The Database at the End of the Universe: Making the Most of PubMed

1. The Database at the End of the Universe: Making the Most of PubMed

2. The Database at the End of The Universe Introduction and Overview to the Course

3. Aim & Objectives Aim To introduce features and provide experience in using PubMed. Objectives Participants will be able to: • Understand differences between PubMed and Dialog/Ovid • Navigate PubMed and MeSH controlled vocabulary. • Carry out free-text/field searching • Build search strategy, use limits, locate single citations • Manipulate result sets (i.e. saving, printing, emailing) • Set up personalised accounts with PubMed. • Use special queries and clinical queries functions. • Describe other useful PubMed/MEDLINE related resources

4. PROGRAMME 10.15 Introduction and Overview to the Course 10.30                  Making the Most of PubMed MeSH 11:10                  Exercise: Finding MeSH on PubMed 11.30                  Guided ATM Tour 12.00                 Cites for Sore Eyes 12.15                 Exercise: Tracking Elusive Citations 12.30 LUNCH 13:00 Using Clinical and Special Queries on PubMed 13:45 Exercise: Answering Clinical Questions 14:15 Using Added Features from PubMed 14:45                 Exercise: Getting added value from PubMed 15:15                 Other PubMed/Medline related tools and projects 15:.55                 Evaluation 16:00 CLOSE

5. PubMed the Basics • National Library of Medicine’s own version of ‘MEDLINE’ with some additions • Started in 1997 partly as replacement for Internet GratefulMed • First free access to ‘Medline’ via Internet • Accessible anywhere in the world without password at http://www.pubmed.com

6. Did you spot the deliberate mistake?

7. Why do you use PubMed? • Single Citation Matcher? – for checking inaccurate references • For finding most up to date references? – more up to date that Dialog? • Because you do not need a password? – quick access • Because some of your users use it? – Why do they use it?

8. How do you react to users using PubMed? • Help them as best you can with your knowledge of searching?? • Throw your hands in the air and tell them to use DIALOG (as it is a more intuitive interface, other biomedical databases are available through it and full text of journals can be accessed)?? • Somewhere in between??

9. Why do people use PubMed? • Simple to use??- demonstrate that it is different rather than simpler than Dialog • Currency of the records??- probably only slightly more current (more in a moment) • You can use it anywhere in the world without a password??- cannot argue with that!

10. Is PubMed Medline? • PubMed is not synonymous with Medline • Medline records since 1966 make up the vast majority of PubMed’s records • All but 2% of PubMed’s records are included in Medline produced by those who ‘lease’ Medline such as Ovid and Dialog • Also includes other records whose status is slightly different

11. What are these different status records? • In process records without full MeSH etc • Records sent to publishers by NLM in advance of publication of issue • Out of scope articles – non biomedical articles from Medline journals, e.g. geology articles from Scientific American • OLDMEDLINE – partial records, e.g. they do not have full MeSH have been added covering 1950 to 1965

12. Currency of PubMed • Completely unscientific survey of journals comparing currency of PubMed and Dialog • Ten randomly selected journals – 6 monthly journals and 4 weekly journals • For ‘In process’ i.e. basic record- two journals were more up to date in PubMed than Dialog - Only by only one issue

13. Currency of MeSH • However, for full record i.e. with MeSH, publication type etc. - six journals more up to date in PubMed. - All four weeklies (including Lancet & JAMA) more up to date by three or four issues • Different comparison in OVID as has separate ‘in process’ database

14. The Database at the End of The Universe Making the Most of PubMed MeSH

15. The Perfect Search- Recap • Clearly focused question (e.g. using PICO). • Plenty of planning! • Exploiting database features…MeSH controlled vocabulary, exploding /focusing, subheadings, special queries etc. • Free-text searching when appropriate • Add it together using Boolean Logic (AND, OR, NOT)

16. MeSH in PubMed- the same as Dialog/Ovid?? • Like Dialog, PubMed has a thesaurus or controlled vocabulary called Medical Subject Headings (MeSH) • Same principles as Dialog/Ovid thesaurus with which you are familiar i.e. controlled list of terms to describe what a database record is about • As you already know....This allows for different spellings and synonyms - For e.g. Using the MeSH term for myocardial infarction will retrieve articles that talk about either myocardial infarction or heart attack

17. MeSH in PubMed-some differences • Theory behind the Thesaurus/MeSH is the same but accessed a little differently • MeSH is accessed by choosing the MeSH database on PubMed: either by the PubMed side bar or the dialog box at the top of the page • MeSH terms are automatically exploded (more on this later) • Perhaps less intuitive than Dialog/Ovid?

20. MeSH terms for cardiovascular disease

21. Searching MeSH • Searching MeSH database is equivalent to ticking Thesaurus Mapping checkbox in Dialog • To search for a term, enter a term in the query box • Click on go

22. List of MeSH terms…. • Like Dialog, searching thesaurus/MeSH produces a list of terms that match your search term • Scope notes for each term are provided under the MeSH term • If you use the PubMed database rather than the MeSH database, PubMed automatically selects MeSH considered most relevant – there is no choice! (more on this later) • PubMed also automatically runs a textword search for the term you have entered

24. Using a MeSH term: Send to Search box • This next step is a little different to Dialog! • In Dialog to use a MeSH term, you tick the box next to the term, then click on search • In PubMed, you use the “Send to Search Box” feature. • Tick the box next to the MeSH term you wish to use • Go to “Send to” dialogue box- click Send to Search box with AND/OR/NOT • Click on “Search PubMed” in new dialogue box that appears

27. Supplementary Concept Records in PubMed • The MeSH controlled vocabulary contains Supplementary Concept Records (SCRs) as well as main MeSH headings. • (You won’t use these terms to search but they are occasionally retrieved when you carry out a MeSH search so it is useful to know what they are). • SCRs are typically chemicals for e.g. calcium acetate. • They are NOT true MeSH headings but are mapped to an appropriate MeSH term.

29. Why have Supplementary Concept Records? • SCRs exist so that the names by which chemicals are indexed in the database are controlled i.e. following same principle of MeSH vocabulary. • For e.g. The substance name IGSF4 protein is used for TSLC1 protein and tumor suppressor in lung cancer 1 protein which are alternative names for this substance.

30. Using MeSH terms • Display terms in a hierarchy i.e. Thesaurus tree • Exploding • Majoring/Focusing • Subheadings • Combining terms and building a search strategy

31. Displaying terms in a hierarchy • Exactly the same as Dialog- click on a MeSH term and it’s position in the thesaurus tree is displayed • At the bottom of the page, the MeSH term is displayed in the relevant part of the thesaurus tree

33. Exploding • PubMed automatically explodes MeSH terms whilst Dialog gives users the option to explode a term • It is possible to override automatic explosion by entering a field tag • For example: • Angina [MeSH:NOEXP]

34. Or another way to prevent explosion of MeSH terms... • Tick the box “Do Not Explode this term (i.e., do not include MeSH terms found below this term in the MeSH tree). ” • This can be found once you’ve clicked on a MeSH term

36. Focusing/majoring a MeSH term in PubMed is very different from Dialog but the theory is the same Need to use the “Links” functions “Links” can be found in tiny (!) writing to the right of the MeSH term Click on “Links” and a menu comes up Choose PubMed Major Topic and this automatically carries out a MeSH (major) query on the term Alternatively, use the appropriate field tag : Angina [MeSH Major Topic] Focusing/Majoring

38. To focus a MeSH term, click on “Links” which can be found to the right of the screen

39. Or another way of focusing MeSH terms... • Tick the box “Restrict Search to Major Topic headings only” • This is found once you’ve clicked on a MeSH term

41. Subheadings • As we’ve seen, clicking on the MeSH term produces a list of applicable subheadings • As in Dialog, choose one or more subheadings by ticking appropriate box(es)

43. Automatic explosion of subheadings • Choosing a particular subheading automatically explodes that “family” of subheadings (e.g. Ticking subheading “therapy” searches for therapy, drug therapy, surgery etc) • In Dialog, each subheading is chosen individually • Automatic explosion is overidden by ticking the “Do Not Explode this term (i.e., do not include MeSH terms found below this term in the MeSH tree)” box

44. In summary... • Theory behind PubMed MeSH is exactly the same as Dialog MeSH • Same tools: Exploding, focusing, subheadings etc • Just need to know which button to press!

45. Mixing it all together • To combine MeSH terms and build a search strategy, there are two ways: • Using the SEND to SEARCH BOX feature • Using the SEARCH HISTORY (to be covered later)

46. Send to Search Box Feature • You may also construct a search strategy by using the Send to Search Box feature. • Whenever you carry out a search on the MeSH database, each MeSH term will have a little checkbox to the left. • Select a MeSH term by ticking the checkbox

47. Send to Search Box Feature cont... • The Send to Search box feature is found below Limits/Preview/Index/History/Clipboard/Details tabs • In the box which says “Send to”, use the drop down list to choose appropriate Boolean operator. • Click Go, and search box appears with beginnings of your search strategy. • Add as many MeSH terms as you like by searching the MeSH database- each time sending your chosen MeSH term to the Search Box • Then click on Search PubMed