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MEDLINE, EMBASE & CINAHL SEARCHING:

a manual to support learning in LIBR534

TABLE OF CONTENTS

INTRODUCTION ....................................................................... 2

What is MEDLINE? ................................................................................2 Medical Subject Headings (MeSH) ................................................ 2

What are MeSH? ...................................................................................2 MeSH Trees...........................................................................................2 Poly-hierarchical structure of MeSH....................................................... 3 MeSH for indexing ................................................................................. 3

Medical subject headings 1960-2017 ................................................... 3 MeSH Subheadings ...........................................................................4

Using MeSH in health-related searching ................................................4 Using MeSH in health libraries ...............................................................4 Canadian context for MeSH ...................................................................4 Building a MeSH set in Ovid .................................................................. 5

Explode a MeSH heading .........................................................................6 Combining Terms ...................................................................... .6

Focus a MeSH heading .........................................................................8 Post-Qualification ............................................................................... 10 Command Line Syntax ........................................................................ 10 Truncation........................................................................................... 10 Nesting ............................................................................................... 11 Appendices ........................................................................................ 12

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INTRODUCTION – WHAT IS MEDLINE?

MEDLINE is the premier international database in biomedicine produced by the National Library of Medicine (NLM) in Bethesda, Maryland. Medline indexes 5700+ peer-reviewed journals, covering allied health, biomedicine and the life sciences, nursing, pharmacy, dentistry and information science as it relates to medicine.

MEDLINE & PubMed Update 2017

File / database Total #

Records

Date

range

Indexed

Records Added

Date

Added

PubMed ~26,900,000

1940s-present

800,000-

2016

MEDLINE ~24.4 million 1966-present

In Process Varies Last six to 12 months

OLDMEDLINE ~2.5 million 1940-65

WHAT ARE MESH?

Medical Subject Headings (MeSH) is the controlled vocabulary used to index articles in Medline. MeSH are used to catalogue and search for biomedical information. The 2017 MeSH Thesaurus has ~27,800 descriptors under sixteen (16) major trees.

The MeSH Tree Contains 16 Major Categories at the Top

1. Anatomy [A] 2. Organisms [B] 3. Diseases [C] 4. Chemicals and Drugs [D] 5. Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 6. Psychiatry and Psychology [F] 7. Phenomena and Processes [G] 8. Disciplines and Occupations [H] 9. Anthropology, Education, Sociology and Social Phenomena [I] 10. Technology, Industry, Agriculture [J] 11. Humanities [K] 12. Information Science [L] 13. Named Groups [M] 14. Health Care [N] 15. Publication Characteristics [V] 16. Geographic areas [Z]

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THE STRUCTURE OF MESH

MeSH terms are arranged from the broadest terms at the top to narrowest terms at the bottom in a poly-hierarchical tree like structure. At the top are the following: "Anatomy (A)” , “Organisms (B)” and “Diseases (C)” with increasing levels of specificity below. With

~27,800+ descriptors and 224,000 Supplementary Concept Records, MeSH is one of the largest controlled vocabularies of its kind. MeSH provides cross-references and see-

references in its scope notes. Vitamin C, for example, leads you to Ascorbic Acid.

USE explode and focus to help you manage recall and precision in your searches.

MeSH for indexing

The MeSH thesaurus is used by NLM librarians to index articles from ~5,700 biomedical journals in MEDLINE. Each article is assigned between ten to fifteen subject terms to

describe its content; MeSH terms are used in bibliographic records for books, audiovisual materials and digital items. The MeSH thesaurus is updated annually, and NLM creates new headings with cues from the biomedical literature. Health professionals in various scientific disciplines are consulted about proposed changes to

MeSH. There is close coordination with other health organizations.

Medical subject headings 1960-2017

New MeSH terms are published every January

NLM has been indexing biomedical literature since 1879 to provide health professionals with access to information for research, healthcare and education.

Once a printed index, Index Medicus is now MEDLINE. MEDLINE contains

journal citations and abstracts for biomedical literature from around the world.

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SUBHEADINGS IN MEDLINE

Medline uses 82 floating subheadings or qualifiers. The 82 topical qualifiers bring out

specific facets of the main term during indexing. Some common subheadings include: drug therapy, diagnosis, etiology and surgery. To search for specific subheadings, find

your MeSH and subheading associated with your topic health care reform/ec for economics of health care reform. Post-coordinate searching is also possible in Ovid and

widely-used by health librarians in systematic review searching. Searchers can also use "Families of Subheadings (see appendix in this manual) to locate specific types of literature. (Ask a health librarian for more information.)

Using MeSH in health-related searching

PubMed at pubmed.gov, NLM’s public search interface to Medline, provides access to ~26 million+ citations from 5,700 international journals in 37 languages; 60 languages for older journals see NLM Indexing practices. The core of PubMed is Medline.

Health librarians use keywords to search for information when they don’t know the exact MeSH to use to satisfy their information need. When relevant citations are found,

look at the MeSH terms applied to a citation to get ideas to rerun your search. Librarians can (re)strategize searches based on a combination of natural language (See

Gault et al) “keywords” and MeSH. Keywords are useful for novice searchers and when current articles have not been well indexed.

Using MeSH in health libraries

To improve subject use and access in health library OPACs To develop taxonomies for indexing in databases of various kinds

To create print and digital pamphlet files To assign key words to journal article submissions by authors

To look up definitions in a medical dictionary To assign metadata to digital publications

To catalogue items for later search engine retrieval To use in reference interviews to identify concepts and synonyms

Canadian context for MeSH

Due to a slight American bias, MeSH does not always address specifics to Canadian health care. Geographic subdivisions - Canada, and the provinces - are used to locate

information for specific areas of Canada ie. HIV infection in the downtown Eastside of Vancouver, try "British Columbia" or "Canada"[MeSH] & "downtown eastside" ….

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BUILDING MESH SETS IN OVID

Question: “….is BLACK COHOSH effective in treating HOT FLASHES” ?

1) To find your MeSH term for COHOSH in Ovid – see the controlled term in blue

Explode and Focus – Playing with Recall & Precision

FOCUS A MESH TERM (AS A MAJOR DESCRIPTOR)

Focus refers to limiting your search to articles where a MeSH term is one of the *major

descriptors. This will improve the precision of your search. Focus is used in searches where the topic is quite large, and the health librarian knows there may be plenty of information to wade through …

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EXPLODE A MESH TERM (TO INCLUDE NARROWER TERMS)

Explode allows you to select all MeSH terms indented underneath. This will increase your recall. By checking the explode box next to Ranunculaceae all terms indented

underneath will be included such as Aconitum, Actaea, Adonis, Anemone and so on

1) Scroll to the top of the page and click Continue. 2) For now, disregard the Subheadings page. Press Continue GO BACK TO the Main Search page where you can see our first set of results in the Search History box (you may need to click Search History to open the box).

3) Repeat the steps on Pages 5-8 that we followed for our second concept hot flashes

4) Your search history should now look like this:

COMBINE MESH TERMS USING BOOLEAN OPERATORS

There are two ways to combine your terms in MEDLINE with AND / OR.

Use the Boolean Operator OR to find articles about Hot Flashes OR Cimicifuga

Use AND to find articles about both Hot Flashes AND Cimicifuga

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1) Combine your terms by selecting the checkboxes of each set; click AND

2) You should now see that your search terms have been combined (1 and 2)

TRY DOING “POST-QUALIFYING” TO YOUR SEARCH SET

Postqualification allows you to make changes to a search set. Ovid translates a command to re-do a search statement. Use postqualification to save time.

Example I

Add the Subheading Adverse Effects to your MeSH term or first set

1) Click Search – note that you have done post-qualification and brought your set

down to 46 results

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Example II FOCUS

Focus the MeSH term “Hot Flashes”

1) Use an asterix * and your set number

2) Click Search; notice the difference in the retrieval numbers

Example III USING “AND” Add terms 4 and 5 together

1) Type 4 and 5 in the search box to combine your two searches

2) Click Search.

Command Line Syntax

Command Line Syntax is similar to Post-Qualification in that it allows you to enter

shortcut commands into the command line bypassing the icon bars.

Example I Confirm the definition and date of entry for Hot Flashes

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1) Type scope <hot flashes> in the search box

2) Click Search

see PREVIOUS INDEXING for “Hot Flashes” to search before 1998

3) Return to the Main Search Page at top

Example II View subheadings associated with Cimicifuga

1) Type ……sh <cimicifuga> into the search box

2) Click Search. The Subheading Display will open

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3) Select the subheadings Adverse Effects, Drug Effects, Poisoning and Toxicity

Example I

Limit the last search by journal using Field Qualifiers:

1) Type 7 and medical journal of australia.jn in to the search box.

2) Click Search

Truncation

Truncation is an important tool to use where there are no MeSH terms for your

concept. It allows you to search for different forms of words by placing wildcards $ after a word stem

Adjacency is a proximity command used to find words adjacent to each other.

Example I:

1) Type Enterprise adj2 Resource adj2 Plan$

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2) Deselect the Map Term to Subject Heading

Nesting

Nesting refers to the use of brackets to organize the order of words being searched. Operations in parentheses are performed first, then combined with other statements

Example I Find the sentence pregnancy and childbirth in the title of articles

1) Type (pregnancy and childbirth).ti. into the search box

2) Click Search

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Appendices – Subheadings aa - Analogs & Derivatives ab - Abnormalities

ad - Administration & Dosage ae - Adverse Effects

ag - Agonists ah - Anatomy & Histology ai - Antagonists & Inhibitors an - Analysis bi - Biosynthesis bl - Blood bs – Blood Supply cf - Cerebrospinal Fluid ch - Chemistry ci - Chemically Induced

cl - Classification cn - Congenital

co - Complications cs - Chemical Synthesis

ct - Contraindications cy - Cytology de – Drug Effects df - Deficiency dh – Diet Therapy di - Diagnosis dt – Drug Therapy

ec - Economics ed - Education

eh - Ethnology em - Embryology

en - Enzymology ep - Epidemiology

es - Ethics et – Etiology

gd – Growth & Development

ge - Genetics hi - History

im - Immunology in - Injuries

ip - Isolation & Purification ir - Innervation

is – Instrumentation

lj - Legislation & Jurisprudence ma - Manpower

me – Metabolism mi - Microbiology

mo - Mortality mt - Methods nu - Nursing og - Organization & Administration pa - Pathology pc - Prevention & Control pd - Pharmacology ph - Physiology pk - Pharmacokinetics po - Poisoning

pp - Physiopathology ps - Parasitology

px - Psychology py - Pathogenicity

ra - Radiography re - Radiation Effects rh - Rehabilitation ri – Radionuclide Imaging rt - Radiotherapy sc - Secondary sd - Supply & Distribution

se - Secretion sn - Statistics & Numerical Data

st - Standards su - Surgery

td - Trends th - Therapy

tm - Transmissioin to - Toxicity

tr - Transplantation

tu - Therapeutic Use ul - Ultrastructure

ur - Urine us - Ultrasonography

ut - Utilization ve - Veterinary

vi - Virology

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PubMed / MEDLINE Subheading Families

Adverse Effects - AE *Etiology - ET *Physiology – PH Poisoning - PO Chemically induced – CI Genetics – GE Toxicity - TO Complications - CO Growth & Development – GD Secondary – SC Immunology – IM Analysis - AN Congenital – CN Metabolism – ME Blood – BL Embryology – EM Biosynthesis – BI Cerebrospinal fluid – CF Genetics – GE Blood – BL Isolation & purification – IP Immunology – IM Cerebrospinal Fluid – CF Urine – UR Microbiology – MI Deficiency – DF Virology – VI Enzymology – EN *Anatomy & Histology – AH Parasitology – PS Pharmacokinetics – PK Blood Supply – BS Transmission – TM Urine – UR Cytology – CY Physiopathology – PP Pathology – PA Metabolism – ME Secretion – SE Ultrastructure – UL Biosynthesis – BI Embryology – EM Blood – BL *Statistics & numerical data –

SN Abnormalities – AB Cerebrospinal fluid – CF Epidemiology – EP Innervation – IR Deficiency – DF Ethnology – EH Enzymology – EN Mortality MO *Chemistry – CH Pharmacokinetics – PK Supply & distribution – SD Agonists – AG Urine – UR Utilization – UT Analogs & derivatives – AA Antagonists & inhibitors – AI Microbiology – MI Surgery – SU Chemical synthesis – SC Virology – VI Transplantation – TR Complications – CO *Organization & administration –

OG *Therapeutic use – TU

Secondary – SC Economics – EC Administration & dosage – AD Legislation & jurisprudence – LJ Adverse effects – AE Cytology – CY Manpower – MA Contraindications – CT Pathology – PA Standards – ST Poisoning – PO Ultrastructure – UL Supply & distribution – SD Trends – TD *Therapy - TH *Diagnosis – DI Utilization – UT Diet Therapy – DH Pathology – PA Drug Therapy – DT Radiography – RA Pharmacology – PD Nursing – NU Radionuclide imaging – RI Administration & dosage – AD Prevention & control – PC Ultrasonography – US Adverse Effects – AE Radiotherapy – RT Poisoning – PO Rehabilitation – RH Embryology – EM Toxicity – TO Surgery - SU Abnormalities – AB Agonists – AG Transplantation – TR Antagonists & inhibitors – AI Epidemiology – EP Contraindications – CT Ethnology – EH Diagnostic use – DU Mortality – MO Pharmacokinetics – PK

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PubMed® Subset Searching

Topic and Limits Subsets

AIDS aids [sb] History of Medicine history [sb]

Bioethics bioethics [sb] MEDLINE® medline[sb] Cancer cancer [sb] OLDMEDLINE oldmedline [sb]

Core clinical journals jsubsetaim Space Life Sciences space [sb]

Comparative Effectiveness Research

effectiveness [sb] Systematic Reviews systematic [sb]

Complementary Medicine

cam [sb] Toxicology tox [sb]

Dietary Supplements dietsuppl [sb] Veterinary Science veterinary [sb] Additional Search Links to Queries and Interfaces

ALTBIB - animal alternatives for biomedical research and testing

CAM on PubMed Healthy People 2020

Cancer Topic Searches MedlinePlus Health Topics Electronic Health Records National Institutes of Health Funding Support

Health Disparities Research Reporting Guidelines and Initiatives Health Literacy Retracted Publication

Health Services Research (HSR) Queries Smallpox

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Publication Types Found in PubMed

For a full list, see: https://www.nlm.nih.gov/mesh/pubtypes.html

For the following, use [publication type], [PT] or [pt]; e.g. clinical trial [pt] (or use the Limits tab) In addition to Clinical Queries, use bolded publication types for evidence-based medicine

searches.

Addresses Journal Article (excludes letter, editorial, news, etc.) Autobiography Lectures

Bibliography Legal Cases Biography Legislation

Case Reports Letter

Classical Article (republished seminal articles) Meta-Analysis (quantitative summary combining results of independent studies)

Clinical Conference (reports of clinical case conferences only)

Multicenter Study

Clinical Trial (includes all types and phases of clinical trials)

News (for medical or scientific news)

Clinical Trial, phase I Newspaper Article

Clinical Trial, phase II Overall (collection of articles) Clinical Trial, phase III Patient Education Handout

Clinical Trial, phase IV Periodical Index (cumulated indexes to journals) Collected Works Portraits

Comment (comment on previously published work) Practice Guideline (specific to health care) Comparative Study Publication Components (specific parts of publications)

Congresses Publication Formats (specific genre of publications)

Consensus Development Conference Published Erratum Consensus Development Conference, NIH Randomized Controlled Trial

Controlled Clinical Trial Research Support, American Recovery and Reinvestment Act Corrected and Republished Article Research Support, N.I.H., Extramural

Dictionary Research Support, N.I.H., Intramural Directory Research Support , Non-U.S. Gov't Research Support, U.S.

Gov't, Non-P.H.S.

Duplicate Publication Research Support, U.S. Gov’t, P.H.S. Editorial Retracted Publication (work later retracted by author)

English Abstract (of foreign article) Retraction of Publication Review (author’s statement of retraction)

Evaluation Studies Review articles

Festschrift Study Characteristics (identify any type of study)

Government Publications Support of Research Guideline (administrative, procedural guidelines in

general) Technical Report

Historical Article (articles about past events) Twin Study In Vitro Validation Studies

Interactive Tutorial Video-Audio Media Interview Webcasts

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Big Four (4): major biomedical databases at a glance

Database Date coverage

Sources Geographic / linguistic

Abstracts Subject Scope Indexing Notes

MEDLINE (via PubMed & Ovid) Major biomedical database

1940s – present ~26 million citations Updated daily

5,700 journals (~1,600 indexed cover-to-cover)

85 countries (47% titles originate in US) 37 languages 74% English

61% of records added from 1975 have abstracts; none from 66-74; back to 1949; Index medicus back to 1879

Premier int’l biomedical database produced by NLM; 60% + US papers so slight American bias

- MeSH subject headings; ~27,800 thesaurus terms - 82 topical subheadings - uses USAN terms for drugs - no added indexing for medical devices or manufacturer names

EMBASE (on Ovid) Major biomedical database

1974 – present ~25 million citations Updated daily

~5,700 journals (~1,500 cover-to-cover)

90-100 countries (30-40% overlap with Medline) 34 languages 80% English

64% records accompanied by abstracts (backfiles available for 1947-1973 at Embase.com)

International. Published by Elsevier. Comparable to Medline but more preclinical citations Pharmaceutical coverage is good. European & Asian content

- EMTREE subject headings ~60,000 thesaurus terms, detailed drug name indexing 78 drug-focused subheadings - uses INN terms and CAS registry numbers

EBM Reviews (Cochrane Library on Ovid) Evidence based tool

1991 – Present Updated quarterly

~375,000 records; 10,000 added annually

Cochrane Collaboration, Cochrane groups

Most have abstracts; some fulltext systematic reviews

Central tool in EBM; systematic reviews of treatments; narrative reviews and definitive controlled trials

- Keyword, phrase searchable - Some records from Medline included

CINAHL fulltext – Cumulated index to nursing and allied health literature (on EBSCO)

1981 – present ~ 5.1 million records Updated weekly

5000+ journals, dissertations, books, theses, alternative therapies

17 foreign languages since 1994

Most citations have abstracts

- nursing and allied health literature; Cochrane citations; 55% content is unique not in Medline or Embase

- 12,000+ CINAHL headings - 68 topical subheadings