Scientific writing: EndNote and literature databases...Scientific writing: EndNote and literature databases 5 October 2016 Matthias Bank Faculty of Medicine, Library & ICT. Lunds universitet

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


• Information Embase

• Demo

• Exercise in Embase

• Reference management in EndNote

– Downloading references to EndNote

– Using different bibliographic styles

– Citations in Word


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?


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


Structure your question with PICO


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


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


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?


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


Boolean operators

• AND (will be added automatically)

• OR

• NOT


PubMed facts

• 26 million references from the biomedical literature

• Covers preclinical and clinical medicine, nursing, allied

health

• Back to 1940s

• Covers 5 800 journals


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.


Find literature on the following cell types

• JIMT-1 cells

• PanC-1 cells

• MiaPaCa-2 cells


PubMed: select search terms

• free text terms

• MeSH terms (Medical Subject Headings)

• combination of free text and MeSH


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


MeSH terms


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


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


Filters/limitations

• How to delimit the search? This is done via

Filters.

– Age group

– Humans/animals

– Language

– Time aspect

– Article type

– …..


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


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


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


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


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


Emtree versus MeSH

Emtree MeSH


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


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


Example

• How does exposure to cigarette smoke affect

the recruitment of neutrophils to the lungs of

mice or rats in animal models of COPD?


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.


EndNote

• Downloading references to EndNote

• Downloading fulltexts

• Using different bibliographic styles

• Citations and bibliography in Word


Thank you! Questions?

Contact:

• [email protected]

046-2223307

mailto:[email protected]

Documents

Scientific writing: EndNote and literature databases...Scientific writing: EndNote and literature databases 5 October 2016 Matthias Bank Faculty of Medicine, Library & ICT. Lunds universitet