literature search & reference management

• Choose a topic & scope
• Select keywords
• Search databases
• Identify relevant references
• Export results to a reference manager

• Identify the core constructs of your topic
• For each construct, make a list of synonyms
• Useful tools for identifying related words:
  • https://www.ncbi.nlm.nih.gov/pubmed --> pull down MeSH in search bar
  • When reading an article, look for its keywords

Example: for the construct "emotion" we could choose the keywords emotion, affect, & arousal

• MeSH search
• View related papers on PubMed

Choose the database(s) to query:

• PubMed
  • Helpful feature: create an account to save your searches and collections of articles
• Google Scholar
  • Helpful features: "Cited by", "Find it @USC"
• PsycInfo
• Access more databases at https://libraries.usc.edu/ --> Database Quicklinks

Use boolean operators to combine your keywords and query each database.

• Generally, use the Advanced Search feature if it exists
• Use quotation marks around terms with multiple words
• Boolean operators: AND, OR, NOT

Let's try a search on emotion, memory and aging, using the PubMed & PsycInfo databases.

Choose keywords:

Combine keywords with boolean operators:

(emotion OR affect OR arousal) AND (memory OR recall OR recognition) AND (aging OR older adulthood)

PubMed:https://www-ncbi-nlm-nih-gov.libproxy2.usc.edu/pubmed?otool=uscnmlib

PsycInfo: https://search-proquest-com.libproxy2.usc.edu/psycinfo?accountid=14749

Depending on the scope of your search, you may have a large number of results. Some ways to filter through those results:

• Restrict to only articles published within the last X years
• Restrict the keyword search to look in "Title/Abstract" only

Regardless, you will need to review your results to identify which references are relevant. If you have a large number of results, my recommendation is to:

• Start by reviewing titles and eliminating titles that are obviously irrelevant
• After title review, review the abstract of each article
• After identifying relevant abstracts, download relevant articles for full-text review

Now, let's practice reviewing & downloading the results of our earlier search in PubMed.

• In PubMed, there are two useful options for saving the results of a search.
• Once you have identified relevant articles to read, select them all using the checkbox feature.
• Then use the Send to feature, and choose one of the following options:
  • Collections: Here you can send results of a search to a "Collection" which stays saved on your PubMed account. I use this feature often, particularly for searches with large sets of results that take me multiple days to filter through the results.
  • Citation manager: Here you can export the results of your search as a .nbib file which can be read into a citation manager.

Try exporting 5 results with the Citation manager option.

Citation management programs allow you to store and organize references, easily extract citations for references, and create bibliographies for collections of references. There are a number of citation management tools available, including:

• Mendeley
• Zotero
• RefWorks

The remainder of today's tutorial will focus on Mendeley.

• Register for an account: https://www.mendeley.com/
• Download Mendeley Desktop: https://www.mendeley.com/download-desktop/
  • This download includes the desktop reference manager as well as the Word plug-in
• Web Importer (on your own): https://www.mendeley.com/reference-management/web-importer/#id_2

Set up a directory where Mendeley "watches" for new references:

• Mendeley Desktop --> Preferences --> Watched Folders
• I use a separate directory within my Downloads folder to store articles for reading and organization
• Download/place PDFs into this directory
• They will be added into the Unsorted section for subsequent organization

Set up how Mendeley automatically names and organizes references:

• Mendeley Desktop --> File Organizer
• Select Organize my files and choose the directory where they should be copied
• Set up how you would prefer articles to be named when they are copied by Mendeley

Create folders and subfolders corresponding to projects, classes, etc.

• From a search in PubMed, etc.
  • File --> Import --> .bib (or choose your format of choice)
  • File --> Add Files --> select PDF, etc.
• Using a PMID or doi identifier
  • File --> Add Entry Manually --> add PMID or doi identifier of desired reference
• Always check the Details of each reference you import, and update them as necessary

• Double click an article to read
• Use the Notes feature on the right panel to keep track of questions, etc.
• Use the Note feature on the top toolbar to add notes within the text
• Use the Highlight feature to highlight text or a rectangle within the text, in a color of your choice

• Choose a citation format
  • View --> Citation Style --> Choose your style of interest (often APA 6th et.)
• Export formatted citation(s):
  • higlight reference(s) of interest --> CTRL + click reference(s) --> Copy As --> Formatted Citation
  • paste the formatted citation(s) into word processor
• For writing papers, the Mendeley word plug-in is invaluable. Use it to add in-text citations and automatically generate a corresponding bibliography.

• Share references in Mendeley using the "Groups" feature:
  • Edit --> New Group --> Create your group & add members
• Web import tool: useful if you are not using your personal machine
  • Add references and your local Mendeley Desktop will sync later
• Word citation plug-in

Now, let's practice importing references using two methods.

• First, add the references you saved earlier by importing the .nbib file into Mendeley
• Second, use your own method to import the following article:

Mather & Sutherland. (2011). Arousal-Biased Competition in Perception and Memory. Perspect Psychol Sci. 6(2), 114-33. doi: 10.1177/1745691611400234.

Introduction to R: syntax, variables, & data types

Please prepare for the next tutorial by installing R and R Studio:

• To install R: https://cran.cnr.berkeley.edu/
• To install R Studio: https://www.rstudio.com/products/rstudio/download/#download