BIOMEDICAL SEARCHING FOR HEALTH LIBRARIANS:

An introductory student manual to support LIBR534, October 2014

Dean Giustini, UBC Biomedical Branch Librarian

1

TABLE OF CONTENTS

INTRODUCTION..................................................................................................................3What is MEDLINE?....................................................................................................3

Medical Subject Headings (MeSH).....................................................................................3What are MeSH?......................................................................................................3MeSH Trees..............................................................................................................3Poly-hierarchical structure of MeSH.........................................................................4MeSH for indexing....................................................................................................4

Medical subject headings 1960-2015........................................................................4MeSH Subheadings....................................................................................................4

Using MeSH in health-related searching...................................................................4Using MeSH in health libraries..................................................................................5Canadian context for MeSH......................................................................................5

Applying MeSH...................................................................................................................5OvidSP Search Interface............................................................................................5

Permuted Index (PI)...........................................................................................................6Scope Notes provide a definition of the MeSH heading....................................................6MeSH Tree......................................................................................................................... 7Explode and Focus – Playing with Recall & Precision.........................................................8

Focus (Precision).......................................................................................................8Explode (Recall)........................................................................................................8

Combining Terms...............................................................................................................9Post-Qualification.....................................................................................................9Command Line Syntax............................................................................................11Field Qualifiers.......................................................................................................12Truncation..............................................................................................................13Nesting...................................................................................................................14Appendices .......................................................................................................16

2

INTRODUCTION

What is MEDLINE?MEDLINE is the premier international database in biomedicine that is produced by the US National Library of Medicine (NLM) in Bethesda, Maryland. The Medline database indexes 5600+ peer-reviewed journals, covering the fields of allied health, biomedicine and the life sciences, nursing, pharmacy, dentistry and information science as it relates to medicine.

MEDLINE & PubMed Update October 2014

File / database Total # RecordsDate range

Indexed Records Added

Date Added

PubMed~24,256,861

1940s-present

MEDLINE ~22 million 1966-present

In Process 449,898 N/A OLDMEDLINE 519,953 1940-65

What are MeSH?

Medical Subject Headings are the controlled vocabulary used for biomedical searching by health librarians. MeSH are created to index, catalogue and search for biomedical information. The 2015 MeSH Thesaurus contains ~26,556 descriptors and sixteen (16) major trees. Every year, MeSH is updated to account for new concepts in biomedicine appearing in the journal literature.

MeSH Tree structures

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

Poly-hierarchical structure of MeSH

MeSH terms are arranged from the broadest categories down to the narrowest in a poly-hierarchical tree structure. At the top categories, there are broad groupings such as "Anatomy” and “Organisms” which are organized towards increasing levels of specificity. With ~27,000 descriptors and 172,000 Supplementary Concept Records, MeSH is one of the largest controlled vocabularies of its kind in the world. The MeSH database provides thousands of cross-references and see-references within its scope notes. Vitamin C, for example, leads you to Ascorbic Acid. Using explode and focus functions will help you manage recall and precision in your searching.

MeSH for indexing

The MeSH thesaurus is used by NLM librarians to index articles from ~5,600 international biomedical journals in MEDLINE. Each article is given from between ten to fifteen subject terms to describe its content; MeSH are used in bibliographic records for books, audiovisual materials and digital items. The MeSH thesaurus is updated annually, and NLM incorporates new headings 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 1960-201 5

MeSH 2015 will be published officially in early January 2015 NLM has been indexing the biomedical literature since 1879, to help provide health

professionals access to information necessary for research, health care, and education. What was once a printed index to articles, the Index Medicus, became a database now

known as MEDLINE. MEDLINE contains journal citations and abstracts for biomedical literature from around the world.

MeSH Subheadings

In Medline, there are 83 floating, allowable subheadings or qualifiers. These 83 topical qualifiers are used to bring out specific facets during indexing.

Common subheadings include drug therapy, diagnosis, etiology and surgery. To search for specific subheadings, find your MeSH term and the subheading associated with your topic health care reform/ec for economics of health care reform. Post-coordinate searching is also possible in OvidSP and widely-used by health librarians in systematic review searching.

Certain pre-arranged "Families of Subheadings (see appendix in this manual) can also be used.

4

Using MeSH in health-related searching

PubMed at pubmed.gov, NLM’s public search interface to Medline, provides access to ~24.25 million+ citations from 5,600 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 which MeSH to use. When a relevant citation is found, look at the MeSH terms applied to the citation to gather ideas to rerun your search. Librarians are always (re)strategizing searches based on combinations of natural language (See Gault et al) “keywords” and MeSH. Keywords are useful tools for novice searchers and when current articles that have not been indexed are needed.

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 the American bias in MeSH, specific issues pertaining to Canada may not be addressed by MeSH. Geographic subdivisions - Canada, and the provinces - are recommended to locate information pertaining to specific areas of Canada ie. HIV infection in the downtown Eastside of Vancouver, try "British Columbia" or "Canada"[MeSH] and "downtown eastside" [keyword].

Applying MeSH

OvidSP Search Interface

1) In OvidSP, click on the Search Tools tab above the search box, to view the MeSH database

2) Select Permuted Index from the drop down

5

3) Type your term in the box. Note: Enter one term at a time

4) Click the Search button to view possible MeSH terms

Permuted Index (PI)

The Permuted Index is an alphabetical list of terms, and includes a number of potentially-useful MeSH terms with the word you typed in (and want to find) in the search box

Far left, in Black Bolded Terms = Commonly-used natural language terms or “Non-MeSH “

Hyperlinked See references in blue are MeSH terms

See = Refers you to a term that you might consider for the search. However you may need to scroll down the permuted index alphabetically to see other appropriate terms for your search

1) Above, instead of “Black Cohosh” the index suggests using “Cimicifuga”. To see the

definition and ensure this is correct MeSH term, click on the small icon

Scope Notes provide a definition of the MeSH heading and information to ensure it is correct

6

Scope Note is the definition of the controlled term as defined by the controlled vocabulary.This is the why reading scope notes are essential for online searchers

Note = the Note will direct you to more specific terms the MeSH may not cover

Year of Entry = when the term was created. The date represents how far back you can search with the term. If you need information earlier, you will need to use the Previous Indexing terms

Previous Indexing = Tells you which MeSH terms were used for searching Medline prior to this one being created. For articles before this date, you must search by using the older index terms

Note: Not all Scope Notes will include all this information. It depends on the term.

1) Click on at the top of Scope Note to return to the permuted index 2) Since Cimicifuga is the correct term for search, click on the term hyperlinked in blue to see

the MeSH Tree

MeSH Tree

The MeSH Tree view shows us a list of related terms; it is organized by one of the 16 major groupings or hierarchies; broader topics are located above, narrower ones below

1) To find your term scroll in the list in OvidSP – it will often be highlighted in blue

7

3) See the term Cimicifuga

Explode and Focus – Playing with Recall & Precision

Focus (Precision)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 …

Explode (Recall)

Explode allows you to select all the MeSH terms indented underneath your term. This function 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

2) Scroll to the top of the page and click Continue. 3) For now, disregard the Subheadings page. Press Continue

You should now be back at 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).

8

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

5) Your search history should now look like this:

Combining Terms

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

Take for example our two concepts: Use the Boolean Operator OR to find articles about Hot Flashes OR Cimicifuga

Use AND to find articles about both Hot Flashes AND Cimicifuga

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)

9

TIP: Consider Post-Qualification, Command Line Syntax, Field Qualifiers,

Truncation & Nesting in your searching

Post-Qualification

Postqualification is a shorthand command for making changes to existing sets. OvidSP translates shorthand commands, re-executes the previous search statement, and posts a new set. Use postqualification to save yourself 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

Example II

Focus the MeSH term “Hot Flashes”

10

1) Use an asterix * and your set number

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

Example III

Add terms 4 and 5 together1) Type 4 and 5 in the search box to combine our two searches

2) Click Search.

Command Line SyntaxCommand 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

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

11

2) Click Search

3) Return to the Main Search Page at top

Example IIView subheadings associated with Cimicifuga

1) Type sh <cimicifuga> into the search box

2) Click Search. The Subheading Display will open

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

12

Field Qualifiers

In OvidSP, you can search for specific words, phrases, terms or numbers using Field Qualifiers such as author (.au.), journal (.jn.), institutional address (.in.) and year (.yr.).

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

Example I

When searching for an author who may or may not publish using their last, first and middle initials you would use truncation and the field qualifier for author. For example, Robert Mann

1) Type Mann R$.au into the search box under Advanced Search Options.

2) Click Search

13

Adjacency

Adjacency is a proximity search command that we use to find words adjacent to each other

Example I

For “Enterprise Resource Planning” we want each word to be within 2 words of the other words

1) Type Enterprise adj2 Resource adj2 Plan$

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

14

Appendices – Subheadingsaa - Analogs & Derivativesab - Abnormalitiesad - Administration & Dosage ae - Adverse Effectsag - Agonistsah - Anatomy & Histologyai - Antagonists & Inhibitorsan - Analysisbi - Biosynthesisbl - Bloodbs – Blood Supplycf - Cerebrospinal Fluidch - Chemistry ci - Chemically Inducedcl - Classificationcn - Congenitalco - Complicationscs - Chemical Synthesisct - Contraindicationscy - Cytologyde – Drug Effectsdf - Deficiencydh – Diet Therapydi - Diagnosisdt – Drug Therapydu - Diagnostic Useec - Economicsed - Educationeh - Ethnologyem - Embryologyen - Enzymologyep - Epidemiologyes - Ethicset – Etiologygd – Growth & Developmentge - Geneticshi - Historyim - Immunologyin - Injuriesip - Isolation & Purificationir - Innervationis – Instrumentation

lj - Legislation & Jurisprudencema - Manpowerme – Metabolismmi - Microbiologymo - Mortalitymt - Methodsnu - Nursingog - Organization & Administrationpa - Pathologypc - Prevention & Controlpd - Pharmacologyph - Physiologypk - Pharmacokineticspo - Poisoningpp - Physiopathologyps - Parasitologypx - Psychologypy - Pathogenicityra - Radiographyre - Radiation Effectsrh - Rehabilitationri – Radionuclide Imagingrt - Radiotherapysc - Secondarysd - Supply & Distributionse - Secretionsn - Statistics & Numerical Datast - Standardssu - Surgerytd - Trendsth - Therapytm - Transmissiointo - Toxicitytr - Transplantationtu - Therapeutic Useul - Ultrastructureur - Urineus - Ultrasonographyut - Utilizationve - Veterinaryvi - Virology

see Appendix for Families of Subheadings

15

PubMed / MEDLINE Subheading Familieshttp://www.nlm.nih.gov/mesh/2014/introduction/subhierarchy.html

Adverse Effects - AE *Etiology - ET *Physiology – PH Poisoning - PO Chemically induced – CI Genetics – GE Toxicity - TO Complications - CO Growth & Development – GD

Secondary – SC Immunology – IMAnalysis - 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 – AECytology – 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 – RHEmbryology – EM Toxicity – TO Surgery - SU Abnormalities – AB Agonists – AG Transplantation – TR

Antagonists & inhibitors – AIEpidemiology – EP Contraindications – CT Ethnology – EH Diagnostic use – DU Mortality – MO Pharmacokinetics – PK

16

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 InterfacesALTBIB - animal alternatives for biomedical research and testingCAM on PubMed Healthy People 2020Cancer Topic Searches MedlinePlus Health TopicsElectronic Health Records National Institutes of Health Funding SupportHealth Disparities Research Reporting Guidelines and InitiativesHealth Literacy Retracted PublicationHealth Services Research (HSR) Queries Smallpox

Journal/Citation SubsetsFor the following, use jsubsetcode without the [sb]; e.g. jsubsetk

AIM Abridged Index Medicus - list created 20 years ago and includes 119 core clinical English language journals; corresponds to "Core clinical journals" subset in Limits

D Dentistry journalsE Citations from bioethics journals or selected bioethics citations from other journalsH Health administration journals, non-Index MedicusIM Index Medicus journalsK Consumer health journals, non-Index MedicusN Nursing journalsOM OLDMEDLINE citations from the Cumulated Index Medicus (CIM) and the Current List of Medical

Literature (CLML) – 1947-1965 (plus some earlier) – not available in NLM CatalogQ History of medicine journals and selected citations from other journalsQIS Citations from non-Index Medicus journals in the field of history of medicineS Citations from space life sciences journals and selected citations from other journalsT Health technology assessment journals, non-Index MedicusX AIDS/HIV journals (selected citations from other journals 1980-2000)

Additional Selected Subsets

all [sb] All citations in PubMedfree full text [sb] Citations which include links to free full text articlesfull text [sb] Citations which include links to full text articlesloall [sb] Citations with LinkOut links in PubMed

loprovmedlib [sb]LinkOut holdings in medical library – see provider name abbreviations at http://www.ncbi.nlm.nih.gov/projects/linkout/journals/htmllists.cgi?type_id=6

pubmed pmc [sb] Free full-text article available in PubMed Central

17

Citation Status Tags and Search Codes

Search Term Status Tag Descriptionpublisher [sb] PubMed - as supplied by

publisherCitation as supplied by publisher, not yet indexed (may be an E-Pub)

pubstatusaheadofprint PubMed - as supplied by publisher

E-Pub – citations available in advance of journal issue's print release (no [sb])

in process [sb] PubMed - in process Citation is in the review processmedline [sb] PubMed - indexed for

MEDLINEFully indexed and cross-linked citations

oldmedline [sb] PubMed - OLDMEDLINE Pre1966 citations not yet mapped to current MeSH

pubmednotmedline [sb] PubMed Processed, not indexed for MEDLINEpubstatusnihms PubMed Author manuscript from non-MEDLINE journal

submitted to PMC (no [sb])pubstatuspmcsd PubMed Non-MEDLINE journal citations in PMC (no [sb])ppmcbookpmcbooktitlepmcbookchapter

PubMed Book and book citations available on the NCBI Bookshelf (no [sb])

PubMed® Stopwords (ignored by PubMed even in “quoted phrases”, unless phrases are in MeSH)

a both have ml seen theyabout but having mm several thisagain by here most should thoseall can how mostly show throughalmost could however must showed thusalso did i nearly shown toalthough do if neither shows uponalways does in no significantly useamong done into nor since usedan due is obtained so usingand during it of some variousanother each its often such veryany either itself on than wasare enough just our that weas especially kg overall the wereat etc km perhaps their whatbe for made pmid theirs whenbecause found mainly quite them whichbeen from make rather then whilebefore further may really there withbeing had mg regarding therefore withinbetween has might seem these without

would

18

Available by searching the PubMed Help manual for Stopwords or go directly to: http://www.ncbi.nlm.nih.gov/books/NBK3827/?rendertype=table&id=pubmedhelp.T43

Publication Types Found in PubMed®

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 LecturesBibliography Legal CasesBiography LegislationCase Reports LetterClassical Article (republished seminal articles) Meta-Analysis (quantitative summary combining results of

independent studies)Clinical Conference (reports of clinical case conferences only) Multicenter StudyClinical Trial (includes all types and phases of clinical trials) News (for medical or scientific news)Clinical Trial, phase I Newspaper ArticleClinical Trial, phase II Overall (collection of articles)Clinical Trial, phase III Patient Education HandoutClinical Trial, phase IV Periodical Index (cumulated indexes to journals)Collected Works PortraitsComment (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 ErratumConsensus Development Conference, NIH Randomized Controlled TrialControlled Clinical Trial Research Support, American Recovery and Reinvestment ActCorrected and Republished Article Research Support, N.I.H., ExtramuralDictionary Research Support, N.I.H., IntramuralDirectory 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 Scientific Integrity Review (US Office of Scientific Integrity reports)Festschrift Study Characteristics (identify any type of study)Government Publications Support of ResearchGuideline (administrative, procedural guidelines in general) Technical ReportHistorical Article (articles about past events) Twin StudyIn Vitro Validation StudiesInteractive Tutorial Video-Audio MediaInterview Webcasts

19

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

Database Dates CoveredUpdating

Sources Geographic / linguistic

Abstracts Subject Scope Indexing Notes

Medline (via PubMed & onOvidSP)

1949 – present

Updated daily

~23 million citations

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

85 countries (47% titles originate in US)

37 languages74% 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; 60% + of papers in clinical medicine with slight American bias

- MeSH subject headings ; ~27,000 thesaurus terms- 83 topical subheadings- uses USAN terms for drugs- no added indexing for medical devices or manufacturer names

Embase(on OvidSP)

1974 – present

Updated weekly

~21 million citations

5,000 journals(~1,000 cover-to-cover)

90-100 countries (40% content overlap with Medline)

34 languages80% 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 lit coverage is excellent. European and Asian content

- EMTREE subject headings~60000 thesaurus terms, detailed drug name indexing78 drug-focused subheadings- uses INN terms and CAS registry numbers

EBM Reviews (Cochrane Library)(on OvidSP)

1991 –Present

Updated quarterly

~375,000 records; 10,000 added annually

ACP, Cochrane Collaboration, Cochrane groups & UK NHS Dare (phasing out in 2015)

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 included from Medline

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

1981 – present

~2 million citations

Updated bi-monthly

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

18 foreign languages since 1994

Most citations have abstracts

- nursing and allied health literature from 1981; includes Cochrane citations; 55% content is unique not in Medline or Embase

- 12,000+ CINAHL headings- 68 topical subheadings- American Nurses Association journals are fully indexed; includes legal cases, research instruments, peer-reviewed and consumer materials

20