PubMed Basics. Stephanie Friree Outreach and Technology Coordinator NN/LM New England Region (800)

Transcription

1 PubMed Basics 1

2 PubMed Basics 2

3 PubMed Basics 3

4 PubMed Basics Stephanie Friree Outreach and Technology Coordinator NN/LM New England Region (800)

5 Overview! Introductions! Conducting research! Good vs. bad data! PubMed, Medline & PMC differences! MeSH! Searching PubMed! Automatic Term Mapping! Subject Searching! Related Articles! Journal Searching (Single Citation Matcher)! My NCBI! Other resources: MedlinePlus, PhPartners.org, ClinicalTrials.gov, Pubmed Health, The Community Guide PubMed Basics 5

6 Video Clip * videos/original/medline mp4 PubMed Basics 6

7 Conducting Research and Evaluating Data * PICO * Evidence Acquisition locating the highest quality, relevant literature from the nursing and medical literature to begin to answer your question * Careful choice of sources filtered or unfiltered PubMed Basics 7

8 Medline, PubMed & PubMed Central * Medline (1966) has 19 million+ citations from 5,600 journals. It is a subset of PubMed. * PubMed (1996) has 23 million+ citations - includes Medline plus in- process citations, out- of- scope articles and ahead of the print edition, and citations to books in NCBI. * PubMed Central (PMC) (2000) is a free archive of 3 million full- text biomedical and life science journal articles PubMed Basics 8

9 What s in PubMed? includes: records for online books & chapters out of scope articles PubMed Basics 9

10 MEDLINE Basic Bibliographic Citation * Journal Source Information * Title of the journal article * Names of the Authors * First Author Affiliation * Abstract published with the article * Language in which the article was published * Publication Type (description of the type of article, e.g., Review, Letter, etc.) * Controlled Vocabulary search terms (Medical Subject Headings) PubMed Basics 10

11 PMC PubMed Basics 11

12 What are Medical Subject Headings? * Represent concepts found in the biomedical literature * Like keywords on other systems * Used to describe the subject of journal articles for MEDLINE * Used for cataloging books and audiovisuals * Used by searchers * Revised annually (tweaked) * Gives uniformity and consistency to the indexing of the biomedical literature PubMed Basics 12

13 MeSH * There are four types of MeSH: * Headings * Subheadings * Publication Types * Supplementary Concept Records * MeSH uses synonyms known as Entry terms * MeSH is organized in a hierarchy or tree * Indexers designate the major points of articles as MeSH Major Topics * Use the MeSH Database to find MeSH terms PubMed Basics 13

14 Medical Subject Headings (MeSH Vocabulary) MeSH Vocabulary Type Headings Examples Body Weight, Kidney, Dental Cavity Preparation, Self Medication, Brain Edema, Oseltamivir Subheadings adverse effects, genetics, contraindications, ultrastructure Publication Types Letter, Review, Practice Guideline, Twin Study Supplementary Concept Records PubMed Basics 14 cordycepin, albuterol- ipratopium, carbon monoxyde dehydrogenase, nocturnin

15 MeSH Headings (Examples) * Lung Neoplasms * Erythrocytes * Quality of Life * Diabetes Mellitus * Ascorbic Acid * Birth Order * Glycolysis * Patient Dropouts PubMed Basics 15

16 MeSH (Medical Subject Headings) terms are added by NLM indexers to reflect the content of the article. Indexers assign the most specific term possible. PubMed Basics 16

17 The MeSH Database (cont.) PubMed Basics 17

18 Subheadings are used with MeSH headings to be more specific. Mouth Mucosa/pathology Nail Diseases/immunology * = a major concept. PubMed Basics 18

19 PubMed Basics 19

20 How do I search PubMed? 1) Identify the key concepts for your search. 2) Enter the terms or key concepts in the search box. 3) Automatic suggestions will display as you type your search terms. 4) Click Search. PubMed Basics 20

21 PubMed Search Tips and Tricks * Designed to be easy to use * A few tricks make it even more powerful * Tutorials help you master the skills to become an efficient, expert searcher PubMed Basics 21

22 3 ways to speed up your search 1. Use clinical queries to limit to clinical research areas 2. Use filters to limit your search quickly 3. Once you have one good article, click Related Citations to see more like it. PubMed Basics 22

23 Clinical Queries Evidence- based search filters Systematic Reviews Etiology Diagnosis Therapy Prognosis Clinical Prediction Guides PubMed Basics 23

24 Example: Is cinnamon an effective complementary and alternative treatment for diabetes? The key concepts are? * cinnamon * diabetes PubMed Basics 24

25 PubMed Basics 25

26 A PubMed Subject Search * Be specific * Use key words for main concepts * Don t use punctuation (quotation marks) * Don t worry about capitalization * Leave out words like the, of, for * Author and journal key words work too! PubMed Basics 26

27 Search Results PubMed Basics 27

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29 Searching by author! Enter the author s name in the format of last name followed by initials. Omit punctuation. Examples smith ja jones k! Full author names may be searched for citations published from 2002 forward if the full author name is available in the article. Example Joshua Lederberg; Garcia Algar, Oscar PubMed Basics 29

30 Stop words * What are stop words? * Example can, just, mainly, perhaps, etc. * If the author name includes only stopwords, use the author search field tag [au] to search in combination with other terms * e.g. just by[au] seizure PubMed Basics 30

31 How can I limit my search? PubMed Basics 31

32 PubMed Record Status Tags

33 Automatic Term Mapping (ATM) PubMed uses Automatic Term Mapping which recognizes thousands of concepts and maps to an appropriate term. ATM checks these tables: * Subjects (MeSH Medical Subject Headings ) * Journal Titles * Authors PubMed Basics 33

34 See the Difference: cancer drugs + breast feeding = 1 cancer drugs breast feeding = 67 (processed using ATM) PubMed Basics 34

35 Mesh vs searching with quotes * cancer drugs + breast feeding performs search = "cancer drugs"[all Fields] AND "breast feeding"[all Fields] * ("neoplasms"[mesh Terms] OR "neoplasms"[all Fields] OR "cancer"[all Fields]) AND ("pharmaceutical preparations"[mesh Terms] OR ("pharmaceutical"[all Fields] AND "preparations"[all Fields]) OR "pharmaceutical preparations"[all Fields] OR "drugs"[all Fields]) AND ("breast feeding"[mesh Terms] OR ("breast"[all Fields] AND "feeding"[all Fields]) OR "breast feeding"[all Fields]) PubMed Basics 35

36 Boolean operators * PubMed applies an AND operator between concepts * OR is also applied in phrases * E.g vitamin c common cold is translated as vitamin c AND common cold * Enter Boolean operators in uppercase to combine or exclude terms PubMed Basics 36

37 Subject Subset Filter * Subjects Subsets are on Filters sidebar but also searchable with tags * Strategies can be found at (use PubMed Help) * aids [sb] developed from AIDSLINE work * cancer [sb] developed with the National Cancer Institute * All strategies reviewed at least annually PubMed Basics 37

38 Journal subset search * Jsubsetletterofsubset AND search term * Ex. Jsubsetn AND asthma * Nursing journal subset tag = n PubMed Basics 38

39 PubMed Basics 39

40 Search example: Nursing shifts * How would you go about researching the following question in PubMed? * Can you find me data/research/best practices that support or negate 8, 10, or 12 hour shifts for nursing? PubMed Basics 40

41 Single Citation Matcher PubMed Basics 41

42 Abstract & Related Citations PubMed Basics 42

43 Links Between Databases PubMed Basics 43

44 How do I find the full text? * On the Abstract display: * Publisher link icons * Library link icons * On the Summary display: * Free Article label * Free PMC Article label PubMed Basics 44

45 What s New? PubMed Basics 45

46 Structured Evidence Queries at PhPartners.org 46

47 Structured Evidence Queries at PhPartners.org 47

48 PubMed Using My NCBI My NCBI allows you to:! Save records (Collections, My Bibliography)! Save searches (Saved Searches)! Customize your results (Filters, My NCBI Preferences, select highlighting, set display tabs) PubMed Basics 48

49 Register for an account! Register for a My NCBI account if you don t already have one. PubMed Basics 49

50 My NCBI homepage PubMed Basics 50

51 Nursing Journal filter PubMed Basics 51

52 Use of My NCBI /highlighting when searching with MeSH PubMed Basics 52

53 Highlighting PubMed Basics 53

54 Online Help and Training PubMed Basics 54

55 PubMed Health * What Works? Clinical Effectiveness PubMed Basics 55

56 MedlinePlus: Trusted Health Information For You 56

57 ClinicalTrials.gov

58 ClinicalTrials.gov * 4 ways to search: Basic, Advanced, See Studies by Topic, See Studies on a Map * Search Results page shows: study record title, condition and interventions used, study status * Display options * Modify Search * Save Search * Search Details PubMed Basics 58

59 The Guide to Community Preventive Services: 59

60 To summarize:! The MEDLINE database of biomedical journal citations is the heart of PubMed.! MEDLINE includes only good quality journals deemed important and relevant by a committee of experts.! MEDLINE is available for free using PubMed, but it is also available from other database searching systems (ie., OVID, Medscape, EBSCO).! MEDLINE is enhanced with Medical Subject Headings (MeSH), which improve access to the literature and can be used for searching. PubMed Basics 60

61 ! Search PubMed by entering the main concepts of your search without punctuation. Your terms will automatically map to MeSH.! Enter components of references (author, title, journal) to find a known article or set of articles.! The full text article may be linked from the PubMed record using an icon in the upper right of the abstract display.! Explore related citations and related information from the right column of your search results and the abstract display.! Customize your PubMed search experience using My NCBI PubMed Basics 61

62 Conclusions You will now be able to:! Distinguish between a MEDLINE and non- MEDLINE record in PubMed.! Understand MeSH headings and their purpose in PubMed! Conduct a basic PubMed search! Locate Articles from Nursing Journals! Manipulate the results display! Move from your PubMed results to other resources! Identify where to customize your use of PubMed (My NCBI) PubMed Basics 62

63 Questions Stephanie Friree Outreach Coordinator NN/LM New England Region (800)