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Advanced PubMed Presentation (with Endnote)

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KUMCGlass

Research and Learning Presentation on Advanced PubMed search strategies and EndNote support.

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May 23, 2014
 Will learn techniques for constructing
effective search strategies
 Explore PubMed related tools
 Will increase efficiency in utilizing PubMed
and other databases
 Will be sharing trends and ways to stay
current
 Identifying resources for citation
management support
Topic: Intra-aortic balloon pumps intra-aortic balloon pump counterpulsation for refractory
symptomatic vasospasm
 Search Builder
◦ Advanced search
◦ Boolean Search (AND/OR/NOT)
 doctors OR physicians
 tumor OR tumour
 doctors AND managed care
 injuries AND automobiles
OR AND
Boolean operators:
AND, OR, and NOT
must be entered in UPPERCASE.
 Enclose a phrase in double quotes
◦ Example: “spinal surgery”
 Try without quotes first
 Truncate a search by using an asterisk (*).
This is commonly referred to as a “wildcard
search”
◦ Example: mimic*
 PubMed searches: mimic, mimics, mimicing etc..
 “Nest” search terms in parentheses. The
terms inside the set of parentheses will be
processed as a unit and then incorporated
into the overall strategy.
◦ Example: salmonella AND (hamburger OR eggs)
 PubMed will retrieve records that contain the term salmonella, as well
as one or both of the terms hamburger OR eggs.
PubMed also refers to a list of
commonly found words that are
referred to as "stopwords."
Stopwords are words that, if indexed,
could potentially return every
document in the database if the word
was used in a search statement.
Consequently, commonly found words
are not indexed and PubMed will
ignore them.
Search Details
The Search Details portal is an important tool to use when building a search.
If you notice that the results PubMed has retrieved for a search are not
relevant, you should check the Search Details section to see exactly how
PubMed has translated your query.
An example would be a broad search for nursing (profession). While
you have just searched the word nursing, PubMed translated that as:
"nursing"[Subheading] OR "nursing"[All Fields] OR
"nursing"[MeSH Terms] OR "nursing"[All Fields] OR "breast
feeding"[MeSH Terms] OR ("breast"[All Fields] AND
"feeding"[All Fields]) OR "breast feeding"[All Fields]
PubMed mapped “nursing” to “breast feeding” and returned 578358
results. While taking out those terms in red will return 550360. A
28,000 article difference!

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Advanced PubMed Presentation (with Endnote)

  • 2.  Will learn techniques for constructing effective search strategies  Explore PubMed related tools  Will increase efficiency in utilizing PubMed and other databases  Will be sharing trends and ways to stay current  Identifying resources for citation management support
  • 3. Topic: Intra-aortic balloon pumps intra-aortic balloon pump counterpulsation for refractory symptomatic vasospasm  Search Builder ◦ Advanced search ◦ Boolean Search (AND/OR/NOT)  doctors OR physicians  tumor OR tumour  doctors AND managed care  injuries AND automobiles
  • 4. OR AND Boolean operators: AND, OR, and NOT must be entered in UPPERCASE.
  • 5.  Enclose a phrase in double quotes ◦ Example: “spinal surgery”  Try without quotes first  Truncate a search by using an asterisk (*). This is commonly referred to as a “wildcard search” ◦ Example: mimic*  PubMed searches: mimic, mimics, mimicing etc..  “Nest” search terms in parentheses. The terms inside the set of parentheses will be processed as a unit and then incorporated into the overall strategy. ◦ Example: salmonella AND (hamburger OR eggs)  PubMed will retrieve records that contain the term salmonella, as well as one or both of the terms hamburger OR eggs. PubMed also refers to a list of commonly found words that are referred to as "stopwords." Stopwords are words that, if indexed, could potentially return every document in the database if the word was used in a search statement. Consequently, commonly found words are not indexed and PubMed will ignore them.
  • 6. Search Details The Search Details portal is an important tool to use when building a search. If you notice that the results PubMed has retrieved for a search are not relevant, you should check the Search Details section to see exactly how PubMed has translated your query. An example would be a broad search for nursing (profession). While you have just searched the word nursing, PubMed translated that as: "nursing"[Subheading] OR "nursing"[All Fields] OR "nursing"[MeSH Terms] OR "nursing"[All Fields] OR "breast feeding"[MeSH Terms] OR ("breast"[All Fields] AND "feeding"[All Fields]) OR "breast feeding"[All Fields] PubMed mapped “nursing” to “breast feeding” and returned 578358 results. While taking out those terms in red will return 550360. A 28,000 article difference!
  • 8.  Filters ◦ Article Types ◦ Publication Dates ◦ Subjects ◦ Journal categories ◦ Language  Custom Filters ◦ KUMC Research: university of kansas medical center [ad] ◦ BMJ, JAMA, & NEJM: "BMJ (Clinical research ed.)"[Jour] OR "JAMA : the journal of the American Medical Association"[Jour] OR "The New England journal of medicine"[Jour]
  • 9.  Related Citations 134 Related Citations! Related Citations View the full record for an article (Abstract or Summary view) and click on the Related Citations link to retrieve closely related citations, based on shared MeSH (Medical Subject Heading) terms. Reviews To narrow your search results to review articles, click on Review in the left-hand column of your search results, under Article types. Or, from the Advanced Search screen, select Publication Type from the pull-down Search Builder menu. Enter Review in the Search Builder box, then click Add to Search Box. Enter any additional search terms, then click Search.
  • 10. Mine citations from related articles to build your citation base!
  • 11.  1. Find five citations on using dog therapy with dementia patients. Write down their PMIDs  2. Find a list of articles written by someone from the University of Kansas Medical Center.  3. Find citations in English on randomized control trials that address the treatment of fibromyalgia using alternative medicine. How many did you get? How many are available Free Full Text?  4. (ADVANCED) You are watching a documentary on how Abraham Lincoln died. According to the documentary, Lincoln died because a doctor inserted the tip of his finger into the bullet hole in his skull during the examination. Is this true? Find an article to back up your answer.
  • 12. What is MeSH and when should you use it?
  • 13. Why should you use MeSH?  If you use two or more words in a keyword search there is no guarantee that they will be linked.  MeSH headings are an efficient way to find information on “concepts” or topics where authors use different language to discuss the same ideas.  For example: Accidental Falls
  • 14.  Do a Title word search; display results in Citation format; identify MeSH OR  Search the MeSH database ◦ Scope Note ◦ Subheadings ◦ Major Topics ◦ Explode
  • 15. Thorough search Quick search  MeSH ◦ Provides ‘true’ meaning of term where a word might be use in more than one context ◦ Includes synonyms ◦ Deals with homonyms ◦ Aids in term discovery ◦ Helps with spelling variations and/or errors  Keyword search ◦ Recent publications (in process) ◦ Records supplied by publishers ◦ New phenomenon
  • 16. Article: Use of intra-aortic balloon pump counterpulsation for refractory symptomatic vasospasm.
  • 17.  Find MeSH Headings for your topic ◦ Do an Advanced Search for your topic  Use MeSH and Keywords Extra: Using the Advanced Search builder, determine how many articles are available on the psychology of bullying (MeSH terms). How many did you find?
  • 18. Clinical Queries, PubMed Specific Topics, ClinicalTrials.gov & PubMed Health
  • 19. Three filters: • Clinical Study Categories • Systematic Reviews • Medical Genetics What do you get when you do a broad search on ‘neurosurgery’….
  • 21. Helps with filtering the evidence. The clinical studies side also lets you choose broad or narrow scope. If you choose narrow, the search will be more focused with fewer results, while broad will get you more results but they’ll be less focused.
  • 24. Abridged Index Medicus (AIM) Journals • 119 titles • Considered “core clinical journals” You can search just the core journal subset by searching the NLM Catalog using: jsubsetaim[All Fields]
  • 26.  PubMed Health provides information for consumers and clinicians on prevention and treatment of diseases and conditions.  PubMed Health specializes in reviews of clinical effectiveness research, with easy-to-read summaries for consumers as well as full technical reports  Clinical effectiveness research finds answers to the question “What works?” in medical and health care.  Can subscribe to RSS feeds
  • 27.  You are writing a literature review and need a list of seminal resources ◦ Answer: Topic Specific Queries
  • 28.  You wish to quickly find bedside information regarding therapy and prognosis for moyamoya disease. ◦ Answer: Clinical Queries
  • 29.  You are in a morning huddle and you need to quickly access clinical effectiveness research, which you must share with the patient. ◦ Answer: PubMed Health
  • 30.  You need to find information regarding current clinical trials. ◦ Answer: ClinicalTrails.gov
  • 31. Tips and Tricks for Searching and Using PubMed
  • 32. PMID will link you directly to the article. You can link to any PubMed article using the format: http://www.ncbi.nlm.nih.gov/pubmed/PMID# Example: http://www.ncbi.nlm.nih.gov/pubmed/19112134
  • 33. Some articles will have a PMID and a PMCID. The PMCID will link you to the ePub Reader.
  • 35. Use when you know exactly what you need .  The Single Citation Matcher, available from the PubMed Home page and the Advanced Search page, allows you to fill in the information you have about a citation (e.g., author, title, journal, volume, issue, page) by field.
  • 36. Useful when you are determining possible publishing avenues.
  • 37.  How to Search the Catalog ◦ Title ◦ Author ◦ Subject ◦ Phrase ◦ Boolean search ◦ Index
  • 38.  Send to  Favorites  Save Searches  Collections  My Bibliography Using MyNCBI Tutorials
  • 40.  http://www.nlm.nih.gov/mobile/  PubMed Mobile  UnBound MEDLINE  GoPubMed  PLoS One  PubChase  PubMedster  PubMed Trends  PubMed4Hh  PubSearch  PubGet  PubMedHH (PICO) http://pubmedhh.nlm.nih.gov/nlmd/pico/piconew.php
  • 41.  Ability to do basic searches in PubMed  Ability to view “Free Articles” only  Open PDF documents on your mobile device  Not device specific  Automatically directs you to the mobile site when on a mobile device
  • 42.  Log in only once and access any journal from your library’s subscription  Search all of PubMed and more  Save full-text PDFs to take with you and read offline  Add notes to any PDF while reading  Share papers with friends and colleagues
  • 43.  PICO search  askMEDLINE  Consensus Abstracts  Search MEDLINE/PubMed journal abstracts
  • 44.  Search trends for more than 230,700 phrases / terms based on MeSH  Trend graph 1: Growth [%], in relation to published articles  Trend graph 2: Number of related PubMed articles p.a.  Trend graph 3: Number of occurrences in articles p.a.  Trend graph 4: Associated articles in MeSH category  Option to aggregate multiple phrases in a single graph  View MeSH category tree (hierarchical structure) for a given phrase  Suggestions (similar / related phrases) for a given phrase  Browse available phrases for a given term  FAQ explaining the graphs in more detail PubMed Trends is a meta-database containing aggregated information from 7.14 million scientific papers published over the last 10 years. Get trends for a large set of phrases / terms based on MeSH 2012 (Medical Subject Headings), a hierarchically structured vocabulary for the purpose of indexing journal articles in life sciences.
  • 45.  A simple PubMed interface  Limited searching options  Real functionality comes from being able to access your account via a web browser (desktop or mobile)  If you work on a computer, but also want to access your research on a mobile device, consider this app
  • 46.  Retrieves lists of citations and, if available, free full text articles from PubMed Central  Quickly retrieves articles, sorted in descending order of similarity  Search results can be emailed, printed or copied to the clipboard  LinkOut’s connect to free full text articles if available
  • 47. PubMed “New and Noteworthy” topics are located at: http://www.ncbi.nlm.nih.gov/feed/rss. cgi?ChanKey=PubMedNews
  • 48.  The Abstract display for PubMed clinical trial citations may now include a "Cited by systematic reviews" portlet if the trial is cited in a PubMed Health systematic review.
  • 49.  PubMed Advanced Search Builder (embedded)  Use MeSH to Build a Better PubMed Query  PubMed Commons  Retrieving Citations from a Journal Issue  E-mail Alerts for Articles from Your Favorite Journals
  • 50.  To be eligible to use PubMed Commons, you must be an author of a publication in PubMed.  You will need an invitation to join PubMed Commons and an NCBI account. This is free of charge
  • 53. Let’s Play a Game! The PubMed® Game From PubMed for Experts Brought to you by NN/LM Pacific Southwest Region February 2013 rev 5. 5x4
  • 55.  http://endnote.com/training Citation Management Subject Guide: http://guides.library.kumc.edu/citation management Guide includes: • How-to Guides (Mac & PC) • KUMC specific EndNote links • Information on output styles • Information on filters • Additional EndNote support options* *You can also call Thomson and Reuters tech support at 800-336-4474 (at the prompts dial 4, 1, 1).
  • 57. Easy to use playlists: • Learn EndNote Podcast • Starting & Upgrading • Adding References • Groups, Preferences, and Miscellany • EndNote Full Class Recordings • EndNote for iPad • Creating Bibliographies https://www.youtube.com/user/End NoteTraining/playlists
  • 58. Contact us: • by email: dykesresearch@kumc.edu • by phone: 913-945-5990 • by IM: (Lync) • by walk-in: G023 Murphy Heather Collins Assistant Director, Research and Learning hcollins@kumc.edu Sara Robertson Research and Learning Specialist srobertson@kumc.edu Christina Magnifico Research and Learning Specialist cmagnifico@kumc.edu