Scientific writing: EndNote and
literature databases
5 October 2016
Matthias Bank
Faculty of Medicine, Library & ICT
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Agenda
• Search process and preparations
• Information PubMed
• Brief demo
• Exercise in PubMed
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
• Information Embase
• Demo
• Exercise in Embase
• Reference management in EndNote
– Downloading references to EndNote
– Using different bibliographic styles
– Citations in Word
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Needs assessment – what are you looking for?
- Get an overview over a new field
- New aspects in your specific field of research
- The most recent literature
- Broad search?
- Very focused / narrow search?
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
The search process – step by step
3. Choice of search terms
Subject headings or freetext
Combine with AND, OR, NOT
Filters
5. Assess relevancy
of result
6. Revise search
2. Identify key information sources /
databases
4. Search
1. Research question, information need
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Structure and limit your question
• Patients/population/animal species/cell line
– disease, disease severity, age groups, co-morbidities
• Interventions
– treatment, diagnostic methods
• Comparison, outcome criteria, time limit
• Study type/publication type
– study design, original research vs reviews, case reports
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Split up your question: Building blocks
strategy
Concept 1
Combine
terms with
OR
Concept 2
Combine
terms with OR
AND AND
Concept 3
Combine
terms with OR
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Example
• Are there studies about the recruitment of
CD4-positive T-lymphocytes to the lungs of
mice or rats in animal models of asthma or
COPD?
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Part 1 Part 2 Part 3
COPD
OR
asthma
Mice OR rats CD4+ T-lymphocytes
OR
CD4-positive T-
lymphocytes OR
CD4-positive T-cells
AND AND
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Boolean operators
• AND (will be added automatically)
• OR
• NOT
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
PubMed facts
• 26 million references from the biomedical literature
• Covers preclinical and clinical medicine, nursing, allied
health
• Back to 1940s
• Covers 5 800 journals
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Exercise PubMed
• Choose one of the exercises.
• Start with looking up the disease in Mesh and search it
both via Mesh and freetext
• The other aspects can be searched either in Mesh or
freetext, depending on how much you want to limit the
result.
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Find literature on the following cell types
• JIMT-1 cells
• PanC-1 cells
• MiaPaCa-2 cells
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
PubMed: select search terms
• free text terms
• MeSH terms (Medical Subject Headings)
• combination of free text and MeSH
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
What is MeSH?
• Our natural language is imprecise
• Large literature databases often have a thesaurus –
various synonyms are mapped to ”preferred terms”
• Diabetes mellitus, type 1– Sudden-Onset Diabetes Mellitus; Diabetes Mellitus, Type I; IDDM;
Insulin-Dependent Diabetes Mellitus 1
• Relevant articles are indexed/classified with MeSH
• Searches become more focused while covering all
synonyms
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Searches in Mesh
Searching with Mesh works well for
• Diseases
• Cell types
• Animal species
Less useful for
• Drugs/pharmaceutics
• Newer therapeutic approaches
• Extremely specific terms
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Select search terms
• Free text terms– often work well
– help in PubMed with automatic linking to Mesh terms. Free text words must be used to search among recently added references, not yet having MeSH terms
• Mesh terms– 28 000 terms which are used to tag/index the articles
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Filters/limitations
• How to delimit the search? This is done via
Filters.
– Age group
– Humans/animals
– Language
– Time aspect
– Article type
– …..
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
PubMed references to EndNote
• Make a search
• Select references (check the box to the left of the
reference)
• Send to – Citation manager
• Create File
• Open with – EndNote X7
• References will be automatically added to your EndNote
library
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Embase facts
• 28 million literature references within human medicine and
related areas, goes back to 1966
• > 800 000 new references/year
• Covers 8200 journals
• Produced by Elsevier
• Target group are researchers within
– Experimental medicine
– Clinical medicine
– Pharmaceutical industry
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Subject coverage Embase vs. PubMed
• Embase focuses on
– Human medicine
– Very good coverage of
clinical disciplines
– Drug-related research
– Health policy and
management
– Basic biological research
• Embase imports from
Medline/PubMed
• PubMed focuses on
– Human medicine
– Dental medicine
– Nursery
– Veterinary medicine
• PubMed is narrower in
the coverage of certain
clinical disciplines, e.g.
– Oncology,
gastroenterology,
cardiology
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Search result Embase versus PubMed
Search term Embase PubMed
Neoplasms
- breast neoplasms
- intestinal neoplasms
- lung neoplasms
3 428 000
365 000
274 000
268 000
2 588 000
216 000
168 800
173 000
Cardiovascular diseases
- myocardial infarction
3 064 000
276 000
1 871 000
146 000
Multiple sclerosis 81 000 44 000
Quality of life 275 000 117 000
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Emtree
• Embase’ thesaurus, contains 70,000 descriptors (preferred
terms) and 290 000 synonyms
• Covers the entire MeSH, automatic mapping av MeSH-
termer till Emtree-termer
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Search functionality
• Quick Search with autocomplete function for simple
searches
• Filters (e.g. year, journal, study type)
• Emtree as entry point for more systematic searches
• Limits: humans/animals, with abstract, from
Embase/Medline, EBM, patient age groups, gender, etc.
• Email alerts, Saved searches
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Search functionality (cont.)
• Phrase searches (i.e. multiple-word expressions) in citation
marks, e.g. ’football injuries’
• Truncate with the asterisk, one or more letters can follow,
e.g. injur*
• question mark to mask exactly one letter, e.g. wom?n
• Field-specific searches possible in Advanced Search
– :ab – abstract
– :ad – author address
– :em – author email address
– :ti – article title
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Example
• How does exposure to cigarette smoke affect
the recruitment of neutrophils to the lungs of
mice or rats in animal models of COPD?
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Exercise Embase
• Choose one of the exercises.
• Start with looking up the disease in Emtree and search it
both via Emtree and freetext
• The other aspects can be searched either in Emtree or
freetext, depending on how much you want to limit the
result.
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
EndNote
• Downloading references to EndNote
• Downloading fulltexts
• Using different bibliographic styles
• Citations and bibliography in Word
Lunds universitet / Medicinska fakulteten / Bibliotek & IKT
Thank you! Questions?
Contact:
046-2223307