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

1. Searching BioMedical
Literature
Jean Song, MSI
Health Sciences Libraries Informationist
National Center for Integrative Biomedical
Informatics
Bioinformatics 800.6

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. 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. 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

6. 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

7. Translated Search

8. Search Results
Summary format
Icons
No abstract
Abstract
PMC
Free full-text
Display
PMID
Not Google
Related Articles

9. Single Citation View

10. Displaying Results
Action Bar
Display format
AbstractPlus
Citation
MEDLINE
Show
Sort By
Send To

11. Citation View
MeSH Headings
Publication Types
Substances
Grant Support

12. MeSH – What it is
Medical Subject Headings
Controlled vocabulary
Hierarchical
Specific
Descriptive
Exploding Terms
MeSH database

13. MeSH Details
Manually indexed citations
Up to 15 headings
Major/Minor
Subheadings
Limitations
Lengthy process – indexing and adding new
terms
Colloquial terms – “vending machines”

14. Killer Pop Machines

15. Related Articles
Google-like
Algorithm uses title, abstract, and MeSH

16. Refining the Search
Limits
Dates
Language
Humans
Gender
Age
Subsets
Full-text
Article Type
Tag Terms
Preview/Index
History
Details

17. 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]

18. Citation Management
Send To
Clipboard
Text
File
Printer

19. Citation Management
Bibliographic management software
Endnote,
Refworks…
MEDLINE
display
RSS Feed
Order vs
Full-text

20. RSS Feeds
Many readers
CTools

21. My NCBI
Login first
Save searches
Automatic updates
Save citations
Clipboard
Send to my NCBI
Collections
Set filters
User
preferences

22. PubMed Services
Journals
Database
MeSH
Database
Single
Citation
Matcher
Clinical
Queries

23. MeSH Database

24. 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

25. Full-Text

26. 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.

27. Motive behind the Policy
http://publicaccess.nih.gov/
Ensure public access
Publicly funded
Advance science and improve human
health
Not open access - not immediate

28. 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

29. 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)

30. 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

31. 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

32. Results
Symbol Boolean operators
Cited references Google search
Related article search
Authors related to search

33. Google Scholar @ UM
http://scholar.google.com.proxy.lib.umich.edu/

34. Limitations
No controlled vocabulary
No clear source listing
No combining of searches
Older citation bias
Limited field search – title or entire article
vs

35. 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

36. 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

38. Cited Reference Search
Web of Science
Science Citation Index
Cited Ref
Search

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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”

47. 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

48. Quick Search

49. Advanced Search

50. European Patent Office
http://www.epo.org
“uniform application procedure for
individual inventors and companies
seeking patent protection in up to 38
European countries”

51. 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

52. Acknowledgements
NCBI
http://www.ncbi.nlm.nih.gov/
Dr. David States
Dr. Oliver He