HINTS on usingliterature databases
Louis Volkers & Gerdien de Jonge
Medical Library - Erasmus MC
phone 87785
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Introduction
1. Literature retrieval: the procedure
2. Available databases
3. How to access fulltext articles
4. Hints on PubMed
5. Demonstration
6. Questions?
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Literature retrieval: the procedure Problem definition
What is the problem? What do you want to know? Put the question into words as a full sentence, the best one is a
question that can be answered with 'yes' or 'no‘ Which are the important items in the question?
Generate synonyms and equivalencies Be aware of British / American differences in spelling:
tumour OR tumor; haemoglobin OR hemoglobin What type of combinations? AND OR NOT Which database(s) to use? Perform searches, and find references Evaluate the results Eventually repeat previous steps Collect relevant articles, read and interprete those Did this answer your question?
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Available literature databases
Primary literature (results of original research)
articles in journals (printed, electronic)
books, reports, etc.
Secundary literature (derivations of primary literature)
compilations, often with summaries (indexes)
PubMed (Medline), PsycInfo, Web-of-Science, PiCarta(EMbase is not available; at this moment it is too expensive for us, there is an
extensive overlap with the free Medline)
Scopus (test), Google Scholar, searchable sites of publishers (Elsevier SciDir)
Reviews, systematic reviews, meta-analyses
Cochrane Library (Database of Systematic Reviews)
UpToDate (a kind of an e-book on internal medicine and pediatrics)
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How to access fulltext articles?
Available in Erasmus MC: a collection of about 700 printed journals (in the Medical Library)
a connection to about 4000 electronic journals (on the internet)
Which? See the Alphabetic List of All Journals on MB home
Journal not available?Request a photocopy (online request form; not for free)
PubMed opens up for about 4500 journals start PubMed from MB home to see fulltext links
change Display = Abstract for clickable links to accessible fulltext:
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Types of search strategies
(Example: PubMed)
Free-text search
search words in all fields
Subject search
search subjects with standardized keywords (MeSH)
PubMed combines both searches, depending on search terms
Limit search
restrict to several attributes (f.e. age groups, type of research)
Index search
search by selecting terms in alphabetic lists
Combine searches: AND OR NOT
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Combinations
union intersection exclusion
vegetables OR fruit
vegetables AND
intestinal cancer
#8 NOT #4
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Types of search strategies
(Example: PubMed)
Free-text search
search words in all fields
Subject search
search subjects with standardized keywords (MeSH)
PubMed combines both searches, depending on search terms
Limit search
restrict to several attributes (f.e. age groups, type of research)
Index search
search by selecting terms in alphabetic lists
Combine searches: AND OR NOT
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Subject search in Medline:Subject search in Medline: standard keywords standard keywords
MeSH: Medical Subject Headings
Genotype
Follow-Up Studies
additional subheadings
(depends on type of keyword)
Peptidyl-Dipeptidase A/genetics*
Cardiovascular Diseases/mortality
used as major topic* or minor topic
functional tree structure > explosion of terms
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Subject search in Medline:Subject search in Medline: standard keywords standard keywords
MeSH: Medical Subject Headings
Genotype
Follow-Up Studies
additional subheadings
(depends on type of keyword)
Peptidyl-Dipeptidase A/genetics*
Cardiovascular Diseases/mortality
used as major topic* or minor topic
functional tree structure > explosion of terms
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Record in PubMed (Display = Citation)
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Subject search in Medline:Subject search in Medline: standard keywords standard keywords
MeSH: Medical Subject Headings
Genotype
Follow-Up Studies
additional subheadings
(depends on type of keyword)
Peptidyl-Dipeptidase A/genetics*
Cardiovascular Diseases/mortality
used as major topic* or minor topic
functional tree structure > explosion of terms
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MeSH - treeMeSH - tree
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Types of search strategies
(Example: PubMed)
Free-text search
search words in all fields
Subject search
search subjects with standardized keywords (MeSH)
PubMed combines both searches, depending on search terms
Limit search
restrict to several attributes (f.e. age groups, type of research)
Index search
search by selecting terms in alphabetic lists
Combine searches: AND OR NOT
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How to find search terms?How to find search terms?
just type your words (not the optimal way for a scientist)
click [MeSH Database] > type word > see MeSH terms > see MeSH tree
> select MeSH term or select subheadings > add to search box
> perform search
type the word(s)
> [Go] > [Details] > see Automatic Term Mapping
(next slide)
type the word(s) restricted to Title field
f.e. genet*[ti] AND statist*[ti]
> [Go] > change [Display=Summary] into [Display=Citation]
> see the records indicated by 'indexed for MEDLINE'
> usefull terms in the MeSH field?
(demonstration)
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Automatic Term MappingAutomatic Term Mappingsearch terms are automatically mapped to MeSH terms
Conditions for searching:
do NOT search with word roots and a wildcard (*)
do NOT search "quoted phrase"
do NOT search by indexes (except for MeSH index)
do NOT search in special fields (f.e. title)(except ALL fields or MeSH field)
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Automatic Term MappingAutomatic Term Mappingsearch terms are automatically mapped to MeSH terms
Conditions for searching:
do NOT search with word roots and a wildcard (*)
do NOT search "quoted phrase"
do NOT search by indexes (except for MeSH index)
do NOT search in special fields (f.e. title)(except ALL fields or MeSH field)
When term mapping succeeded, PubMed searches like this (click Details):
subject in MeSH fields OR text word in all text fields
f.e. search term = red blood cell =>erythrocytes[MeSH Terms] OR red blood cell[Text Word] (n=127877)
f.e. search term = red blood cell* =>red blood cell[All Fields] OR red blood cells[All Fields] (n=34658)
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SDI: What's new in Medline?SDI: What's new in Medline?automatical updates via "My NCBI"
In "My NCBI" you can:
save your searches
automatic check for new citations by e-mail
special filter selections
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SDI: What's new in Medline?SDI: What's new in Medline?automatical updates via "My NCBI"
In "My NCBI" you can:
save your searches
automatic check for new citations by e-mail
special filter selections
Actions:
First time: register; next time: log in with username and password
Configure display filters
Save searches, and configure e-mail updates
View "My NCBI"; make updates manually
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Locations in the Medical Library
(2nd floor building Ee)
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Demonstration
go to the home page of the Medical Library:
http://www.erasmusmc.nl/medbib
http://www.erasmusmc.nl/bibliotheek
via Erasmus MC Intranet: click > Bibliotheek
via Erasmus MC Internet: click > Bibliotheek
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