1. The Literature Search: PubMed and Zotero
Deb Werner
Director of Library Research in Medical Education

2. About me BA, Biology MLIS (Master of Library and Information Science)
Worked in libraries in:
San Francisco
UC Berkeley
University of Minnesota
UChicago (since 2006)

3. Interesting fact
I round with Internal Medicine once a week. This photo is at Comer with Peds and Riley Brian, who some of you may know—we all worked on a project together which is why the photo was taken there.

4. Learning Objectives
Develop a search strategy using keywords and controlled vocabulary in order to find relevant articles.
Retrieve the full text of articles in order to read and evaluate them.
Organize references using Zotero in order to easily find and cite articles.
In today’s workshop, I’ll provide an overview of PubMed and Zotero. Here are the learning objectives for this session.
Please feel free to ask questions at any time, however, if you are having technical issues that are unique to you, we will have to discuss those separately at the end. If it is an issue that many people are experiencing, we’ll try to address it as a group, if possible.

5. Outline PubMed Zotero Accessing PubMed Developing a search strategy
Retrieving the full text of articles
Zotero
Overview
Setting up online sync
Saving citations
Creating a bibliography
Here is the outline:
We’ll start with PubMed—how to access it; how to most effectively search it, and how to get the full text of articles.
We’ll then cover Zotero
Overview of Zotero
Set Up Online Sync
Save Citations in Zotero
Create a Bibliography

6. John Crerar Library
This is the Crerar Library. It is the combined biomedical and physical sciences library on campus. There is not a separate medical library—this is it!

7. Crerar Library Spaces Two Reservable Group Studies Reading Room
Crerar Café
Credit: Photos by Jean Lachat

8. Your literature review
Have you begun your lit review?
For those who have begun, when did you start? How far into it are you? Are you using something other than Zotero to manage the process?

9. The literature search in PubMed

10. PubMed Biomedical database with 29 million citations from:
MEDLINE
PubMed Central (PMC)
life science journals
online books
PubMed is the public interface for searching MEDLINE
In addition to MEDLINE, PubMed includes:
Out-of-scope citations (e.g., articles on astrophysics) from some MEDLINE journals in the general sciences and chemistry, for which the life sciences articles are indexed for MEDLINE.
Additional life science journals that submit full text to PubMedCentral and receive a qualitative review by NLM.
Citations that precede the date that a journal was selected for MEDLINE indexing.
From

11. What is MEDLINE?
Premier biomedical database containing citations to articles in biomedicine Created and maintained by the National Library of Medicine (NLM) and National Institutes of Health Citations from more than 5,600 worldwide biomedical journals published in about 40 languages Coverage back to 1940s

12. Crerar Library website
Open PubMed now.

13. Finding full text – click
Find It links a citation to the full text, if the Library subscribes to it.
When in a database, PubMed is the example here, the Library’s Find It button appears on an abstract or citation. Click Find It to link to try to get the full text of the article. The presence of the Find It button does not guarantee that we have online access, it just links you to the Library’s ejournal subscriptions, and if we do subscribe, you’ll get the full text.
Make sure you open PubMed through the library’s website, remember it is on the Science Databases Quicklinks, or through links on the hospital's intranet, in order for the Find It button to appear.
Also, if you cannot open an article that it appears we should have access to, please let us know! Often, the Library is not aware of problems accessing a journal until it is reported by a patron.

14. Exercise: PubMed Search
Find an article that answers: What current tools are available to help prescribe opioids?

15. Discussion How many results did you retrieve?
Review the Search Details
Were any MeSH terms searched?
Do you need to revise your search?
Demo search.
--current tools available prescribe opioids (1 result)
--current tools prescribe opioids (4 results)
--current tools prescribing opioids (11 results)
--tools prescribing opioids (70 results)
What are you noticing is happening with these different searches?
--Removing non-essential words retrieves more results
--Changing word forms (e.g. prescribe to prescribing) changes the number of results

16. What is MeSH?
Medical Subject Headings A controlled vocabulary (thesaurus) Gives uniformity and consistency to describing and searching the biomedical literature Developed and maintained by NLM MeSH terms found in MeSH Database:
There is one preferred term, so you don’t have to search all the synonyms.

17. MeSH
Pros
Searches synonyms, multiple word endings, variant spellings
Disambiguation of terms
Targeted results
Cons
Newest citations do not have MeSH terms and so not searched
Some concepts (e.g. newer treatments) do not have MeSH terms
Humans apply subject headings. In doing so, they
consider negating words like but, not, except so your results won’t include citations in which your search terms are specifically excluded
weigh the relative importance of the search term to the whole article

18. MeSH examples Cold MeSH terms: Residents MeSH terms: Air temperature
Condition caused by a virus
MeSH terms:
“Cold Temperature”
“Common Cold”
Residents
People in medical training
People in long-term care facilities
MeSH terms:
“Internship and Residency”
“Nursing Homes”

19. Accessing MeSH database
Use the droplist next to the search box in PubMed to access the MeSH database

20. Exercise: MeSH search
Find a MeSH term that will retrieve articles from the last five years on the detrimental effects of chocolate.
What MeSH term(s) represent the concept of chocolate?
What year was the term introduced?
How are the ‘detrimental aspects’ represented with MeSH?
1. Chocolate; Cacao

21. Answer

22. Keywords (aka text words)
Pros
Retrieves newest citations
Uses current terminology
Necessary when MeSH term does not exist
Cons
Does not search synonyms and spelling variations
Ignores context
Homonyms (cold, residents, etc.)
Negating expressions (but, except, never…)

23. Exercise
Find a newer RCT that answers: Is nicotine replacement therapy an effective smoking cessation treatment for pregnant women?

24. Identify individual concepts & synonyms
Is nicotine replacement therapy an effective smoking cessation treatment in pregnant women?
What are the individual concepts?
Nicotine replacement therapy / smoking cessation / pregnant women
What are some synonyms for each concept?

25. Search concepts separately, then combine
nicotine replacement therapy OR nicotine patch OR nicotine gum OR Nicorette OR “nicotine chewing gum”[MeSH]
smoking cessation OR quitting smoking OR quit smoking OR “smoking cessation”[MeSH]
pregnant OR pregnancy OR gravidity OR “pregnancy”[MeSH]
#1 AND #2 AND #3
Retrieve 304

26. Limit your results with Filters
Use the Article Types filter to get RCTs
Select Customize to access the RCT filter
Use the Publication Dates filter for recent publications
Some Filters are Mesh!
Age
Species
Sex
Article Type*
Limit to RCTs, retrieve 33
Limit to last 5 years, retrieve 15
Some Filters are MeSH searches and therefore eliminate the newest articles not yet indexed. Articles Types can be submitted by publishers, when this happens, the filter can retrieve non-indexed articles.

27. Review your results
Do your results appear to answer the question? How many results did you retrieve? Is that too many or too few?

28. Improving your search Narrow results Broaden results
Use more specific search terms
Apply additional filters: Language, Publication Date, Article Type
Broaden results
Use additional synonyms
Broaden the search terms
Remove filters
Find an article right on target?
Look at its MeSH terms to identify other potential search terms
Searching is an iterative process; revise your search until you are satisfied with the results or satisfied you’ve done all you can

29. General search tips

30. Search tips for any database
Use multiple synonyms for concepts Glean additional search terms from article titles and abstracts Use controlled vocabulary (e.g. MeSH) Use citation chaining to locate more articles Take advantage of database functionality

31. Multiple synonyms Contact Dermatitis Contact Sensitivities
Contact Sensitivity
Contact Eczema
Contact Hypersensitivities
Contact Hypersensitivity

32. Use titles & abstracts for search terms

33. Controlled vocabulary (e.g., MeSH)

34. Citation chaining
Search citations backward and forward in time Search an article’s references to find older articles Use Google Scholar to find newer articles a relevant article Example:
Aka pearl growing, snowballing, reference chaining

35. Search an article’s references

36. Use Google Scholar to find newer articles

37. Search citing articles using Google Scholar

38. Database functionality: PubMed
Create a personal account:
Highlight search terms
Save searches
Have PubMed run search and results to you
Use Filters
Article types
Publication dates
Languages
Use “Similar articles” feature

39. Set up a personal account

40. Use Filters

41. Use Similar articles

42. Zotero
Zotero is a reference manager that facilitates collecting and organizing references.
Zotero is a reference manager, or citation management tool, that helps you collect and organize references from databases, websites, catalogs, etc.

43. Which reference manager do you use?
EndNote EndNote Online
Mendeley Papers
RefWorks Other

44. Zotero
This is what Zotero looks like when it is populated with references.

45. Zotero Library
Your Zotero library refers to your collection of citations and any files and research notes that you attach to them – basically, all your stuff.

46. Zotero Connector Connects your browser to Zotero
Zotero uses what are called browser extensions to connect your browser. It’s the extension that builds the bridge between the browser and Zotero, enabling you to easily save citations, and, in some cases, PDFs to your Zotero library.

47. Set Up Online Sync Go to Zotero.org Click ‘Log In’ in upper right
Click ‘Register’ in upper right
Create your account
Verify your account
You should have Zotero and a Connector for your browser already installed. Are there any problems so far?
Next, there are a few settings that I’d like to walk you through. The first is setting up online sync.
The purpose of Online Sync is for Zotero to synchronize your data across as many devices as you choose. All of your notes and bibliographic data remain seamlessly and silently up to date.

48. Set Up Online Sync (continued)
Open Zotero (desktop app)
Go to Preferences:
Windows
Mac

49. Set Up Online Sync (continued)
Set Sync preferences
If you want to sync files, like PDF attachments, you need to click the check box for that. Note that you have 300 MB of free Zotero File Storage for attached files, with larger storage plans available for purchase.

50. Set Up PDF Indexing
Go to Preferences > Search Click ‘Check for Update’
There’s another setting that I want to make sure we configure now because it really enhances the functionality of Zotero.
Again in the Preferences menu, from the options at the top of the window, choose Search. In the middle of the window, you should see a large button that says “Check for Update.” Go ahead and click that button.
What this will do is enable you to search the full text of any PDFs you save to Zotero AND extract citation information from many PDFs just by dragging and dropping PDF files into your Zotero library.

51. Save Citations
Zotero icon appears in browser location bar Click icon to save citations to Zotero Firefox Chrome Safari
Now let’s talk about getting citations into Zotero. Zotero makes it easy to pull citations from websites, provided there is Zotero translator code running in the background. The translator is what enables Zotero to detect, interpret, and import citation information from a given website.
If a Zotero translator exists, a Zotero capture icon appears in the location bar of your browser. Here is an example.
In the top example, we’re looking at the location bar of a JSTOR webpage and at the end of the location bar there is a page icon. If I were to move my mouse over the icon, a text box would appear, which reads “Save to Zotero” – this tells me that there is a Zotero translator for this page, which can interpret any citation information that appears here.

52. Save Citations from PubMed
Okay, next let’s begin saving citations to our Zotero library and let’s start by saving citations from PubMed.
I’m going to do a keyword search. Go ahead and do a keyword search of your choice. Okay, now that I have a list of search results displayed on the page, I have a question for you. This is a review of something I touched on earlier, when introducing you to Zotero terminology. Where on this page does the Zotero capture icon appear? Remember that the Zotero capture icon is what enables Zotero to interpret the information on this page and it’s what enables us to save citation information with one click.
It’s up in the location bar or URL bar of the browser. You can see there’s a file folder icon near the end of the location bar and when I move my mouse over it, it reads “Save to Zotero.”
When I click on the icon, I see a list of all the citations listed on this page of results. That’s a product of the way Zotero works – remember, it’s translating the information displayed on this web page.

53. Save Multiple Pages from PubMed
Select “Send to” Select “File” Under Format, select “XML” Click “Create File” button In Zotero, Import file

54. Drag & Drop PDFs
Drag PDFs into My Library; right click to retrieve Metadata.

55. Zotero with Word – Windows
Zotero ribbon in Word installed with Zotero installation Add citations and bibliographies to papers
Now, let’s move on to using Zotero with Microsoft Word.
When you installed the Zotero, bundled with that installation was the Zotero add-on for Microsoft Word. So, when you open Microsoft Word, on the Windows operating system, you’ll be able to find a new toolbar in the ribbon.

56. Zotero with Word – Mac
Depending on what version of Word for Mac you have, you will find the Zotero toolbar in a few different locations.
The top screen shot is of Word 2016 for Mac , which includes Zotero under the Add-Ins tab on the ribbon.
In Word 2011 for Mac, you will have a floating Zotero toolbar, which is the middle screenshot. My next slide shows you how to display the toolbar if you don’t currently see it.
And lastly, in Word 2008 for Mac you can access Zotero functions by using the script menu.

57. Zotero with Word – Mac View > Toolbars > Zotero
You can display the Zotero toolbar on the Mac by going to the View menu, choosing Toolbars, and then finding the Zotero option to display the toolbar, which is very similar to what Windows users see.

58. Create a standalone bibliography
Right-Click > Create Bibliography from Items

59. Create a standalone bibliography
Choose a citation style: Vancouver Output Mode: Bibliography Output Method: Save as RTF (for best results)

60. Do More with Zotero
Folders – organize your library Duplicates – find & reconcile duplicate citations Notes – take research notes in Zotero Groups – share citations with collaborators

61. Learn More & Get Help Zotero Guide: guides.lib.uchicago.edu/zotero
your questions or schedule a consultation
Zotero.org
Quick Start Guide
Screencast tutorials
Discussion forums

62. Questions?