HINTS on usingliterature databases

Louis Volkers & Gerdien de Jonge

Medical Library - Erasmus MC

info.mb@erasmusmc.nl

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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