PubMed: Medline with a Future

1. PubMed: Medline with a Future Laura Larsson Research Librarian Health Services revised November 16, 2014 larsson@u.washington.edu

2. Objectives • learn how to use this new Web-based software to perform online database searches • learn basic and advanced searching • specialized tips for finding citations

3. PubMed • New development in the area of online database searching

4. MEDLINE • bibliographic citations and author abstracts • All fields of medicine • 3,900 current biomedical journals published in the United States and 70 foreign countries • >9 million records dating from 1966+ • Medline is updated weekly and the records incorporated into PubMed

5. PREMEDLINE • Basic citation information and abstracts done first, then MeSH added and record checked later on • New records added to PREMEDLINE daily

6. PubMed's Homepage • http://www.ncbi.nlm.nih.gov/pubmed • The sidebar provides help, an overview, gives you NLM news and announcements, and gives you clinical queries with built in search "filters”

7. Graphic of Search Modes

8. Marvellous Features Include: • The Journal Browser • The Citation Matcher program • Related articles, or, “More Like This!!!!”

9. The Journal Browser • The Journal Browser enables the viewer to look up journal titles by the title, keyword, title abbreviation or ISSN number.

10. The Citation Matcher • if you only have • the author’s family name and the date, you can locate the citation • the author’s family name and the pages, you can locate the citation • the date and pages • other variations on this theme

11. Related Articles • once you’ve found one article, you can click on Related Articles and find ones which have similar indexing and content • very, very useful • more on this feature, below

12. Four different modes of searching • Basic Search • Advanced Search • Boolean Search • Clinical Queries

13. Basic Search Mode • Enter the terms in the query box • Terms are automatically ANDed together so that all terms or concepts appear in the records displayed • Click on Search after all terms are added to enable the search

14. Author Searches • enter author as: surname ii • if you enter larsson l, you will get back larsson la, larsson lb, and so on • use quotes to prevent truncation from occurring: “larsson l”

15. Author + Subject • health care administration “ross a”

16. Author + Article title • “ross a” moving into the twentieth

17. Journal Title Searches • enter the journal’s full name, e.g., journal of nutrition • enter the journal’s abbreviated name, e.g., j nutr • enter the ISSN, e.g., 0022-3166 • retrieval will be limited to the specified journal • links to full text if articles are available on the Web

18. Journal Title + Subject • j nutr obesity therapy

19. Subject 1 and Check Tag

20. Advanced Search Options • Click on Advanced Search from the Homepage sidebar • Field specific searches (use Search Field pull-down menu) • continue to Add Terms to Query box • terms are ANDed together • search statement is displayed at the top of the screen with the number of citations (if any)

21. Lists of MeSH Terms • select Mode | List Terms • select the term/s you want by highlighting and clicking on Select • scroll up and down the alphabetic display • modify the query as desired

22. Subheadings • are used with MeSH to arrive at a more specific aspect of a subject • examples include: /epidemiology, /trends, /complications, /diagnosis (and so on • look at the handout for subheadings • enter the term/subheading; e.g., asthma/drug therapy

23. Boolean Searches • construct your search using the Boolean operators: AND, OR, NOT • AND - (reduces the number of hits) includes only those citations which contain ALL the specified terms • OR - (expands the number of hits) citations which contain the terms

24. Boolean Searches, continued... • NOT - (limits) excludes those citations • RANGE - (limits) ranges the specified term (e.g., publication date) • Boolean operators must be entered in UPPERCASE

25. Truncating Terms • Called wild card searching • use an asterisk * • use when youwant to use singular or plural, or when you have a word which might have several endings

26. Other Boolean Information • Boolean search statements are processed left to right • sample search: ((neoplasms/etiology [majr] AND sexually transmitted diseases {majr]) NOT hiv infections [mh]) AND english [la] AND 1994:1993 [dp]

27. Graphic of Clinical Searches Screen

28. Clinical Searches • for clinicians • has built-in search “filters” • four study categories - therapy, diagnosis, etiology, prognosis are provided • increase sensitivity (most relevant articles with some less relevant ones) or specificity (includes most relevant articles but does omit a few)

29. Clinical Searches, continued… • select Clinical Queries from the PubMed Homepage sidebar • type in your subject and select the study Category and Emphasis | Search • do not use this search method if you wish to retrieve everything • this filter is designed to report research conducted with specific methodologies • retrieval is limited!!!!

30. Citation Matcher • match a list of citations to PubMed entries using journal, volume, issue, page number, and year • select Journal Browser from the PubMed Homepage sidebar • then select Citation Matcher on the Journal Browser sidebar • use to locate a single article by selecting Citation Matcher for Single Articles

31. Retrieving Citations • if you click or Search (or Enter) in Basic Mode, or if you select: Retrieve # of Documents (Advanced Mode) the search will be run • citations are displayed in batches of 20 • citations appear on a document summary page

32. Retrieving Citations • to print or save a larger number of citations, click on the Docs Per Page pull-down menu and select a number larger than your total retrieval • then select Search • this redoes the search and re-displays all the citations

33. To Display and Print or Save Citations • to view citations, or to print or save them, you must first display the citations • click on the Display button • click on the check box to the left of each item to select them • no selectons = display all citations

34. Display Formats • Abstract report is the default: Journal Citation, Title, Authors, Address or Affiliation, and Abstract • MEDLINE report: two-character tagged field • use for importing into bibliographic management software!!!!!

35. Formats, continued... • Citation report: Journal Citation, Title, Authors, Address or Affiliation, Abstract, MeSH terms, chemical substances, MEDLINE and PubMed unique identifiers • ASN.1 report: A structured format for the full records, in which each data element is explicitly represented

36. Printing • File | Print or Print icon • to save the items to a file, you must first go to the bottom of the page and select your computer (e.g. UNIX, Mac, PC, select the desired file format (text or HTML), then Save • use text for saving to citation managers such as ProCite or EndNote

37. Print Warning • the number of citations per page is set at 20 (the default) • if you want to print more than 20 citations at a time, click on the Docs Per Page pull-down menu and select some number greater than the number of citations you found and click Search. • you wil then be able to rerun your search and Save or Print from your browser

38. Saving • scroll to bottom and specify the kind of computer you are using: Mac, PC, UNIX • select format (text or HTML) from the pull-down menus • click on Save, select the subdirectory and give the file a name: filename.txt • save as Text if you want to save to citation management software

39. Printing into a Citation Manager • to change the display format, select the Display pull-down menu at the top of the document summary page • to import records into a citation manager, select Medline Report

40. Printing or Saving Citations • display all the items, click on the check boxes to the left of the citations and then click on the Display button

41. Specialized Tips for Finding Citations • verifying a citation when all you have is the volume and pages • use the Citation Matcher • type in what you have

43. MeSH Browser displays MeSH terms in a hierarchical structure lets users select terms for searching searcher can attach subheadings directly and limit terms to a Main Concept

44. Stop Words these words do not get processed when you search so don’t bother to type them in examples: a, about, many, meanwhile, myself, sufficiently, where, yet, you

45. Other Points of Interest some shortcomings with the Related Articles algorithm those articles "related" to an article without an abstract seem to generally also not have abstracts updates and changes to the PubMed program are noted at: http://www.ncbi.nlm.nih.gov/PubMed/news.html

46. Where to Get Help The NLM PubMed Project. PubMed Overview http://www.ncbi.nlm.nih.gov/PubMed/overview.html PubMed Help http://www.ncbi.nlm.nih.gov/PubMed/pubmedhelp.html

47. Interesting Search Rural AND obstetrics AND access AND outcomes what do you get when you type this search in? what does clicking on Related Articles get you?