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How to search the pharmaceutical literature


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A handout to support informatics training for UBC pharmacy residents

A handout to support informatics training for UBC pharmacy residents

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  • 1. UBC PharmD Students Library Workshop, August 22nd, 2014 “Using the UBC Library and Finding Drug Information” Dean Giustini (DG) – UBC Biomedical Branch librarian Dr. James McCormack (JMc) – Faculty, UBC Faculty of Pharmaceutical Sciences Schedule Topic Resources UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 1 9:30am Introduction(s)  UBC Library homepage  Library catalogue “search”  “Find” eJournals & Indexes & databases 9:45-10:20am Strategies to find best evidence about drugs Appraised & synthesized sources of information  Individual e-books & online book collections  AccessMedicine, Books@0vid  MDConsult, MedicinesComplete  Natural Standard  e-Therapeutics, eCPS Break Try some searching  Using tools above, compare versions 10:30-11:00am Clinical practice guidelines Point of care tools  Clinical guidelines sources  BC Guidelines, CMA Infobase, etc.  Point of care decision-making tools  BMJ Clinical Evidence & DynaMed 11:00 – 12noon Article indexes & databases  Overview of major drug databases (handout)  Drug nomenclature; how it affects searching Search practice  OvidSP Platform Lunch Lunch Free time 12:50 – 1:30 Problem sets/primary sources review  OvidSP & Medline, EMBASE  International Pharmaceutical Abstracts  PICO review 1:30 – 2:00 EBM databases  Cochrane Database of Systematic Reviews  Cochrane Controlled Trials Register  ACP Journal Club & DARE & TRIP 2:00 – 3:00 Other databases  Google Scholar  Web of Science (ISI platform) 3:00 to end Pharmacy Jeopardy  Team competition
  • 2. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 2 Introduction The following handbook is for UBC pharmacy students who are searching for drug-related information during their programs in 2014. See also: UBC Pharmacy_Handout (HLWIKI International). UBC Hospital Library at the Diamond Centre, Vancouver hospital The University of British Columbia Library operates a hospital library at the Vancouver General Hospital (Diamond Centre, Floor 2). The Library licenses thousands of ebooks, ejournals and databases and digital resources are being purchased regularly. The UBC Library maintains a free document delivery service for articles that it does not own at any of the UBC libraries. The BMB Library provides access to computers, printers, copiers and Wifi access (Wireless Internet) via ‘ubcsecure’ at UBCCard The UBCCard (which functions as a library card also) can be obtained from the UBC Carding Office on the Point Grey Campus, UBC Bookstore. For information about library cards, see How to Get a Library Card. UBC LIBRARY WEBSITE Pharmacy databases, journals and e-books  UBC Library resources -- such as pharmacy databases, journals and e-books -- are subscription-based (i.e. the library pays for access), so you must authenticate as a UBC user when at home or at a non-UBC computer. See also: Pharmacy subject guide How to search  For an overview of searching pharmacy-related databases, see page 10 of this handout  It is aimed at those who already have a basic understanding of search principles and how to use common indexes and databases such as EMBASE and PubMed  See also our OvidSP Tutorial or
  • 3. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 3 Access Off-Campus  Campus wide login (CWL) –; for more information, see the UBC Library homepage under: Connecting from home  If you are off-campus, you must authenticate as a UBC user in order to get into our databases and online journal collections using your UBC library card or CWL.  EZProxy prompts you to log in using your CWL or library barcode when accessing a resource. Online books  Before you buy any textbooks, check to see if UBC library has an online version. Many classic titles are available in AccessMedicine, Books@Ovid, eTherapeutics+, MedicinesComplete & MD Consult More e-books  e-Books are most often grouped into collections of online books (such as those below)  UBC Library provides access to thousands of e-books through the UBC library catalogue  Want to find e-books in our catalogue? see: AccessMedicine includes:  Harrison’s Principles of internal medicine (Harrison’s online)  Goodman and Gilman’s Pharmacological basis of therapeutics  Tintinalli’s Emergency medicine  Lange educational library, including Olson’s Poisoning & drug overdose Books@Ovid includes:  Briggs' Drugs in Pregnancy and Lactation on Books@Ovid
  • 4. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 4 eTherapeutics+ includes:  e-CPS  Therapeutics: online version of Therapeutic Choices  Lexi-Interact MedicinesComplete In-depth information about drug-drug, drug-food, and drug-herb interactions  AHFS Drug Information  Martindale: The Complete Drug Reference  Stockley's Drug Interactions MD Consult includes:  Goldman's Cecil Medicine (Textbook of Medicine)  Harriet Lane Handbook ; Nelson Textbook of pediatrics  Haddad and Winchester’s Clinical management of poisoning and drug overdose Natural Standard  an international research collaboration that synthesizes data on complementary and alternative therapies Other e-books:  Diagnostic and Statistical Manual of Mental Disorders DSM-V (Psychiatry Online)  Natural Standard  Red Book Online Online journal articles  Many scholarly journals are available via UBC Library. When searching in a biomedical or pharmaceutical database, look for in order to locate an online version of articles  In most cases, we have an online version of the article  If full-text is not available, see whether or not we have the print  If we cannot provide a copy for you, you can order the article via the Interlibrary Loan (ILL) Order page (free to UBC students, faculty and staff)
  • 5. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 5 Clinical practice guidelines British Columbia  BCGuidelines - Guidelines and Protocols Advisory Committee (GPAC) o browse numerous conditions, with particular focus on circumstances in British Columbia Canada  CMA Infobase: Clinical Practice Guidelines (CPGs) - Canadian Medical Association (CMA) o 1200 publicly-accessible evidence-based clinical practice guidelines (CPGs) developed by medical or health organizations in Canada North American (and beyond)  National Guideline Clearinghouse (NGC) o a US-based public resource for evidence-based clinical practice guidelines United Kingdom  NICE National Institute for Health and Clinical Excellence  SIGN Scottish Intercollegiate Guidelines Network  TRIP Database: Turning Research Into Practice - UK meta-search tool; includes clinical guidelines
  • 6. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 6 Current awareness There are numerous ways to keep up to date with current literature, including subscribing to electronic bulletins and newsletters, setting up RSS feeds for tables of contents from key journals, creating alerts for specific database searches, and participating in a journal club. Here are some ideas for you to explore as you customize your strategy for keeping up with current evidence.  Bulletins, newsletters, etc.  British Columbia Pharmacy Association, The Tablet (student members free)  Canadian Healthcare Network  Canadian Pharmacists Letter (members)  College of Pharmacists of BC  Medical Letter - (member access)  Therapeutics Letter (UBC Therapeutics Initiative) -  The Therapeutics Education Collaboration offers entertaining and informative podcasts. Episode 40 deals with keeping up to date with the medical literature.  UC Berkeley Wellness Letter - (some free, member access)  UBC Continuing Education Professional Development -  eNews updates  CADTH – Canadian Agency for Drugs and Technology in Health: What’s New RSS feed available -  Health Canada Advisories, Warnings and Recalls: See the “Subscribe to news” link -  Sign up for daily news email or set up RSS feed -  Natural Medicines Comprehensive (NMCD) eUpdate - (subscribers only; eUpdate is free)  MedEffect – from Health Canada: Use the MedEffect e-Notice link to sign up -  US FDA MedWatch: Safe alerts available by email or as RSS feed -
  • 7. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 7 News & media  Globe and Mail   NY Times   Reuters   Media Doctor  (goal is to improve media coverage of drugs)  RetractionWatch  RSS feeds for TOCs  Set up RSS feeds to custom searches (including searches by journal title) in PubMed and in OvidSP  Annals of Internal Medicine o  Annals of Pharmacotherapy o  American Journal of Health-System Pharmacy o  British Medical Journal (BMJ) o  Canadian Medical Journal o  Canadian Pharmacists Journal (CPhA) / Revue des pharmaciens du Canada (RPC)  Journal of the American Medical Association (JAMA) o  Lancet o  New England Journal of Medicine o  Pharmacotherapy (American College of Clinical Pharmacy) o
  • 8. SEARCHING THE PHARMACEUTICAL LITERATURE In evidence-based practice, it is essential to keep up-to-date with new drugs in your field and to answer patient-related questions effectively. This handout provides an overview of the core pharmacy-relevant databases and evidence-based tools. It provides search tips for those who want to improve their basic to intermediate search skills. Ask the librarian for more information if you need an assessment or assistance. MAJOR INDEXES & DATABASES DESCRIPTION SEARCH TIPS & PEARLS Medline (OvidSP) The US National Library of Medicine’s (NLM) premier bibliographic database covers the biomedicine, nursing, pharmacy, dentistry, veterinary medicine, the health care system and preclinical sciences. Data producer is NLM. OvidSP is a commercial vendor. Contains bibliographic citations and abstracts from ~5500 biomedical journals. Daily update; 1948 – present UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 8 Searching by keyword vs. subject heading  Textword searching finds occurrences of keywords in titles or abstracts (or specified fields). Keyword searching may yield more irrelevant results than subject searching (since words or phrases may have more than one meaning). Keyword searching, however, may be needed for new topics, very specific topics or when an available subject heading is not accurate enough.  When conducting text searches, remember to consider synonymous or related terms, variant spellings (American vs. British), and word endings (singular and plural forms of a word).  Subject searching or controlled searching helps deal with variant spellings as articles on the same topic should be indexed using the same subject heading or controlled terms – regardless of spelling or terminology used in the article.  Subject searching generally yields more precise and relevant results.  In Medline subject headings are referred to as MeSH terms (“Medical Subject Headings”). MeSH are arranged in a hierarchical order, with narrower headings indented under broader headings.
  • 9. NOTE: In this example, exploding the MeSH term “Canada” includes results indexed with more specific MeSH terms for each province and territory. NOTE: Explode and Focus can be used simultaneously. For example, exploding and focusing the MeSH term “Canada” will also retrieve records in which the MeSH term “British Columbia” is a major topic. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 9 TIP: For a comprehensive search USE a combination of subject searching AND keywords Explode function (when using MeSH)  Explode expands a search to include a heading and more specific headings indented below  Indexers assign the most specific subject heading so to include all possible terms, the broader term may need to be exploded. Focus function (when using MeSH)  Focus will limit your search to citations where your MeSH terms are considered a major topic  Articles are indexed from between 15 – 20 MeSH but there may be ~3 MeSH designated as major topics Scope notes (when using MeSH)  Scope notes provide definitions about MeSH terms for indexing  They provide information about when headings were created and what
  • 10. NOTE: KEYWORD SEARCHING  To search variants on a keyword, use $ (for example, wait$ finds wait or waiting, list$ finds list or lists)  Use an asterisk * as a truncation symbol also  To make keyword searches more relevant in OvidSP, TRY limiting keyword searches to the title or abstract field, or using the adjacency function. For example, in search set 4, wait or waiting must be within 3 words of any one of the keywords in the parentheses. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 10 heading(s) were previously used in indexing  Scope notes are especially useful when you have an array of similar MeSH terms to select from and aren’t sure which to use. Keyword search strategies  Careful keyword searching is necessary when no MeSH terms are suitable for your search (concept may be too recent for a new MeSH to have been created)  Remember MeSH indexing is done by librarians. If you use MeSH terms you may miss relevant records indexed incorrectly  Using keywords is a way to make sure your search is as thorough as possible  Keyword searching can be particularly effective when search terms are unique Limits  Use limits to restrict your search results by age, date of publication, language, publication type, etc.  For greater efficiency apply limits to your final search set, rather than to individual sets as you’re searching Embase (OvidSP) International (but European Indexing in EMBASE
  • 11. focused) biomedical and pharmacological database; extensive indexing of drug information; ~5000 journals; comprehensive coverage of pharmacy, pharmacology and toxicology with detailed subject headings for drugs; weekly updates; 1980 – present UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 11  In EMBASE, headings are called EMTREE terms  In Medline they are MeSH; there are important differences to know  EMBASE uses INN names for drugs; Medline uses USAN names; EMTREE provides extensive cross referencing of drug names; Registry numbers are routinely included.  Drug and device brand & manufacture names added by indexers when cited by source author in full text.  References to investigational or recently approved drugs is easier in EMBASE EMTREE subheadings  Subheadings allow the searcher to refine the search further by specifying some aspect of the EMTREE subject heading. For example: antibiotic agent/ae TIP: Subheadings can be useful when applied to subjects that have many articles associated -- but should generally be used with caution NOTE:  The display for subject headings in EMBASE shows broader headings, narrower headings and “used for” references  Used for references are synonymous terms that automatically map to that heading  Although the display in EMBASE is different from MEDLINE, explode, focus and subheadings function similarly NOTE: Subheadings (also referred to as “link terms”) for EMTREE drug subject headings are much more specific and varied than they are in Medline.
  • 12. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 12 US National Library of Medicine’s (NLM) freely available search tool to biomedical literature. Medline (i.e. the indexed portion) forms largest part of PubMed. Pubmed includes OLDMEDLINE , in-process and non-indexed citations. Automatic term mapping  Keywords that are entered into the search box are matched (in this order) against a MeSH translation table, a Journals translation table, the Full Author translation table and an Author Index, the Full Investigator (Collaborator) translation table and an Investigator (Collaborator) index.  When a match is found for a term or phrase in a translation table the mapping process is complete and does not continue on to the next translation table.  If a match is found in this translation table, the term will be searched as MeSH (that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy), and in all fields. TIP: See how Pubmed translates your search, click Details tab Automatic term mapping (translation) is good in Pubmed but not 100%. Drug trade names do not map well, for example, motrin maps to “ibuprofen” but advil fails to map to its non-proprietary name Where term mapping is weak, try the MeSH database or examine relevant records for clues about the most relevant MeSH term available
  • 13. Other Biomedical Databases UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 13 Cochrane Database of Systematic Reviews (CDSR)) on OvidSP Produced by Cochrane, international, non-profit and independent organization producing and disseminating systematic reviews of interventions Contains 2 types of publications: completed systematic reviews & protocols for future reviews Searching in CDSR and DARE  Use UBC Library’s list of Indexes & Databases   Can search individually, or with other databases that comprise EBM Reviews.  NO subject heading searching – keyword only . Searching in CDSR and DARE  Available through UBC Library’s list of Indexes & Databases  Database of Abstracts of Review of Effectiveness (DARE) on OvidSP A filtered source containing critical assessments of systematic reviews published in the literature. Produced by the UK’s National Health Services’ Centre for Reviews and Dissemination. International Pharmaceutical Abstracts on OvidSP Produced by the American Society of Health System Pharmacists. Smaller but more focused database covering pharmacy specialty journals Strengths in biopharmaceutics, drug stability, pharmaceutical technology, pharmacy education, and legal aspects of drugs Monthly update; 1970 – present. Searching in IPA  UBC Library’s list of Indexes & Databases, see International Pharmaceutical Abstracts (IPA)  Generally, searching is by keyword.  Strong for drug brand names. BIOSIS Previews (on ISI) Journal references from Biological Abstracts plus the references to Searching in BIOSIS  Subject headings (aka descriptors descriptors) subdivided into categories, for
  • 14. meetings, reviews, books, and monographs from Biological Abstracts/RRM (Reports, Reviews, Meetings). Covers Agriculture, Biology, Biochemistry, Biotechnology, Botany, Pre-Clinical and Experimental Medicine, Pharmacology, Veterinary Sciences and Zoology 1969 – present. Weekly update. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 14 example major concepts, biosystematic names, etc.  Includes CAS registry numbers but cannot be relied upon to retrieve all references to given compounds.  Provides 2 levels of conference coverage: 1) citations that summarize meeting overall and 2) separate records for individual papers  See BIOSIS Previews Web of Science (on ISI) Multidisciplinary database that coverage a broad range of subjects, including physical sciences, medical sciences, life sciences, applied sciences, agriculture, humanities and social sciences, law, business. 1900 – present. Weekly update. Searching in Web of Science  Searching mostly keyword driven  Excellent source of cited reference searching (i.e. Who has cited a particular paper?)  Good for finding landmark articles Secondary literature: clinical guidelines, reviews, evidence summaries, etc. $$ - FIRSTConsult (UBC subscribes) A point of care/bedside information tool with links to guidelines. A companion product to MDConsult, which includes e-books, patient leaflets, selected e-journals. Available through UBC library’s Indexes and Databases  FREE - TRIP Database Meta-search for finding guidelines, evidence-based synopses, clinical questions and more. Available on the web at:  For a full list of what sources are searched by TRIP, see: 
  • 15. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 15 FREE - CMA Infobase Canadian source maintained by Canadian Medical Association. Guidelines published or reviewed in the last five years. “Currently includes over 1200 CPGs developed or endorsed by authoritative medical or health organization.” Available on the web at:  Keyword searching; also possible to narrow by guideline developer.  Provides full text if possible; full text may not always be available depending on copyright. Short record is given with more detailed record (with analysis) for some.  Archive of guidelines older than 5 years is available. FREE - National Guideline Clearinghouse US source; maintained by US Agency for Healthcare Research and Quality. “Produced under auspices of medical associations; relevant professional societies, public or private organizations, government agencies at the Federal, State, or local level; or health care organizations or plans.” Available on the web at:  Keyword search recommended, though MeSH is available.  Provides guideline syntheses.  Complete summary provides fairly in-depth analysis of guidelines.  Creates on-the-fly comparison charts of multiple guidelines.  Provides archive of guidelines older than 5 years For more information, see how to use: Point-of-care tools in medicine & Expert searching for the systematic review
  • 16. Major biomedical research databases at a glance UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 16 Database Name Dates Covered Updating Sources Geographic Scope & Language Coverage Abstracts Subject Scope Indexing Notes Medline (via PubMed & on OvidSP) 1949 – present Updated daily ~23 million citations 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; 60% + of papers in clinical medicine with slight American bias - MeSH subject headings 2010 - ~26,000 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 languages 80% English 64% records accompanied by abstracts (backfiles available for 1947-1973 at 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 indexing 78 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 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 – Cumulated index to nursing and allied health literature (on EBSCO) 1981 – present ~2 million citations Updated bi- 2900+ journals, disserations, 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
  • 17. monthly legal cases, UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 17 research instruments, peer-reviewed and consumer materials Abbreviations: ACP – American College of Physicians CAS – Chemical Abstracts Service EBM – Evidence-based medicine INN - International Nonproprietary Names ISI - Institute for Scientific Information OA – Open access USANs - U.S. adopted names
  • 18. APPENDIX A Mobile Apps in Pharmacy 2013 Reference: Aungst TD. Medical applications for pharmacists using mobile devices. Ann Pharmacother. 2013 Jul;47(7-8):1088-95. doi: 10.1345/aph.1S035. Epub 2013 Jul 2. UBC PharmD Students Library Workshop, August 22nd, 2014 – Giustini, McCormack page 18