EndNote Desktop

There are  four options for getting citation data into Endnote. 

Option 1: Direct Export

• Pros: Most databases have specific export utilities that allow you to work directly with Endnote, or allow you to download a file that you can then import into your EndNote library. Best Bet for accurately getting citations from article citation databases, like PubMed into EndNote. 
• Cons: Two step process.  

Option 2:  'Capture' References.   

• Pros:  This browser add-on scrapes citation data from a webpage. Best bet for websites like the CDC
• Cons: Does not work with most citation databases, like Scopus or PubMed

Option 3. Connection File

• Pros: You can initiate a journal citation literature search from within the EndNote, connecting to PubMed and a variety of other databases. 
• Cons:  We generally do not recommend this option for a literature review, since you are missing out on the native features of the database you are searching.  

Option 4: Import PDFs. 

• Pros: EndNote may be able to generate a reference from a PDF.  See the Working with PDFs tab on this guide to learn more about this option.
• Cons: Messy or missing data that you need to clean up. May be faster and easier to re-find the citations in an article citation database.

This video covers how to set up the Capture References bookmark as well as the Cite While You Write Word plugin.  You only need to watch the first 51 seconds to see how to set up your Capture button. Capture also works well with sites like Amazon or websites that may be encoded to recognize citation data.  Sometimes when you try to scrape a website, not all the data elements copy over so you may need to manually add the citation elements, but at least this option helps you get started.

Connection files allow EndNote to communicate with another database, allowing you to search a resource like PubMed from within EndNote.

Advantages

1. If you are missing a known reference from your library, you can quickly add the citation and a pdf to your library.

2. If you have a very unique term or author name you are following, it may be easy to have EndNote pull relevant citations to your library.

Disadvantage

This is the big one: PubMed uses something called automatic term mapping.  When you type a word or phrase like heart attack into the PubMed search box, PubMed automatically searches synonymous terms like myocardial infarction at the same time. EndNote does not do this. So if you enter the phrase "heart attack" that is all you'll get and your search results may suffer.  If you are conducting a literature review then its usually best to stick to the native search functions within the database you wish to search. 

EndNote comes with most of the connection files you need. To learn about connection files and how to use them, watch this helpful video.

After you import citations into your library, the next step is to keep them happy and organized.  See the next section of this guide to learn about creating folders, moving references between folders, and managing duplicate records. Read the next section of this guide, "Organize Your References" to learn more.