Searching BioMedical
Literature
Jean Song, MSI
Health Sciences Libraries Informationist
National Center for Integrative Bi...
Overview
 PubMed
   Search and manage citations
   MeSH, Services, PubMed Central
 NIH Public Access Policy
 Google Schola...
PubMed – What it is
 Web-based retrieval system developed by the
 National Center for Biotechnology Information
 (NCBI) at...
PubMed – What it is not
 Hard Sciences
   Biosis Previews
   Engineering Index
   MathSciNet
   Search Tools
   http://sea...
Searching PubMed
 Automatic Term Mapping
   Subject, Journal, Author
   Exploding
   No match – all fields
 Boolean operat...
Translated Search
Search Results
 Summary format
 Icons
   No abstract
   Abstract
   PMC
   Free full-text

 Display
   PMID
   Not Google
...
Single Citation View
Displaying Results
 Action Bar
 Display format
   AbstractPlus
   Citation
   MEDLINE
 Show
 Sort By
 Send To
Citation View
 MeSH Headings
 Publication Types
 Substances
 Grant Support
MeSH – What it is
 Medical Subject Headings
 Controlled vocabulary
 Hierarchical
 Specific
 Descriptive
 Exploding Terms
 ...
MeSH Details
 Manually indexed citations
   Up to 15 headings
   Major/Minor
   Subheadings
 Limitations
   Lengthy proces...
Killer Pop Machines
Related Articles
 Google-like
 Algorithm uses title, abstract, and MeSH
Refining the Search
 Limits
    Dates
    Language
    Humans
    Gender
    Age
    Subsets
    Full-text
    Article Typ...
Tag Term Searching
 Address
   “Ann Arbor”[ad] OR 48109[ad]
   “Mich*”[ad]
 Grant
   da021519[gr]
   8-character serial nu...
Citation Management
 Send To
 Clipboard
 Text
 File
 Printer
Citation Management
 Bibliographic management software
   Endnote,
   Refworks…
   MEDLINE
   display
 RSS Feed
 Order vs
...
RSS Feeds
 Many readers
 CTools
My NCBI
 Login first
 Save searches
 Automatic updates
 Save citations
    Clipboard
    Send to my NCBI
    Collections
 ...
PubMed Services
 Journals
 Database
 MeSH
 Database
 Single
 Citation
 Matcher
 Clinical
 Queries
MeSH Database
PubMed Central
 http://www.pubmedcentral.nih.gov/
 Free digital archive of biomedical and life
 sciences journal literatur...
Full-Text
NIH Public Access Policy
 Newly Enacted
 The Policy implements Division G, Title II, Section 218
 of PL 110-161 (Consolida...
Motive behind the Policy

 http://publicaccess.nih.gov/
 Ensure public access
 Publicly funded
 Advance science and improv...
Who does it apply to?
  Directly funded by an NIH grant or cooperative
  agreement active in Fiscal Year 2008 (October
  1...
Compliance
 Address copyright
   http://www.copyright.umich.edu
   Author’s addendum
 Submit to NIH
   Yourself
   Your in...
Implications
 Text mining, natural language processing
   Increased specificity
   Intelligent proximity indicators
 Appro...
Google Scholar
 http://scholar.google.com
 Broader scope of scholarly literature than
 PubMed
    “peer-reviewed papers, t...
Results


                                         Symbol Boolean operators



        Cited references Google search
    ...
Google Scholar @ UM
 http://scholar.google.com.proxy.lib.umich.edu/
Limitations
 No controlled vocabulary
 No clear source listing
 No combining of searches
 Older citation bias
 Limited fie...
Citation Analysis
 Research productivity measures
   Grant awards, grant dollars
   Publications, cited references
 Streng...
ISI Web of Knowledge
 http://proxy.lib.umich.edu/login?url=http://i
 siknowledge.com/
 Institute for Scientific Informatio...
Cited Reference Search
 Web of Science
 Science Citation Index
 Cited Ref
 Search
Journal Impact Factor
 Journal Citation Report
 Measure applies to journals only, not
 authors (h-index) or individual cit...
Impact Factor
 Immediacy Index - average number of times an article is
 cited in the year it is published
 Cited Half-life...
United States Patent and
Trademark Office
 http://www.uspto.gov/
 Patent database
   Full text for patents issued from 197...
Trademark
 Brand name
 Identify and distinguish the goods of one
 manufacturer or seller from goods
 manufactured or sold ...
Patent
 Grant of property rights by the US gov’t
 Excludes others from making, using, or
 selling the invention in the Uni...
Patents
 Utility, design, plant
 Term – 20 years from new application filing
 Must be NOVEL
 “If the invention has been de...
Patent Database
 http://www.uspto.gov/patft/
 Search prior patents and publications to
 ensure novelty
 Average 24.6 month...
Quick Search
Advanced Search
European Patent Office
 http://www.epo.org
 “uniform application procedure for
 individual inventors and companies
 seekin...
Ask Us
 Health Sciences Libraries
   http://www.lib.umich.edu/hsl
 Art, Architecture & Engineering Library
   http://www.l...
Acknowledgements
 NCBI
 http://www.ncbi.nlm.nih.gov/
 Dr. David States
 Dr. Oliver He
Searching Bio Medical Literature
Searching Bio Medical Literature
Searching Bio Medical Literature
Searching Bio Medical Literature
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Searching Bio Medical Literature

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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 http://searchtools.lib.umich.edu Non-US/English Full-text PubMed Central http://pubmed.gov vs PubMed@UM http://www.ncbi.nlm.nih.gov.proxy.lib.umich.edu/sites/entrez?ot 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 http://www.pubmedcentral.nih.gov/ Free digital archive of biomedical and life sciences journal literature Small percentage of the literature in PubMed Full-text through U of M http://www.ncbi.nlm.nih.gov.proxy.lib.umich.edu/sites /entrez?otool=umichlib http://www.lib.umich.edu http://mirlyn.lib.umich.edu
  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 http://publicaccess.nih.gov/ 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 http://www.copyright.umich.edu 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 http://scholar.google.com 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 http://scholar.google.com.proxy.lib.umich.edu/
  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 http://proxy.lib.umich.edu/login?url=http://i siknowledge.com/ 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 http://www.uspto.gov/ 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 http://www.uspto.gov/patft/ 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 http://www.epo.org “uniform application procedure for individual inventors and companies seeking patent protection in up to 38 European countries”
  47. 47. Ask Us Health Sciences Libraries http://www.lib.umich.edu/hsl Art, Architecture & Engineering Library http://www.lib.umich.edu/aael University Library http://www.lib.umich.edu
  48. 48. Acknowledgements NCBI http://www.ncbi.nlm.nih.gov/ Dr. David States Dr. Oliver He
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