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Searching PubMed

By
Dr. A.P. Kulkarni, MD, PhD, FIAPSM
Pro Vice Chancellor
MUHS, Nasik
What Is PubMed

q  Free resource, developed and
  maintained by the National Center for
  Biotechnology Information (NCBI), at the
  U.S. National Library of Medicine (NLM)
q About 22,000 journals since 1966
q  Uses MEDLINE data base
q Accessible through
  http://www.ncbi.nlm.nih.gov/pubmed
22-Jun-11                                    2
The screen you see on
              http://
              www.ncbi.nlm.nih.gov/
              pubmed




            The screen you
            see on
            www.pubmed.gov

22-Jun-11                             3
Common Problems

§  Lot of unnecessary references
§  Retrieving one or two exact
    references
§  Getting latest on a topic
§  We get abstracts, what about getting
    full text (Free !!)?

22-Jun-11                              4
Structure of PubMed

§ Search Box : Type search words
   àSearch
§ Limits: Select Limiting options that cuts
   down unnecessary references, refines
   your search à Search
§ Display Mode : Select :
  Summary, Abstract Plus etc
22-Jun-11                                  5
Search Box
             “Go” button
            Search Button




22-Jun-11                   6
Lot of Unnecessary
            References
Example:
You are a pediatrician. Want
 references on bronchodilators in
 asthma
Type word bronchodilator in search
 box and click Search à 207,402
 references
22-Jun-11                            7
Search Box Entry


            Display Setting
            (Summary)
            207,402 References
            Lined Up




22-Jun-11                              8
Display Setting
            (Abstract)




22-Jun-11                     9
Lot of Unnecessary
            References
Use other key words
Bronchodilator AND asthma
Here AND is a limiting operand
Other operands: OR, NOT

22-Jun-11                    10
Lot of Unnecessary
            References
Example:
Type word bronchodilator AND
 asthma in search box and click
 Search à 18,636 references
Cut down from 207,402 to 18,636

22-Jun-11                         11
Search :
            Bronchodilator
            AND
            Asthma

22-Jun-11                    12
Lot of Unnecessary
            References
Use of Limits     4.  Human / animal
    facility      5.  Journal group
Common Limits     6.  Type of article
1.  Age
2.  Sex
3.  Language
22-Jun-11                           13
Limits Option




22-Jun-11                   14
Limits Options Displayed
            Type of Article         Language
            Clinical trial,         English, French,
            Editorial, Letter etc   German …etc
            Species (Human,         Sex
            Animals)                M, F
            Subsets                 Age
            AIDS                    Birth- 23 mo
            Bio-ethics              0-18 yrs …. etc
            Cancer… etc

22-Jun-11                                              15
Limits Activated

 §  Type of Article : Clinical trial
 §  Language: English
 §  Species: Human
 §  Sex : M, F
 §  Age: 0-18 years
  Number reduced from 18,636 to: 2116

 22-Jun-11                              16
Limits Activated Displayed
            2116 references


22-Jun-11                                17
1 or 2 Exact References

Example:
§  Article by Kulkarni A.P.
§  On Typhoid Outbreak
§  Or is it Typhoid Epidemic?
§  Or is the word “Enteric Fever”
    used?
22-Jun-11                            18
1 or 2 Exact References

Use “Advanced Search” option on Home
  Screen
(Typhoid OR enteric) AND (outbreak OR
  epidemic)
Also use additional option
Kulkarni AP [First Author]
(Typhoid OR enteric) AND (outbreak OR
  epidemic) AND Kulkarni AP[First Author]
22-Jun-11                               19
Related Citations




            Single Article Displayed


22-Jun-11                                20
Getting Latest
Example : Malaria Vaccine , in last 5 years
In Search Box Type
Malaria Vaccine
Use Limits option
In this use Dates - > “Published In
  Last” option & select “5 years”


22-Jun-11                                 21
Getting Latest
§  Search Builder: Various options like
Author, Book, Publication date
§  Can select one or more
§  Can add it to “Search Box” with
    AND, OR options



22-Jun-11                                  22
Search word
                     “ Malaria Vaccine”

            Limits
            Date
            Last 5 years




22-Jun-11                                 23
22-Jun-11   24
Want Full Text : (Free!!)

 In the Limits Find “Text Option”
    Links To Full Text
 ü Links To Free Full Text
   Abstracts
 In the displayed list : Click on “Free
   Full Text” below the article of interest
 Full text is displayed in Separate
   window
 22-Jun-11                                    25
Full
         List of                    Text
                             Artic       o
                   rticles         le D f Select
              78 A                     ispla     ed
Lis t of 16                                  yed
 Dis  played




  22-Jun-11                                           26
Guide   Tools
                    Clinical Queries
                    Topic specific enquiries



22-Jun-11                                      27
More Websites For Free
       Full Text
§  www.biomedcentral.c
    om
§  Independent
    publishing house
§  Permanent, free
    access to 185
    journals
§  Alphabetical list of
    journals
22-Jun-11                  28
More Websites For Free
       Full Text
§  www.openmed.nic.in
§  Free facility for self
    archive
§  Only archived work is
    accessed
§  2004 ----- 123
§  2005 ----- 211
§  2006 ----- 186

22-Jun-11                    29
More Websites For Free
       Full Text
§  www.medind.nic.in
§  Access to selected
    Indian Journals
§  Search facility directs
    you to URL- link of
    the journal
§  Requires Adobe
    Reader


22-Jun-11                     30
More Websites For Free
       Full Text
§  www.indmed.nic.in
§  Indian MEDLAR
§  Full, free text of
    selected journals in
    pdf format
§  One can know from
    icons if free / full text
    available or not

22-Jun-11                       31
More Websites For Free
       Full Text
§  www.popline.org
§  Journals / articles on
    RCH since 1973
§  Also available to
    institutes on CD
§  Full, free text on
    request ( for
    developing countries
    only)

22-Jun-11                    32
More Websites For Free
        Full Text
§  www.freemedicaljour
    nals.com
§  Some journals
    provide free, full text
    after 6 months –
    2years
§  This is collection of
    such access to 430
    journals like JAMA,
    BMJ
 22-Jun-11                    33
More Websites For Full
Text
§  www.highwire.stanford
    .uk
§  Website of Stanford
    University , UK
§  Search facility
§  Full text on payment
§  Requires registration


   22-Jun-11                34
Cochrane Data base

§  www.mrw.interscience.wiley.com/cochrane
§  Cochrane systematic reviews on various
    topics like clinical trials, vaccine trials




  22-Jun-11                                   35

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Searching pub med

  • 1. Searching PubMed By Dr. A.P. Kulkarni, MD, PhD, FIAPSM Pro Vice Chancellor MUHS, Nasik
  • 2. What Is PubMed q  Free resource, developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM) q About 22,000 journals since 1966 q  Uses MEDLINE data base q Accessible through http://www.ncbi.nlm.nih.gov/pubmed 22-Jun-11 2
  • 3. The screen you see on http:// www.ncbi.nlm.nih.gov/ pubmed The screen you see on www.pubmed.gov 22-Jun-11 3
  • 4. Common Problems §  Lot of unnecessary references §  Retrieving one or two exact references §  Getting latest on a topic §  We get abstracts, what about getting full text (Free !!)? 22-Jun-11 4
  • 5. Structure of PubMed § Search Box : Type search words àSearch § Limits: Select Limiting options that cuts down unnecessary references, refines your search à Search § Display Mode : Select : Summary, Abstract Plus etc 22-Jun-11 5
  • 6. Search Box “Go” button Search Button 22-Jun-11 6
  • 7. Lot of Unnecessary References Example: You are a pediatrician. Want references on bronchodilators in asthma Type word bronchodilator in search box and click Search à 207,402 references 22-Jun-11 7
  • 8. Search Box Entry Display Setting (Summary) 207,402 References Lined Up 22-Jun-11 8
  • 9. Display Setting (Abstract) 22-Jun-11 9
  • 10. Lot of Unnecessary References Use other key words Bronchodilator AND asthma Here AND is a limiting operand Other operands: OR, NOT 22-Jun-11 10
  • 11. Lot of Unnecessary References Example: Type word bronchodilator AND asthma in search box and click Search à 18,636 references Cut down from 207,402 to 18,636 22-Jun-11 11
  • 12. Search : Bronchodilator AND Asthma 22-Jun-11 12
  • 13. Lot of Unnecessary References Use of Limits 4.  Human / animal facility 5.  Journal group Common Limits 6.  Type of article 1.  Age 2.  Sex 3.  Language 22-Jun-11 13
  • 15. Limits Options Displayed Type of Article Language Clinical trial, English, French, Editorial, Letter etc German …etc Species (Human, Sex Animals) M, F Subsets Age AIDS Birth- 23 mo Bio-ethics 0-18 yrs …. etc Cancer… etc 22-Jun-11 15
  • 16. Limits Activated §  Type of Article : Clinical trial §  Language: English §  Species: Human §  Sex : M, F §  Age: 0-18 years Number reduced from 18,636 to: 2116 22-Jun-11 16
  • 17. Limits Activated Displayed 2116 references 22-Jun-11 17
  • 18. 1 or 2 Exact References Example: §  Article by Kulkarni A.P. §  On Typhoid Outbreak §  Or is it Typhoid Epidemic? §  Or is the word “Enteric Fever” used? 22-Jun-11 18
  • 19. 1 or 2 Exact References Use “Advanced Search” option on Home Screen (Typhoid OR enteric) AND (outbreak OR epidemic) Also use additional option Kulkarni AP [First Author] (Typhoid OR enteric) AND (outbreak OR epidemic) AND Kulkarni AP[First Author] 22-Jun-11 19
  • 20. Related Citations Single Article Displayed 22-Jun-11 20
  • 21. Getting Latest Example : Malaria Vaccine , in last 5 years In Search Box Type Malaria Vaccine Use Limits option In this use Dates - > “Published In Last” option & select “5 years” 22-Jun-11 21
  • 22. Getting Latest §  Search Builder: Various options like Author, Book, Publication date §  Can select one or more §  Can add it to “Search Box” with AND, OR options 22-Jun-11 22
  • 23. Search word “ Malaria Vaccine” Limits Date Last 5 years 22-Jun-11 23
  • 24. 22-Jun-11 24
  • 25. Want Full Text : (Free!!) In the Limits Find “Text Option” Links To Full Text ü Links To Free Full Text Abstracts In the displayed list : Click on “Free Full Text” below the article of interest Full text is displayed in Separate window 22-Jun-11 25
  • 26. Full List of Text Artic o rticles le D f Select 78 A ispla ed Lis t of 16 yed Dis played 22-Jun-11 26
  • 27. Guide Tools Clinical Queries Topic specific enquiries 22-Jun-11 27
  • 28. More Websites For Free Full Text §  www.biomedcentral.c om §  Independent publishing house §  Permanent, free access to 185 journals §  Alphabetical list of journals 22-Jun-11 28
  • 29. More Websites For Free Full Text §  www.openmed.nic.in §  Free facility for self archive §  Only archived work is accessed §  2004 ----- 123 §  2005 ----- 211 §  2006 ----- 186 22-Jun-11 29
  • 30. More Websites For Free Full Text §  www.medind.nic.in §  Access to selected Indian Journals §  Search facility directs you to URL- link of the journal §  Requires Adobe Reader 22-Jun-11 30
  • 31. More Websites For Free Full Text §  www.indmed.nic.in §  Indian MEDLAR §  Full, free text of selected journals in pdf format §  One can know from icons if free / full text available or not 22-Jun-11 31
  • 32. More Websites For Free Full Text §  www.popline.org §  Journals / articles on RCH since 1973 §  Also available to institutes on CD §  Full, free text on request ( for developing countries only) 22-Jun-11 32
  • 33. More Websites For Free Full Text §  www.freemedicaljour nals.com §  Some journals provide free, full text after 6 months – 2years §  This is collection of such access to 430 journals like JAMA, BMJ 22-Jun-11 33
  • 34. More Websites For Full Text §  www.highwire.stanford .uk §  Website of Stanford University , UK §  Search facility §  Full text on payment §  Requires registration 22-Jun-11 34
  • 35. Cochrane Data base §  www.mrw.interscience.wiley.com/cochrane §  Cochrane systematic reviews on various topics like clinical trials, vaccine trials 22-Jun-11 35