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Literature Search - PubMed

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This presentation shows you how to search PubMed.

This presentation shows you how to search PubMed.


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  • 1. Literature Search PubMed Somkiat Asawaphureekorn M.D., M.Sc. (Clinical Epidemiology)Wednesday, August 24, 2011
  • 2. Department of Ophthalmology, Faculty of Medicine, Srinagarind Hospital Khon Kaen University, Khon Kaen, Thailand.Wednesday, August 24, 2011
  • 3. PubMedWednesday, August 24, 2011
  • 4. What is PubMed? • A web-basedof Entrez system developed by NCBI (a part retrieval retrieval system) • Free version of MEDLINE on the web • PubMed vs Medline NIH National Institutes of Health NLM National Library of Medicine National Center for NCBI Biotechnology Information 4Wednesday, August 24, 2011
  • 5. PubMed Database • A database of the life sciences literaturedrawn primarily from bibliographic information • PubMed contains links to  Full-text articles at participating publishers Web sites  Other third party sites such as libraries and sequencing centers • All citationsPublication Types assigned MeSH Terms and in MEDLINE are from NLMs controlled vocabulary. 5Wednesday, August 24, 2011
  • 6. What Does MEDLINE Cover? • Not only medicine  medicine  nursing  dentistry  veterinary medicine  health care system  preclinical sciences e.g., molecular biology 6Wednesday, August 24, 2011
  • 7. How Big is MEDLINE? 7Wednesday, August 24, 2011
  • 8. How Big is MEDLINE? • > 5,000 biomedical journals 7Wednesday, August 24, 2011
  • 9. How Big is MEDLINE? • > 5,000 biomedical journals • > 16 million citations back to 1865 7Wednesday, August 24, 2011
  • 10. How Big is MEDLINE? • > 5,000 biomedical journals • > 16 million citations back to 1865 • Published in the U.S. and 70 other countries. 7Wednesday, August 24, 2011
  • 11. How Big is MEDLINE? • > 5,000 biomedical journals • > 16 million citations back to 1865 • Published in the U.S. and 70 other countries. • Coverage is worldwide,sources orrecords are from English-language but most have English abstracts 7Wednesday, August 24, 2011
  • 12. How Big is MEDLINE? • > 5,000 biomedical journals • > 16 million citations back to 1865 • Published in the U.S. and 70 other countries. • Coverage is worldwide,sources orrecords are from English-language but most have English abstracts • MEDLINEprovides links to full-text) (PubMed contains citations, not full-text articles 7Wednesday, August 24, 2011
  • 13. PubMed BasicsWednesday, August 24, 2011
  • 14. Two Types of Searching • Keywords search  Results match the exact terms  May miss alternative terms  Often result in more false hits • Subject search  Results match the concept of that term  MeSH (PubMed), EmTree (Scopus)  Improve precision and save time  Good for well-defined topic 9Wednesday, August 24, 2011
  • 15. Cons of Subject Search • Not work for new or not clearly defined concept • Newly added articles may not have MeSH • Errors or bad judgement of indexers 10Wednesday, August 24, 2011
  • 16. 7 Steps of Searching 1.Define your topic 2.Break the topic into individual concepts 3.Define words or phrases to describe the concept 4.Search each concept as separate set 5.Combining the search sets with AND, OR, NOT 6.Display and evaluate the results 7.Refine your search: limit or broaden 11Wednesday, August 24, 2011
  • 17. PubMed Tools • My NCBI  Save search strategy, search result, email alert • Clinical queries • Advance Search  Limit, Preview, History, Index • Clipboard • MeSH database • Journal database • Single citation matcher 12Wednesday, August 24, 2011
  • 18. Anatomy of a Medline Record 13Wednesday, August 24, 2011
  • 19. Anatomy of a Medline Record 13Wednesday, August 24, 2011
  • 20. Anatomy of a Medline Record 13Wednesday, August 24, 2011
  • 21. Anatomy of a Medline Record 13Wednesday, August 24, 2011
  • 22. Anatomy of a Medline Record field tag 13Wednesday, August 24, 2011
  • 23. Anatomy of a Medline Record field tag content within the field 13Wednesday, August 24, 2011
  • 24. Anatomy of a Medline Record 14Wednesday, August 24, 2011
  • 25. Anatomy of a Medline Record MeSH terms 14Wednesday, August 24, 2011
  • 26. Components of Searching • 3 components for searching  Search terms  Search fields  Search syntax • Example of search  Search for articles about influenza published in the New England Journal of Medicine  influenza [mh] AND n engl j med [ta] term field Boolean operator 15Wednesday, August 24, 2011
  • 27. Search Rules and Syntax 16Wednesday, August 24, 2011
  • 28. Search Rules and Syntax • Boolean operators  AND, OR, NOT (must be in UPPER CASE) 16Wednesday, August 24, 2011
  • 29. Search Rules and Syntax • Boolean operators  AND, OR, NOT (must be in UPPER CASE) • Enclosing individual concepts in parentheses  common cold AND (vitamin c OR zinc). 16Wednesday, August 24, 2011
  • 30. Search Rules and Syntax • Boolean operators  AND, OR, NOT (must be in UPPER CASE) • Enclosing individual concepts in parentheses  common cold AND (vitamin c OR zinc). • Truncation = *  bacter* = bacteria, bacterium, bacteriophage, etc.  Not map to the MeSH term 16Wednesday, August 24, 2011
  • 31. Search Rules and Syntax • Boolean operators  AND, OR, NOT (must be in UPPER CASE) • Enclosing individual concepts in parentheses  common cold AND (vitamin c OR zinc). • Truncation = *  bacter* = bacteria, bacterium, bacteriophage, etc.  Not map to the MeSH term • Phrase search: “peptic ulcer”  Not map to the MeSH term 16Wednesday, August 24, 2011
  • 32. Search Rules and Syntax • Boolean operators  AND, OR, NOT (must be in UPPER CASE) • Enclosing individual concepts in parentheses  common cold AND (vitamin c OR zinc). • Truncation = *  bacter* = bacteria, bacterium, bacteriophage, etc.  Not map to the MeSH term • Phrase search: “peptic ulcer”  Not map to the MeSH term • All fields: [all] 16Wednesday, August 24, 2011
  • 33. Boolean operator • cataract = A + C • glaucoma = B + C • cataract AND glaucoma = C • cataract OR glaucoma = A + B + C • cataract NOT glaucoma = A • glaucoma NOT cataract = B cataract AND glaucoma cataract glaucoma A C B 17Wednesday, August 24, 2011
  • 34. Search Strategy Design When starting your Sensitivity search do not limit your options use MeSH [mh] & Free Text [tw] As your search progresses you can be more specific by adding more terms Specificity 18Wednesday, August 24, 2011
  • 35. PubMed Basic Skills • Search terms  Medical subject heading (MeSH) • Search fields • Search syntax • PubMed search mechanism  Automatic term mapping 19Wednesday, August 24, 2011
  • 36. Automatic Term Mapping • MeSH Translation Table  MeSH, entry term, MeSH Subheadings  Publication Types  Pharmacologic Action terms  Terms from the Unified Medical Language System  Supplementary Concept (Substance) Names • Journals Translation Table  Full journal title, the MEDLINE abbreviation, and the ISSN number. • Full Author Translation Table • Author Index 20Wednesday, August 24, 2011
  • 37. If no match is found? • PubMed breaks apartterm phrase and repeats the above automatic the mapping process until a match is found. • If there is no match,together and searched inbe combined (ANDed) the individual terms will All Fields. 21Wednesday, August 24, 2011
  • 38. Phrase Searches • Automatic term by the MeSH Translation Table are recognized mapping applied to phrases that • To force phrase searches  Entering the phrase in quotes, e.g., "single cell"  Using a search tag, e.g., single cell[ti] 22Wednesday, August 24, 2011
  • 39. ATM Is Suppressed When • Search with truncation  bacteri* • Search with quote  “deep vein thrombosis” • Search with field tags  venous thrombosis [mh] 23Wednesday, August 24, 2011
  • 40. MeSH (Medical Subject Headings) • NLMs controlled vocabulary used for indexing articles in PubMed • Provide ause differentway to retrieve information that may consistent terminology for the same concepts • Impose uniformity and consistency to the indexing of biomedical literature • MeSH termsmanner called in a hierarchical categorized are arranged MeSH Tree Structures and are updated annually 24Wednesday, August 24, 2011
  • 41. Example of MeSH 25Wednesday, August 24, 2011
  • 42. Example of MeSH 26Wednesday, August 24, 2011
  • 43. Example of MeSH 27Wednesday, August 24, 2011
  • 44. Example of MeSH 28Wednesday, August 24, 2011
  • 45. Turn Off Automatic Inclusion • To turn off the automatic inclusion of the more specific terms, use the syntax [field:noexp]  hypertension [mh:noexp]  hypertension [majr:noexp]  hypertension/therapy [mh:noexp]. • The latter example turns off the more specific terms in both parts, searching for only the one Subheading therapy attached directly to only the one MeSH term hypertension. 29Wednesday, August 24, 2011
  • 46. Search Field Tags As of Aug 2011 30Wednesday, August 24, 2011
  • 47. Field: Comment/Correction Type • Comment in: hascommentin • Comment on: hascommenton • Erratum in: haserratumin • Erratum for: haserratumfor • Republished in: hasrepublishedin • Retraction in: hasretractionin • Retraction of: hasretractionof 31Wednesday, August 24, 2011
  • 48. Field: Publication Date [DP] • Format  yyyy/mm/dd [dp]  yyyy/mm/dd : yyyy/mm/dd [dp]  “last X days”[dp]  “last X months”[dp]  “last X year”[dp]  Search for electronic dates only use [epdat]  Search for print dates only use [ppdat] • The electronic date will not be searchable if it is later than the print date, except when range searching. • 2006 [dp] vs 2006:2006 [dp] 32Wednesday, August 24, 2011
  • 49. Searching for date range • Example [dp] 1993:1995 1997/01:1997/06 [epdat] 2002:2009[ppdat] • Comprehensive searches for a full year should be entered as 2000:2000[dp] rather than 2000 [dp] to retrieve citations with a different print and electronic year of publication  The electronic date will not be searchable if it is later than the print date, except when range searching. 33Wednesday, August 24, 2011
  • 50. Field: Journal Name British Medical Journal The New England Journal of Medicine จ.พ.ส.ท. 34Wednesday, August 24, 2011
  • 51. Field: Journal Name The Cochrane Library Clinical Evidence ACP Journal Club 35Wednesday, August 24, 2011
  • 52. Field: Publication Types [pt] • clinical trial, phase I • randomized controlled trial • editorial • journal article • lecture • meta-analysis • multicenter study • practice guideline • review literature • retracted publication(article later retracted by author) • retraction of publication (author’s statement of retraction) 36Wednesday, August 24, 2011
  • 53. Field: Subsets [SB] • 4 types of subsets in PubMed  Subject  Citation status  Journal/Citation  PubMed Central • 2 ways to access subsets  PubMeds “Limits” screen pull-down menu  Use the [SB] search tag 37Wednesday, August 24, 2011
  • 54. Subject Subsets • Citations to articles on specialized topics  Systematic Reviews : systematic [sb]  Veterinary science : Veterinary [sb]  AIDS : aids [sb]  Bioethics : bioethics [sb]  Complementary Medicine : cam [sb]  History of Medicine : history [sb]  Space Life Sciences : science [sb]  Toxicology : tox [sb] • Example of search syntax  asthma AND systematic [sb] 38Wednesday, August 24, 2011
  • 55. Searching Systematic Review • Use the “Clinical Queries” screen • Use the search field tags  epilepsy AND (systematic [sb] OR meta-analysis [pt]) • Search from “Limit” screen pull-down menu  If search for both systematic reviews and meta- analysis, it will search for: systematic [sb] AND meta-analysis [pt] 39Wednesday, August 24, 2011
  • 56. Citation Status Subsets • Citations in a particular stage of processing • Citation Status tags displays next to the PMID  PubMed - as supplied by publisher : publisher [sb]  PubMed - in process : in process [sb]  PubMed - indexed for MEDLINE : medline [sb]  PubMed - pubmednotmedline [sb]  PubMed - OLDMEDLINE for Pre1966 : oldmedline [sb]  All – total number of PubMed citations : all [sb] • Example of search syntax  n engl j med AND in process [sb] 40Wednesday, August 24, 2011
  • 57. Journal/Citation Subsets (1) • Citations to articles from specialized journals or to articles on specialized topics in other journals (11)  AIM - Abridged Index Medicus • a list created 20 years ago of 120 core clinical English language journals  D - dentistry journals  E - citations from bioethics journals or selected bioethics citations from other journals  H - health administration journals, non-Index Medicus  IM - Index Medicus journals 41Wednesday, August 24, 2011
  • 58. Journal/Citation Subsets (2)  K - consumer health journals, non-Index Medicus  N - nursing journals  Q - history of medicine journals and selected citations from other  S - citations from space life sciences journals  T - health technology assessment journals, non- Index Medicus  X - AIDS/HIV journals (selected citations from other journals 1980 - 2000) • Search syntax : use ”jsubset?”  diarrhea AND jsubsetx 42Wednesday, August 24, 2011
  • 59. PubMed Central Subset • Citations with links to full-text in PubMed Central (PMC) • 2 ways to search  PubMeds “Subset” menus in “Limits” screen  Use the pubmed pmc [sb] search tag • protein p53 AND pubmed pmc [sb] • protein p53 AND pubmed pmc local [sb] 43Wednesday, August 24, 2011
  • 60. Citations with Abstracts • Search only for citations that have abstracts • 2 ways to search  Use the “Limit” screen  Use the value “hasabstract” • sars AND hasabstract 44Wednesday, August 24, 2011
  • 61. Citations with Full-Text • Search only for citations that have full-text  free full text [sb] - Citations that include a link to a free full-text article  full text [sb] - Citations that include a link to a full-text article 45Wednesday, August 24, 2011
  • 62. Ahead of Print Citations • Articles thatissues release web in advance of the journal appear on the • Theseahead of print] immediately following the [epub citations display the tag date of publication • Search syntax : use “pubstatusaheadofprint”  gene AND pubstatusaheadofprint 46Wednesday, August 24, 2011
  • 63. Article Identifier [AID] • Article identifiers submitted by journal publishers  doi (digital object identifier) 47Wednesday, August 24, 2011
  • 64. Location Identifier [LID] • The DOI orto locate an onlineserves the role of pagination publisher ID that article 48Wednesday, August 24, 2011
  • 65. Investigator Name [IR], [FIR] • Names of principal investigator(s) or collaborators who contributed to the research  Search names following the Author field format 49Wednesday, August 24, 2011
  • 66. Secondary Source [SI] • Identifies secondary source databanks and accession numbers  ClinicalTrials.gov, ISRCTN  GenBank, GEO, PubChem • The field is composed of the source followed by a slash followed by an accession number and can be searched with one or both components  genbank [si], AF001892 [si]  genbank/AF001892 [si] 50Wednesday, August 24, 2011
  • 67. Age Group Limits (1) • Newborn (0-1 m) -> “infant, newborn” [mh] • Infant (1-23 m) -> “infant” [mh:noexp] • All infant (0-23 m) -> “infant” [mh] • Preschool child (2-5 y) -> “child, preschool” [mh] • Child (6-12 y) -> “child” [mh:noexp] • Adolescent (13-18 y) -> “adolescent” [mh] • All child (0-18 y) -> “infant” [mh] OR “child” [mh] OR “adolescent” [mh] 51Wednesday, August 24, 2011
  • 68. Age Group Limits (2) • Adult (19-44 y) -> “adult” [mh:noexp] • Middle aged (45-64 y) -> "middle aged” [mh] • Aged (65+ y) -> “aged” [mh] • 80 and over (80+ y) -> "aged, 80 and over” [mh] • All adult (19+ y) -> “adult” [mh] • Middle aged + Aged (45+ y) -> “middle “aged” [mh] OR aged”[mh] 52Wednesday, August 24, 2011
  • 69. Number of Authors in PubMed • 1966 - 1984  No limit for number of authors • 1984 - 1995  Limit authors to 10, with "et al" as the eleventh • 1996 - 1999  Limit authors to 25  If > 25 authors, the first 24 were listed, the last author was used as the 25th, and the twenty-sixth and beyond became "et al." • 2000 - Present  No limit for number of authors 53Wednesday, August 24, 2011
  • 70. Author Search 1 54Wednesday, August 24, 2011
  • 71. Author Search 1 • Author Names  last name plus initials (no punctuation) • smith ja [au]  Use double quotes around the authors name • "smith j" [au] 54Wednesday, August 24, 2011
  • 72. Author Search 1 • Author Names  last name plus initials (no punctuation) • smith ja [au]  Use double quotes around the authors name • "smith j" [au] • Search for full name (start 2002)  somkiat asawaphureekorn [fau] 54Wednesday, August 24, 2011
  • 73. Author Search 2 55Wednesday, August 24, 2011
  • 74. Author Search 2 • Searh only as first author  smith dj [1au] 55Wednesday, August 24, 2011
  • 75. Author Search 2 • Searh only as first author  smith dj [1au] • Searh only as last author  smith dj [lastau] 55Wednesday, August 24, 2011
  • 76. Author Search 2 • Searh only as first author  smith dj [1au] • Searh only as last author  smith dj [lastau] • Search for the only author  (smith dj [1au] AND smith dj [lastau]) 55Wednesday, August 24, 2011
  • 77. Knowledge & WisdomWednesday, August 24, 2011
  • 78. Knowledge & Wisdom Knowledge … is proud that he has learnt so much,Wednesday, August 24, 2011
  • 79. Knowledge & Wisdom Knowledge … is proud that he has learnt so much, Wisdom … is humble that he knows no more.Wednesday, August 24, 2011
  • 80. Knowledge & Wisdom Knowledge … is proud that he has learnt so much, Wisdom … is humble that he knows no more.Wednesday, August 24, 2011
  • 81. Knowledge & Wisdom Knowledge … is proud that he has learnt so much, Wisdom … is humble that he knows no more. The Task (1785) byWednesday, August 24, 2011
  • 82. Knowledge & Wisdom Knowledge … is proud that he has learnt so much, Wisdom … is humble that he knows no more. The Task (1785) by William Cowper (1731 - 1800)Wednesday, August 24, 2011
  • 83. Wednesday, August 24, 2011
  • 84. THANK YOUWednesday, August 24, 2011