This document provides an overview of searching for articles in bibliographical databases. It discusses key concepts such as bibliographical databases and indexes, search strategies, Boolean logic, truncation, and thesaurus searching. Specific examples are provided to illustrate searching the Medline database for articles on non-invasive prenatal testing using the PICO framework. Indexing processes for Medline are also summarized, including how indexers assign major and non-major subject headings.

1. Searching for articles
in bibliographical databases
Concepts and examples
2014-10-03 Patrice X. Chalon, M.Sc. 1

2. What is this?
2
Image source: https://www.flickr.com/photos/glooze_photos/3693153103/

3. What is this?
3
Image source: https://www.flickr.com/photos/donutgirl/273061411/

4. Image source: http://www.flickr.com/photos/-cavin-/2209548445/
4
What is this?
4

5. Image source : http://www.flickr.com/photos/34878947@N04/4605875739
http://www.flickr.com/photos/yeliseev/2283085538
http://www.flickr.com/photos/ericbegin/2462706533/
http://ellenblickman.com/wp-content/uploads/2009/05/books-computer.jpg /
5
1994 1999 2004
5

6. Knowledge Management
Knowledge
6
Explicit
knowledge
Implicit (tacit)
knowledge
http://www.flickr.com/photos/lac-bac/7797313986/
http://www.flickr.com/photos/janeladeimagens/170838066/
Record and distribute
(Formalisation, structuration,
diffusion)
Develop and disseminate
(Training, coaching, feedbacks..)

7. Sources
7
Image sources:
http://www.flickr.com/photos/jcmejiaacera/11646975845/
http://www.flickr.com/photos/georgmayer/126254265/
http://www.flickr.com/photos/sloanpix/8205071402/
http://www.flickr.com/photos/raster/3380860520/

8. 8
Who are you?
8

9. And example…
THE CONCEPTS
9
http://www.flickr.com/photos/jakeandlindsay/5524669257/

10. BIBLIOGRAPHICAL
DATABASES
10
Source: http://www.flickr.com/photos/omcoc/6751047205/

11. Bibliographical indexes
11
Source: http://nlm.nih.gov/hmd/sowhatsnew/images/3a7-a.jpg

12. Content of a record
So = Jo, Dp, Vo, Is, Pg
Eur J Nucl Med, 2000, 27 (1): 91-7
Au
Mijnhout GS, Hooft L, van Tulder MW, Deville WL, Teule GJ and Hoekstra
OS
Ti
How to perform a comprehensive search for FDG-PET literature.
Ab
In this study, a comprehensive, unbiassed search strategy for identifying
literature on fluorine-18 fluorodeoxyglucose positron emission tomography
(FDG-PET) in Medline, Embase and Current Contents was developed, …
Kw, SH.
Abstracting and Indexing ; Databases, Bibliographic ; Fludeoxyglucose F
18/ diagnostic use ; Fluorine Radioisotopes/ diagnostic use; Human ;
Medline ; Periodicals ; Radiopharmaceuticals/ diagnostic use ; Research ;
Subject Headings ; Tomography, Emission-Computed
Others : Ad, ISSN, La, URL, References,…
Accurate ?
Particle !
Traduced
title ?
Manual /
Automatic ?
Keywords or
Subject
Headings ?
Manual / Automatic ?
Source: MedLine
12 12

13. 13
Evolution of databases
13

14. A world of datbases
14

15. HOW TO SEARCH?
15
Source: http://www.flickr.com/photos/omcoc/6751047205/

16. Search strategy quadrant
pertinent
Not
pertinent
Not
identified SILENCE
identified NOISE
16 16

17. Sensitive vs Specific search
Sensitive
 For a sensitive search you
need to think of all the
possible ways an author or
an indexer might describe
each of your key words in
phrases. You might find it
useful to check with a
medical thesaurus or a list of
subject heading such as
MESH (Medical Subject
Headings).
 The more alternative terms
you use the more results
you will get from the search.
Specific
 For a specific search you want to use only terms that
relate directly to your question, so you would use
only one (or at the most two) way to describe
each search term. You may need to check with the
MESH as with the databases own thesaurus to
ensure that the terms you are using are the terms the
indexer would use.
 In a specific search, you would apply more Limits.
Limits are search terms such as language, age of
article, journal title, article type or limits on the
populations such as age, gender, ethnic group etc.
 You can limit articles NOT to find certain terms,
for example you could search for stress but NOT
stress fractures.
 The more limits you apply to a search the fewer
results you will get from that search.
Source : NHS FIFE LIBRARY SERVICES: Guide to Literature Searching. Available from: http://www.nhsfifelibraries.scot.nhs.uk/publications/litsearching.doc
17
2010-09-10 Patrice X. Chalon 17

18. Documenting the search
18

19. EBM…
19

20. Source: Guyatt G, Evidence-Based Medicine Working Group. Users' guides to the medical literature : a manual for evidence-based clinical practice. 2nd ed.
New York: McGraw-Hill Medical; 2008.
20
Evidenced- based approach
1. Identify your problem
2. Define a structured question
3. Find the best evidence
4. How valid is the study?
5. What are the results?
6. How should I apply the results to patient care?
20

21. 1. IDENTIFY YOUR PROBLEM
Image source : http://www.flickr.com/photos/crystaljingsr/3914729343/
21 21

22. Example
22

23. 2. DEFINE A
STRUCTURED QUESTION
Image source : http://www.flickr.com/photos/crystaljingsr/3915514014
23 23

24. Frameworks for structured questions
PICO(s) SPICE ECLISPSE
Patient / Population Setting Expectations
Intervention Perspective Client group
Comparison Intervention Location
Outcome Comparison Impact
Study design Evaluation Professionals
Involved
Service
Evaluation
Image source : http://www.flickr.com/photos/nguyendai/502168391
24 24

25. Example
25
Hulstaert F, Neyt M, Gyselaers W. The non-invasive prenatal test (NIPT) for trisomy 21 – health economic aspects. Health Technology Assessment (HTA)
Brussels: Belgian Health Care Knowledge Centre (KCE). 2014. KCE Reports 222. D/2014/10.273/36.

26. Example (cont.)
26

27. Synonyms, derivatives…
LIST YOUR TERMS!
27
Image source : http://www.flickr.com/photos/crystaljingsr/3915514014

28. Example
28
Source: Lancet. 369(9560):474-81, 2007 Feb 10.

29. 29
Example (cont.)
Population
 Pregnant woman
 Pregnant women
 …
Intervention
 NIPT
 Non-Invasive Prenatal
Test
 Noninvasive Prenatal
Testing
 Diagnostic anténatal
non-invasif
 …
29

30. 3. FIND THE BEST EVIDENCE
Image source : http://www.flickr.com/photos/crystaljingsr/3915514724
30 30

31. Where to search?
31

32. Database…S?
« La recherche dans une seconde base permet de récolter de 8 à 40% de
références supplémentaires généralement issues de périodiques possédant un
facteur d’impact, même faible. »
Source: Le traitement médicamenteux de l'insuffisance cardiaque par 3 grands groupes pharmacologiques : Evaluation de la complémentarité des outils
bibliographiques du domaine biomédical de l’Université de Liège. Chalon P, 2002, Report.
32
1999-2001 Diurétiques Digitaliques Beta-bloquants
Medline 619 287 666
Chemical Abstracts
Spécifiques (%)
Journaux suppl
(avec IF)
780
+161 (20.6)
+ 35 (6)
146
+ 81 (22)
+ 23 (3)
170
+ 103 (13.4)
+ 19 (1)
Current Contents
Spécifiques (%)
Journaux suppl
(avec IF)
472
+ 99 (13.8)
+ 15 (12)
162
+ 27 (8.6)
+ 6 (3)
717
+ 445 (40.1)
+ 13 (9)
32

33. Database characteristics
 Time coverage
 Topics
 Source
 Content
 Indexation
 Abstracts
2010-09-10 Patrice X. Chalon 33 33

34. TEXTWORD SEARCH
34
http://www.flickr.com/photos/robbie73/4289385819/

35. 35
SEARCH INTERFACES
35

36. Search interface characteristics
 Truncation
 Booleans
 Thesaurus options
 Related references…
 Query in natural language
 Simple search vs advanced
 Search filters…
36 36

37. TRUNCATION
Variants Economical vs
Economics
Economic* 0-n
Singular vs Plural Test vs Tests Test? 0-1
EN-us vs EN-uk Hematology vs
Haematology
H?ematology 0-1
Prefixes Pre natal vs
prenatal vs pre-natal
Pre?natal 0-1
37 37

38. BOOLEANS
NEAR
 non invasive prenatal
test / in all fields = 7
results
 non invasive prenatal
test / in Title = 1 result
ADJn
 (prenatal and test) /all
fiels = 9689
 (prenatal adj2 test) / all
fields = 348
 Prenatal test / all fields
= 140
2010-09-10 38

39. BOOLEANS (cont.)
ADJn
 (prenatal and test) = 9689
 (prenatal adj2 test) = 348
 Prenatal test = 140
2010-09-10 39

40. BOOLEANS (cont.)
40
Patient AND
Inter
vention
Design
Comparator
OR

41. BOOLEANS (cont)
Breast NeoplamsNOTBreast Neoplasms, male
41
Breast
Neoplasms
Breast
Neoplasms,
Male
Source: http://www.flickr.com/photos/fs999/3508277416

42. Example (cont.)
(pregnant wom?n OR
pregnancy)
AND
(NIPT OR (non invasive ADJ2
prenatal ADJ2 test*))
42 42

43. Example (Cont.)
43

44. THESAURUS SEARCH
Image source : http://www.zazzle.be/dinosaure_de_thesaurus_tapis_souris-144708844640520683
44 44

45. Remember me?
45

46. Taxonomy
 PHYLUM AND SUBPHYLUM - Chordata, Vertebrata
 CLASS AND SUBCLASS - Aves, Neornithes
 ORDER AND SUBORDER - Falconiformes, Falcones
 FAMILY AND SUBFAMILY - Accipitridae, Buteoninae
 GENUS AND SUBGENUS - Haliaeetus,
- SPECIES AND SSP - leucocephalis,
leucocephalis
 SCIENTIFIC NAME - Haliaeetus leucocephalis leucocephalis
Source : http://fwie.fw.vt.edu/WWW/macsis/lists/M040093.htm
46 46

47. Thesaurus : definition
 Alphabetical list of selected words
used to classify documentation
Source: Dictionary French Larousse. Available from http://www.larousse.com/en/dictionaries/french/thesaurus
47
47

48. Thesaurus: relationships
48
Source: http://www.cndp.fr/thesaurus-motbis/

49. Thesaurus : evaluation
Advantages
 Quick results
Less noise
 Updated regularly
Disadvantages
 All concepts are not
covered
 New terms need
some time to be
correctly used
49 49

50. They are working for you!
MEDLINE INDEXING
50
Source: http://ihm.nlm.nih.gov/images/A017410

51. Indexing process
1. Read carefully and understand the title.
2. Read the introduction, looking for the purpose of the article.
3. Scan the body of the article, focus on the Materials & Methods section and the Results section.
4. Note section headings, paragraph headings; italics, boldface; charts, plates, tables, illustrations; laboratory methods,
case reports, etc.
5. Select for indexing only those subjects actually
discussed as opposed to those subjects merely
mentioned.
6. Read the summary or conclusions of the author to determine whether the stated purpose was achieved. Do not
index implications or suggested future applications. Do not index
conclusive statements not supported by the text.
7. Scan the abstract for items missed, verifying that the text supports indexing these concepts.
8. Scan the author's own indexing or the keywords supplied by the publisher to see whether the concepts chosen are
actually discussed in the text.
9. Scan the bibliographic references supplied by the author for clues and further corroboration.
Source : The basics of medical subject headings (MeSH®) in MEDLINE®/PubMed available from http://www.Nlm.Nih.Gov /bsd/disted/mesh/index.Html
51 51

52. Finding terms
 Indexers use the hierarchy to find the most
specific MeSH heading (rather than each of the broader
subjects in which a searcher may be interested)
 Indexers use more than one heading if a
single heading does not cover the concept
 If an exact heading does not exist, indexers
use the MeSH Browser and the hierarchy to
find the most specific heading available.
Source : The basics of medical subject headings (MeSH®) in MEDLINE®/PubMed available from http://www.Nlm.Nih.Gov/bsd/disted/mesh/index.Html
52 52

53. Example
53

54. Major topics
 Asterisks on MeSH headings and subheadings (e.g.,
Wound Healing/radiation effects*) designate that they are
the major topics of the article, usually obtained from the
title and/or statement of purpose
 Non-major (non-asterisked) headings and subheadings
are usually additional topics substantively discussed
within the article, terms added to qualify a major topic
(…).
 The only indexed MEDLINE citations without an
asterisked heading are some biographies in which the
subject’s name may be considered the only major point.
(…)
Source : The basics of medical subject headings (MeSH®) in MEDLINE®/PubMed available from http://www.Nlm.Nih.Gov/bsd/disted/mesh/index.Html
54 54

55. Coordination
 Using a subheading to describe a specific aspect of a MeSH
heading
“Blood analysis of Carbon Monoxyde”
Carbon Monoxyde / Blood
 Using two MeSH headings
"Treatment of HIV infections with HIV protease inhibitors"
HIV Infections/drug therapy
HIV Protease Inhibitors/therapeutic use
 Indexing a "pre-coordinated" MeSH heading which combines
two concepts into one
Pneumonia, Staphylococcal
Source : The basics of medical subject headings (MeSH®) in MEDLINE®/PubMed available from http://www.Nlm.Nih.Gov /bsd/disted/mesh/index.Html
55 55

56. Example
56
Source: http://www.ncbi.nlm.nih.gov/mesh/68019694

57. Rule of three
 More than 3 major concepts: If more than 3 related topics are
each presented as a major topic of the article, the more
general MeSH heading under which they are all
treed is usually designated as the major topic. The
specific headings are usually indexed, but not as major topics.
 More than 3 non-major concepts: If more than 3 related
concepts are discussed in an article but are not a major topic,
the more general MeSH heading under which they
are all treed is usually indexed. The specific headings
usually are not indexed.
Source : The basics of medical subject headings (MeSH®) in MEDLINE®/PubMed available from http://www.Nlm.Nih.Gov /bsd/disted/mesh/index.Html
57 57

58. Example
58
Source: http://www.ncbi.nlm.nih.gov/mesh/68006521

59. COMBINING OPTIONS
59

60. Example
60
Hulstaert F, Neyt M, Gyselaers W. The non-invasive prenatal test (NIPT) for trisomy 21 – health economic aspects. Health Technology Assessment (HTA)
Brussels: Belgian Health Care Knowledge Centre (KCE). 2014. KCE Reports 222. D/2014/10.273/36.

61. Source: http://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Kitchen_Funnel.jpg/1026px-
Kitchen_Funnel.jpg
Limiting results
61 61

62. When?
62
http://www.flickr.com/photos/damaradeaella/2822846819

63. How
 Thesaurus advanced features
 Special queries
 Publication type
 Language
 …
63

64. Thesaurus adv. feat.
Focus
 Pregnant Women/ =
5671
 *Pregnant Women/ =
2765
Sub-headings
 Breast Neoplasms =
221.295
 Breast Neoplasms/di
[Diagnosis] = 26.937
64
Explosion
 Breast Neoplasms =
221.295
 Exp Breast Neoplasms
= 223.494

65. Neyt M, Chalon PX. PharmacoEconomics. (2013 Nov
8. [Epub ahead of print])
Special queries
65
2010-09-10 Patrice X. Chalon 65

66. Evidence pyramid
66

67. Last but not least
COMPLEMENTARY SOURCES
Image source : http://www.flickr.com/photos/redjar/113026147
67
67

68.  Full text database (open access!,
Google scholar,…)
 OAI repositories (REPEC,…)
 Clinical trials registers
 Conference proceedings
 “Hand searching” (Reference lists,
core journals, contacts)
 Networks…
2010-09-10 68

69. SuRe info
69
http://www.sure-info.org
http://vortal.htai.org/?q=node/336

70. Thank you!
70
Source: http://www.flickr.com/photos/omcoc/6751047205/

71. Exercise
71
KCE Reports vol. 217
KCE Reports vol. 189