Searching Pubmed and Medline
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Searching Pubmed and Medline

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Workshop developed to teach MLIS students how to effectively search for evidence-based medical information through Ovid-Medline and PubMed.

Workshop developed to teach MLIS students how to effectively search for evidence-based medical information through Ovid-Medline and PubMed.

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  • PMC (PubMed Central) launched in 2000 as a free archive for full-text biomedical and life sciences journal articles
  • example Head injur* AND memory loss
  • example in pubmed eye [mh] eye [mh: noexp]
  • Date of Publication [dp] - Date searching includes both print and electronic dates of publication. Searching for a single date does not include items when the electronic date of publication is after the print date. Electronic Date of Publication (if applicable) [epdat] Print Date of Publication (if applicable) [ppdat] Entrez Date [edat] - The date the citation first entered PubMed. MeSH Date [mhda] - The date the citation was indexed with MeSH terms. Create Date [crdt] – The date the citation record was first created.
  • Date of Publication [dp] - Date searching includes both print and electronic dates of publication. Searching for a single date does not include items when the electronic date of publication is after the print date. Electronic Date of Publication (if applicable) [epdat] Print Date of Publication (if applicable) [ppdat] Entrez Date [edat] - The date the citation first entered PubMed. MeSH Date [mhda] - The date the citation was indexed with MeSH terms. Create Date [crdt] – The date the citation record was first created.
  • To add additional filter categories to the sidebar, click the “Show additional filters” link, select the additional categories, and then click Show. To activate the additional filters, click the filter selection.
  • To add additional filter categories to the sidebar, click the “Show additional filters” link, select the additional categories, and then click Show. To activate the additional filters, click the filter selection.
  • To add additional filter categories to the sidebar, click the “Show additional filters” link, select the additional categories, and then click Show. To activate the additional filters, click the filter selection.
  • National Center for Biotechnology Information (NCBI)
  • read from John's sheet

Searching Pubmed and Medline Searching Pubmed and Medline Presentation Transcript

  • Accessing Medline- A Workshop in PubMed and Medline-OVID Group members: Vivian, Bridget, Ashley, and Kristen B
  • Today's Workshop 1. Learning Objectives (Kristen) 2. Medline (Kristen) 3. Literature Review (Ashley) 4. PubMed (Bridget) 5. PubMed-NCBI (Bridget) 6. Medline-OVID (Vivian) 7. Medline-OVID - My Workspace (Vivian) 8. Class Activity
  • Learning Objectives 1. Comparison of how MeSH maps natural language differently between PubMed and Medline- Ovid 2. Understand how to save, share, and combine search strategies and auto-alerts for PubMed and Medline-OVID 3. Understand how to export citations into RefWorks from PubMed and Medline-OVID
  • Medline • Premier, comprehensive biomedical database in the United States • Updated daily • 5500 biomedicine and life science journals in nearly 40 languages • English abstracts are including for more than 80% of the records • Full text coverage: 1948-Present • Number of records: 18000000+
  • Literature Review Allison JJ, Kiefe CI, Weissman NW, Carter J, Centor RM. The art and science of searching Medline to answer clinical questions. Intl J of Technology Assessment in Health Care. 1999; 15 (2): 281-296. Delwiche, FA. Searching Medline via Pubmed. Clinical Laboratory Science. 2008; 21 (1): 35-41. De Groote, SL. PubMed, Internet Grateful Med, and Ovid: A comparison of three Medline internet interfaces. Medical Reference Services Quarterly. 2000; 19 (4): 1-13. Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180. Katchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807.
  • Lit Review Findings • Usability and User Preference of Ovid vs. PubMed • Effectiveness of search tool dependant on user’s familiarity with it • Functionality (use of Boolean operators, truncations and proximity searching) • Variations in how Ovid and PubMed map free language onto MeSH • Sensitivity of PubMed vs. Ovid in retrieving all relevant articles • Use of Filters
  • User Preference Thiele RH, Poiro NC, Scalzo DC, Nemergut EC. Speed, accuracy and confidence in Google, Ovid, PubMed, and UpToDate: Results of a randomised trial. Postgrad Med J. 2010; 86: 459-465. Google 45% PubMed 25% Ovid 4% UptoDate 26%
  • Variations in MeSH Mapping Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180. Cannot assume symmetrical retrieval from MeSH in different systems Pubmed and Ovid provide methods for suggesting mesh, but methods are varying
  • SensitivityKatchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807. PubMed has higher sensitivity than Ovid The Study: • PubMed found more results for each concept - rheumatoid arthritis, MTX and randomized control trials • 18 eligible articles were selected, Ovid had
  • Limits and FiltersWinchester DE, Bavry AA. Limitations of the MEDLINE database in constructing meta-analyses. Ann Intern Med. 2010; 153: 347-8 • When search limits are used, researchers miss important and relevant records • Only limits that can be safely used are dates and language – those not based on MeSH • Applying search limits is not an integral part of search strategy - well executed searches benefit from limits when they are applied post hoc to remove unwanted documents
  • Tips and Tricks Revealed in Lit Review 1. Use both MeSH and free text words to limit Eg. search "trial" as free-text in the abstract filed in addition to MeSH 1. Use synonyms and truncation 1. Don't actively limit but use double negation Eg. (NOT (Animals [MeSH] NOT Humans [MeSH])) - ensures no non-indexed human studies are missed
  • PubMed - Introduction • What is PubMed? • Types of Citations • Advanced Search Builder • Automatic Term Mapping • MeSH Subheadings (Qualifiers) • Search Field Descriptions & Tags • Filters • Features (Single Citation Matcher, Clinical Queries & My NCBI)
  • PubMed - What Is It? • Free access to MEDLINE • Links to full-text articles in PubMed Central, publisher web sites, and other related resources • Over 22 million citations • Developed & maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine
  • PubMed - Type of Citations • PubMed - as supplied by publisher • PubMed - in process • PudMed - indexed for MEDLINE • PubMed • PubMed - OLDMEDLINE
  • PubMed - Example:
  • May miss non-indexed papers or "wrongly indexed" papers if only MeSH is used Use both MeSH terms AND keywords, including synonyms, related terms, variant endings and spellings PubMed - Comprehensive Searching
  • PubMed - Advanced Search Builder • • Choose a field (if you like) • Run Search • Combine search strings Isolate concepts
  • PubMed - Automatic Term Mapping (ATM) • Maps keywords to MeSH headings, journal titles or author names • Splits phrases apart and searches each term separately and combines them • Parts of a search can be removed and/or added and rerun
  • PubMed - Keep in Mind... • • PubMed ignores Stopwords (i.e. because, regarding, mostly, however, each, etc.) List of Stopwords: http://www.ncbi.nlm.nih.gov/books/NBK3827/ta ble/pubmedhelp.T43/?report=objectonly
  • PubMed - Use with Caution... • • Phrase searching is possible with "double quotations" *Warning: Using truncation or quotations will automatically turn off mapping and MeSH term explosion (try to use in addition by combining with OR)
  • Use the MeSH database to find a suitable term and "Add to Search Builder", then run your search in PubMed PubMed - Wrong Term Mapped?
  • PubMed - MeSH Search Tags (Qualifiers) [mh] To search a MeSH heading [majr] To search a MeSH heading that is a major topic of an article
  • PubMed - Warning: Warning: Using only MeSH subject terms excludes in-process & publisher-supplied citations & others that do not (or do not yet) include MeSH subject terms
  • PubMed - MeSH Search Tags No Exploding Turn-off automatic explosion by adding :noexp i.e. [mh: noexp] [majr: noexp] Terms will automatically explode
  • PubMed - MeSH Subheadings Want to Get More Specific?Add MeSH Subheadings (also called Qualifiers) by adding a slash and typing in the Qualifier's name or the Qualifier's abbreviation i.e. eye/injuries [majr] or eye/in [majr] *case and spacing don't matter *cannot turn off the explode feature for a subheading
  • PubMed - Subheadings cont'd List of Subheadings: http://www.ncbi.nlm.nih.gov/books/NBK3827/table/ pubmedhelp.T41/ Subheading Definitions: http://www.nlm.nih.gov/mesh/topsubscope.html Qualifier Hierarchies: http://www.nlm.nih.gov/mesh/subhierarchy.html
  • PubMed - Search Field Descriptions/Tags List of PubMed Data Element Field Descriptions: http://www.ncbi.nlm.nih.gov/books/NBK3827/tabl e/pubmedhelp.T44/?report=objectonly Limits your search
  • PubMed - Author Field • i.e. austin j [au] • Will automatically truncate. To stop this, add quotations i.e. "austin je" [au]
  • PubMed - Date Field • • To search for a specific date, use this format: YYYY/MM/DD [date field] *month and year are optional
  • PubMed - Date Field cont'd... Date Field Date ranges can be entered with a colon i.e., 2004:2006 Comprehensive searches for a full year i.e., 2000:2000 (will retrieve citations with a different print and electronic year of publication) Searching by date FAQ:
  • PubMed - Filters • • Select filter (left side of screen) • Click on "Show Additional Filters" if necessary *Filters will remain for all subsequent searches unless they are cleared
  • PubMed - Single Citation Matcher • • Enter the information you have to fill in the blanks • Click go
  • PubMed - Clinical Queries A search interface to find citations in the areas of: • Clinical Study Categories: Find citations corresponding to a specific clinical study category. • Systematic Reviews: Find citations for systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines. • Medical Genetics: Find citations related to various topics in medical genetics.
  • PubMed - My NCBI • • Need to register (free!)
  • PubMed - My NCBI: User Preferences Some include: • Link options • Email options • Display highlighted terms • Single Citation Display
  • PubMed - My NCBI: Filtering Options • • Can customize your own filter and name it
  • PubMed - My NCBI:Save Search Strategy & Alert Setup • Max number of saved searches is 100 per user-name • Saved searches cannot be edited • Limited to one email address per account *related articles cannot be saved; date and date ranges are
  • PubMed - RefWorks Refresher In PubMed... 1) Mark appropriate records in your search 2) Add to Clipboard (from "Send to" menu) 3) Display the Clipboard contents 4) Change "Display Settings" to Medline format 5) Select and Copy all of the text
  • PubMed - RefWorks Refresher Cont'd In RefWorks.... 6) Select References > Import 7) Select NLM PubMed from the Import Filter drop down menu 8) PubMed will appear automatically as the database 9) Click on the From Text link 10) Paste text into the box 11) Click IMPORT
  • Medline-OVID • Uses OvidSP - their flagship research platform • More than 2500 ebooks and collections, including archive collections of critical historical materials, as well as publisher and topical collections • Over 1300 premium, peer-reviews journals, including dozens of journal collections • Over 100 bibliographic and full-text databases • Disciplines: Medicine, Nursing & Health Professions, Behavioural Sciences, Basic Science, Humanities & Technology
  • Medline-OVID Mapping • OVID uses vocabulary mapping which searches using natural language terminology • The mapping process uses OVID's statistical algorithm to determine which terms are associated with certain subject headings • The use of mapping increases a user's retrieval precision • Ovid will automatically maps search terms to the database's controlled vocabulary
  • Medline-OVID Command Line Syntax • Allows shortcut commands to be added to a user's search, circumventing the use of the icon bar • Use of command line in OVID overrides MeSH mapping Examples: • exp <term> - This command within a controlled vocabulary database would explode the term • * <term> - This command within a controlled vocabulary database would focus on that term • <term>.ab. - This command would search term term through the abstract (ab) field of the database
  • Medline-OVID Truncation and Wild Cards • Unlimited truncation - "$" or ":", such as "cancer$" which will retrieve "cancer", along with "cancers" and "cancerous" • Limited truncation - "$" or ":" paired with a number will retrieve the root word with that maximum number of character, i.e. "dog$1" will retrieve "dog" and "dogs", but not "dogma" • Mandated Wild Card - "#" is used within or at the end of a term to substitute one required character, i.e. "wom#n" will retrieve "women" and "woman", however "dog#" will retrieve "dogs", but not "dog" because it require another character to be present • Optional Wild Card - "?", used to substitute one or no characters, useful when dealing with American/British word variants, i.e. "colo?r" will retrieve "color" and "colour", however "?" will not work if there is only one letter before the wild card
  • Medline-OVID Stopwords • Words with that hold little value or meaning • These words are often discarded in a search unless • Ovid has elimated Stopwords, now user's can search words/phrases such as "is there hope.tw"
  • Medline-OVID RefWorks • Bibliographic information can be exported into RefWorks in Ovid
  • Medline-OVID - My Workspace My Searches & Alerts •Search strategies/strings can be saved o Save as Temporary (24hours) o Save as Permanent (valid subscription) o AutoAlert (searches automatically on regular basis and emails the results) o Expert Searches (An expert creates a search strategy that is shared and available to allow multiple users to share searches on the same group account) My eTocs •Email alerts user when the journal they subscribe to updates its
  • Class Activity Follow instructions on your handout and complete exercises. If you have any questions, raise your hand and we can help. Class discussion
  • MeSH Variations Ovid: Depression (default) but there are other choices in list PubMed Automatic Mapping: Depressive disorder OR depression PubMed Mesh Browser: Depression, depressive disorder and more options
  • PubMed Mesh Browser or Default Search? • PubMed Browser is more like Ovid - building block style with user control over which MeSH is selected • PubMed default automatic mapping is intelligent and handy, but it doesn't always account for all MeSH that could be used but can retrieve more documents... Choosing how you want to search is up to you!
  • Differences in Ovid's MeSH list and PubMed's Browser List Ovid provides shortest list of MeSH choices (average is 8 terms) with a selection rate of 62% PubMed has a list 3x longer with a selection rate of 63% (Gault et. al) Not much difference...
  • Combining Concepts and Results PubMed MeSH Browser: ((("Depression"[Mesh]) OR "Depressive Disorder"[Mesh]) AND "Mass Screening"[Mesh]) AND "Women"[Mesh] # of results - 17 PubMed Automatic Mapping: ("depressive disorder"[MeSH Terms] OR ("depressive"[All Fields] AND "disorder"[All Fields]) OR "depressive disorder"[All Fields] OR "depression"[All Fields] OR "depression"[MeSH Terms]) AND ("mass screening"[MeSH Terms] OR ("mass"[All Fields] AND "screening"[All Fields]) OR "mass screening"[All Fields]) AND ("women"[MeSH Terms] OR "women"[All Fields])
  • Combining Concepts and Results Ovid (user selection): Depression and mass screening and women # of results - 6
  • Command Line Answer for PubMed Field Descriptor Question: hepatitis b[mh] AND Murphy TV[au] AND 2012:2013[pd] Answer for Ovid Dot Commands: hepatitis b. and Murphy TV.au and 2012:2013.yr OR hepatitis b. AND Murphy TV.au AND 2012:2013.yr