View
2.466
Download
0
Category
Tags:
Preview:
Citation preview
1
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
2
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]
3
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.
4
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" ….
5
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 …
6
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
7
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
8
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
9
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
10
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$
11
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
12
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
13
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
14
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
15
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
16
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
Recommended