual citations Average number of times articles from a journal published in the past two years have been cited in the following year View aggregate journals or by subject categories
  38. 38. Impact Factor Immediacy Index - average number of times an article is cited in the year it is published Cited Half-life - median age of the articles that were cited in that year 2006 aggregate JCR top 10
  39. 39. United States Patent and Trademark Office Patent database Full text for patents issued from 1976 to the present TIFF images for all patents from 1790 to present Art, Architecture & Engineering Library is a Patent and Trademark Depository Library
  40. 40. Trademark Brand name Identify and distinguish the goods of one manufacturer or seller from goods manufactured or sold by others R May be used once registered
  41. 41. Patent Grant of property rights by the US gov’t Excludes others from making, using, or selling the invention in the United States “Patent Pending” – application filed Protection does not start until patent is granted
  42. 42. Patents Utility, design, plant Term – 20 years from new application filing Must be NOVEL “If the invention has been described in a printed publication anywhere, or has been in public use or on sale in this country more than one year before the date on which an application for patent is filed in this country, a patent cannot be obtained”
  43. 43. Patent Database Search prior patents and publications to ensure novelty Average 24.6 months to process Pending applications only searchable after 18 months
  44. 44. Quick Search
  45. 45. Advanced Search
  46. 46. European Patent Office “uniform application procedure for individual inventors and companies seeking patent protection in up to 38 European countries”
  47. 47. Ask Us Health Sciences Libraries Art, Architecture & Engineering Library University Library
  48. 48. Acknowledgements NCBI Dr. David States Dr. Oliver He