An introduction to biomedical searching for health librarians

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This class is an introduction to Medline and to searching for students in LIBR534 "An introduction to health information sources & services"

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  • 3
  • Subject indexing includes:
    reviewing a journal article (or other material such as a letter or editorial)
    determining its subject content, and
    describing that content using a controlled vocabulary.  
  • An introduction to biomedical searching for health librarians

    1. 1. 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 MeSHSubheadings...........................................................................4 Using MeSH in health-related searching ................................................4 Using MeSH in health libraries ...............................................................4 Canadian context forMeSH...................................................................4 Building a MeSH set in Ovid ..................................................................5 Explode a MeSH heading .........................................................................6 Combining Terms.......................................................................6 Focus a MeSH heading.........................................................................8 Post-Qualification ...............................................................................10 CommandLine Syntax ........................................................................10 Truncation...........................................................................................10 Nesting ...............................................................................................11 Appendices ........................................................................................ 12
    2. 2. 2 INTRODUCTION – WHAT IS MEDLINE? MEDLINE is thepremier internationaldatabasein biomedicineproduced bythe NationalLibrary of Medicine (NLM) in Bethesda,Maryland. Medline indexes 5700+ peer-reviewed journals, covering allied health,biomedicineandthelife sciences, nursing, pharmacy,dentistry and informationscience 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? MedicalSubject Headings (MeSH)is thecontrolled vocabulary used to index articles in Medline. MeSH are used to catalogueandsearch for biomedicalinformation.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. ChemicalsandDrugs [D] 5. Analytical,Diagnostic andTherapeutic TechniquesandEquipment [E] 6. Psychiatry andPsychology [F] 7. PhenomenaandProcesses [G] 8. DisciplinesandOccupations[H] 9. Anthropology,Education,Sociology andSocialPhenomena[I] 10. Technology,Industry,Agriculture [J] 11. Humanities[K] 12. InformationScience [L] 13. NamedGroups [M] 14. HealthCare [N] 15. PublicationCharacteristics[V] 16. Geographic areas[Z]
    3. 3. 3 THE STRUCTURE OF MESH MeSH terms are arranged from thebroadest terms at the top to narrowest terms at the bottomin a poly-hierarchical tree likestructure. At thetop are thefollowing:"Anatomy (A)”, “Organisms (B)” and “Diseases (C)” with increasing levels ofspecificity below. With ~27,800+ descriptorsand 224,000 SupplementaryConcept Records, MeSHis one of the largest controlled vocabulariesof its kind. MeSH providescross-references and see- references in its scope notes. Vitamin C, for example, leadsyou to Ascorbic Acid. USE explode and focus to help you manage recall and precision in your searches. MeSHfor indexing The MeSHthesaurus is used by NLM librarians to index articles from ~5,700 biomedical journals in MEDLINE. Each articleis assigned between ten to fifteen subject terms to describe its content; MeSH terms are used in bibliographicrecordsfor books, audiovisual materialsand digitalitems. TheMeSH thesaurus is updated annually,and NLM creates new headingswith cues from thebiomedicalliterature.Health professionals in various scientific disciplines are consulted about proposed changes to MeSH. There is close coordinationwith otherhealth organizations. Medical subject headings 1960-2017  New MeSH terms are published every January  NLM has been indexing biomedicalliteraturesince 1879 to provide health professionals with access to information for research, healthcareandeducation.  Once a printed index, Index Medicus is now MEDLINE. MEDLINE contains journal citationsand abstracts for biomedicalliteraturefrom around theworld.
    4. 4. 4 SUBHEADINGS IN MEDLINE Medline uses 82 floating subheadingsor qualifiers. The 82 topicalqualifiers bring out specific facets of themain term during indexing. Some common subheadingsinclude: 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-coordinatesearching is also possible in Ovid and widely-used byhealth librarians in systematic review searching. Searchers can also use "Families of Subheadings(see appendixin this manual) to locatespecific typesof literature. (Ask a health librarianfor more information.) UsingMeSH in health-relatedsearching PubMed at pubmed.gov,NLM’s publicsearch 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. Thecore ofPubMed is Medline. Health librarians use keywords to search for information when theydon’t know the exact MeSH to use to satisfy their informationneed. When relevant citationsare found, lookat the MeSHterms applied to a citationto get ideas to rerun your search. Librarians can (re)strategize searches based on a combinationof natural language(See Gault et al) “keywords” and MeSH. Keywords are useful for novice searchers and when current articles have not been well indexed. UsingMeSH in healthlibraries  To improve subject use and access in health libraryOPACs  To develop taxonomiesfor indexing in databasesof various kinds  To create print and digitalpamphlet files  To assign key words to journal articlesubmissions byauthors  To lookup definitions in a medical dictionary  To assign metadatato digitalpublications  To catalogueitemsfor later search engine retrieval  To use in reference interviews to identifyconceptsand synonyms Canadiancontextfor MeSH Due to a slight American bias, MeSH does not always address specifics to Canadian health care. Geographicsubdivisions- Canada, and the provinces - are used to locate information for specific areas of Canada ie. HIV infection in thedowntown Eastside of Vancouver, try "British Columbia"or "Canada"[MeSH] & "downtowneastside" ….
    5. 5. 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 thecontrolled 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 willimprove the precision ofyour search. Focus is used in searches where the topicis quite large,and thehealth librarianknows theremay be plenty of information to wade through …
    6. 6. 6 EXPLODE A MESHTERM(TO INCLUDE NARROWER TERMS) Explodeallowsyou to select all MeSH terms indented underneath. This will increase your recall. By checking theexplodeboxnext to Ranunculaceae allterms indented underneath will be included such as Aconitum,Actaea, Adonis,Anemone and so on 1) Scrollto thetop of thepageand click Continue. 2) For now, disregard theSubheadingspage.Press Continue GO BACK TO theMain Search pagewhere you can see our first set of results in the Search Historybox (youmay need to click Search Historyto openthe box). 3) Repeat thesteps on Pages 5-8 that we followed for our second concept hot flashes 4) Your search historyshould now looklikethis: COMBINE MESH TERMS USING BOOLEANOPERATORS There are two ways to combine your terms in MEDLINE with AND/ OR. Use the BooleanOperatorORto find articles about Hot Flashes OR Cimicifuga Use AND to find articles about both Hot Flashes AND Cimicifuga
    7. 7. 7 1) Combine your terms byselecting thecheckboxes ofeach set; click AND 2) You shouldnow see that your search terms have been combined (1 and 2) TRY DOING “POST-QUALIFYING” TO YOUR SEARCH SET Postqualificationallows youto make changes to a search set. Ovidtranslates a command to re-do a search statement. Use postqualificationto save time. Example I Add theSubheading AdverseEffects to your MeSH term or first set 1) Click Search – note that youhave done post-qualificationand brought yourset down to 46 results
    8. 8. 8 Example II FOCUS Focus theMeSH term “Hot Flashes” 1) Use an asterix * and your set number 2) Click Search; noticethedifference in theretrieval numbers Example III USING “AND” Add terms 4 and 5 together 1) Type4 and 5 in thesearch box to combine your two searches 2) Click Search. Command Line Syntax Command Line Syntax is similar to Post-Qualificationin that it allows you to enter shortcut commands into thecommand line bypassing the icon bars. Example I Confirm thedefinitionand dateof entry for Hot Flashes
    9. 9. 9 1) Typescope <hot flashes> in thesearch box 2) Click Search see PREVIOUS INDEXING for “Hot Flashes” to search before 1998 3) Return to theMain Search Page at top Example II View subheadings associated with Cimicifuga 1) Type……sh <cimicifuga> into thesearch box 2) Click Search. TheSubheading Display willopen
    10. 10. 10 3) Select the subheadingsAdverseEffects, DrugEffects, Poisoning and Toxicity Example I Limit thelast search by journal using FieldQualifiers: 1) Type7 and medical journal of australia.jn in to thesearch box. 2) Click Search Truncation Truncation is an important toolto use where there are no MeSH terms for your concept.It allows you to search for different forms of words byplacing wildcards $ after a word stem Adjacency is a proximity command used to find words adjacent to each other. Example I: 1) TypeEnterprise adj2 Resource adj2 Plan$
    11. 11. 11 2) Deselect theMap Termto Subject Heading Nesting Nesting refers to theuse of brackets to organizethe order of words being searched. Operationsin parentheses are performed first, thencombined with otherstatements Example I Find thesentence pregnancy and childbirth in thetitle of articles 1) Type(pregnancy and childbirth).ti. into thesearch box 2) Click Search
    12. 12. 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 – BloodSupply 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 - RadiationEffects rh - Rehabilitation ri – RadionuclideImaging 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 - TherapeuticUse ul - Ultrastructure ur - Urine us - Ultrasonography ut - Utilization ve - Veterinary vi - Virology
    13. 13. 13 PubMed / MEDLINE SubheadingFamilies AdverseEffects - AE *Etiology - ET *Physiology – PH Poisoning - PO Chemicallyinduced – 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 BloodSupply –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 – SNAbnormalities– AB Cerebrospinal fluid – CF Epidemiology –EP Innervation – IR Deficiency – DF Ethnology –EH Enzymology –EN MortalityMO *Chemistry – CH Pharmacokinetics– PK Supply&distribution– SD Agonists – AG Urine – UR Utilization–UT Analogs & derivatives – AA Antagonists & inhibitors–AI Microbiology – MI Surgery – SU Chemicalsynthesis – 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 Radionuclideimaging – 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 Diagnosticuse – DU Mortality –MO Pharmacokinetics– PK
    14. 14. 14 PubMed® Subset Searching Topic andLimitsSubsets AIDS aids [sb] History of Medicine history [sb] Bioethics bioethics[sb] MEDLINE® medline[sb] Cancer cancer [sb] OLDMEDLINE oldmedline[sb] Core clinicaljournals jsubsetaim SpaceLife Sciences space [sb] Comparative Effectiveness Research effectiveness [sb] SystematicReviews systematic [sb] Complementary Medicine cam [sb] Toxicology tox [sb] DietarySupplements dietsuppl[sb] Veterinary Science veterinary [sb] Additional Search Links to Queries and Interfaces ALTBIB - animal alternatives for biomedicalresearch and testing CAM on PubMed HealthyPeople2020 Cancer TopicSearches MedlinePlus Health Topics ElectronicHealth Records NationalInstitutes of Health Funding Support Health Disparities Research Reporting Guidelines and Initiatives Health Literacy Retracted Publication Health Services Research (HSR) Queries Smallpox
    15. 15. 15 Publication Types Found in PubMed For a full list, see: https://www.nlm.nih.gov/mesh/pubtypes.html Forthe 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 JournalArticle (excludesletter, editorial, news,etc.) Autobiography Lectures Bibliography Legal Cases Biography Legislation Case Reports Letter Classical Article (republished seminal articles) Meta-Analysis(quantitativesummarycombiningresults of independent studies) ClinicalConference(reportsofclinicalcase conferences only) MulticenterStudy ClinicalTrial (includesalltypes and phases ofclinical trials) News (formedical or scientific news) ClinicalTrial,phase I Newspaper Article ClinicalTrial,phase II Overall (collectionofarticles) ClinicalTrial,phase III Patient EducationHandout ClinicalTrial,phase IV Periodical Index(cumulatedindexes to journals) Collected Works Portraits Comment (commentonpreviously published work) Practice Guideline(specific tohealth care) Comparative Study PublicationComponents(specific parts ofpublications) Congresses PublicationFormats (specific genreof publications) ConsensusDevelopment Conference PublishedErratum ConsensusDevelopment Conference,NIH RandomizedControlledTrial ControlledClinicalTrial Research Support,AmericanRecoveryand Reinvestment Act Correctedand Republished Article Research Support,N.I.H.,Extramural Dictionary Research Support,N.I.H.,Intramural Directory Research Support,Non-U.S. Gov'tResearchSupport,U.S. Gov't,Non-P.H.S. Duplicate Publication Research Support,U.S.Gov’t, P.H.S. Editorial Retracted Publication(worklater retracted byauthor) English Abstract(offoreignarticle) Retraction ofPublicationReview (author’sstatement of retraction) Evaluation Studies Reviewarticles Festschrift Study Characteristics(identify any type of study) Government Publications SupportofResearch Guideline (administrative, proceduralguidelines in general) Technical Report Historical Article (articles about past events) Twin Study InVitro Validation Studies Interactive Tutorial Video-AudioMedia Interview Webcasts
    16. 16. 16 Big Four (4): major biomedical databases at a glance Database Date coverag e Sources Geographic / linguistic Abstracts Subject Scope IndexingNotes 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%ofrecords added from 1975 have abstracts;none from 66-74; back to1949; Indexmedicus back to1879 Premier int’l biomedical database producedby NLM; 60%+ US papers so slight Americanbias - MeSH subject headings; ~27,800 thesaurusterms - 82 topical subheadings - uses USANterms fordrugs - noadded indexing formedical 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) 34languages 80%English 64%records accompanied by abstracts (backfiles available for 1947-1973at Embase.com) International. Publishedby Elsevier. Comparable to Medline but more preclinical citations Pharmaceutical coverageis good.European & Asiancontent - EMTREE subject headings ~60,000 thesaurus terms, detailed drug name indexing 78 drug-focused subheadings - uses INNterms and CASregistry numbers EBM Reviews (Cochrane Libraryon 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 recordsfrom Medline included CINAHL fulltext– Cumulated indexto nursingand 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 - nursingand allied health literature; Cochrane citations; 55% contentis unique not in Medline or Embase - 12,000+ CINAHL headings - 68topical subheadings

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