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Citing Sources

How to cite sources in your writing and use citation management software to organize your references and format your bibliography automatically

Citation Management Software

Citation management software, a.k.a. reference management software or personal bibliographic management software,  can help you with:

  • organizing references, PDFs, images, data sets, webpages etc. 
  • taking notes on references and annotating PDFs and searching notes later
  • formatting bibliographies and in-text citations in hundreds of citations styles
  • sharing references and collaborating on projects with colleagues

This guide will overview a few pieces of citation management software, including Zotero, Mendeley, EndNote (Web and Standalone), and Papers,  to help you choose and use them. Remember, if you need to use more than one throughout your academic career, there are methods to transfer your data from one to another. 

Access to Citation Management Software

Factors to consider for choosing a citation management software

  • Cost: free, one-time purchase, or subscription.
  • Types of reference you use the most: research articles v.s. images\media
  • Functions you need the most: organization, annotating, write-n-cite etc.
  • Collaboration needs: share with other within or outside research groups or not.

For example,

If you... Consider to use ...

… archive web pages and import citations from government sites, blogs, social media etc.

Zotero or Mendeley

… annotate and index PDF often

EndNote Desktop or Mendeley

… extract citation data from PDFs often

Mendeley, Zotero, or EndNote Desktop

… use mobile capabilities

Mendeley, EndNote Web, Zotero (3rd party app)

… manage and caption many images


…customize bibliographic style often and need stable Write-N-Cite


… use LaTex editing exclusively or intensively

JabRef or BibTex

… share with others (including external collaborators) a lot

Mendeley, Zotero

Please see the table below for comparison of features across several citation management software. They may help you choose one.

Example Workflows for Using a Citation Management Software

To consider which citation management software to choose, you need to consider which one would work the best for your research workflow involving literature. Here are some example workflows.

Citation Management Workflow 1


Citation Management Workflow 2


Citation Management Workflow 3

Caution with using citation management software

  • Garbage in, Garbage out - Your citations will be only as good as the data fed to the tool. If a database misspelled an author's last name, the citation will have the misspelling, unless you correct it.
  • Be careful with using Find Fulltext function - Some citation management tools specialize in downloading files from databases.  Remember to connect to VPN  or setup proxy to use the function properly if you are off-campus. Our licensing agreements with database vendors prohibit excessive downloading.  Please be aware of any automated file import features that may be activated in your citation management programs! The following links may be needed to setup your Find Fulltext . 
    • Open URL:
    • Mines Proxy prefix:

Comparison of Popular Citation Management Software

  EndNote Basic (Web only)  EndNote Desktop Zotero Mendeley
Comparison of Popular Citation Management Software (Last Updated Dec 2016)

Commercial product started early from Thomson Reuter. Now with Clarivate Analytics

Open source; grant funded startup.

Open source tool originated in biomedical community; now with Elsevier.

Cost - Access/software Free for Mines affiliates

$112.99 Students
$214.99 Faculty and staff

Free Free
Cost - Cloud storage

Unlimited with Mines Web of Science subscription / In general, 2 GB (50,000 references)


First 300MB free; $20/year for next 2 GB and higher for more

First 2GB Free; various charges for storage and group capacity

Linking to PDF and other files Yes Yes Yes Yes
Compatibility with word processing programs MS Word

MS Word, OpenOffice, Mathematica, Pages, LaTex through BibTex

MS Word, OpenOffice,

Google Docs

MS Word, OpenOffice, BibTex

Citation style modification

Most popular styles available. No modification.

Most popular styles available. Can modify /add new styles.

Most popular styles available, difficult to modify

Most popular styles available, difficult to modify

Mobile capabilities

Mobile site

Mobile site. iPad App

Mobile site, Firefox extension

Mobile site, iPhone, iPod, iPad, Android App.

Searching across external database Yes Yes No No
Importing citations from other databases Yes Yes Yes Yes

One click to Find Fulltext

No Yes No No
Extracting citation data from PDF No Yes, quality varies, needs embedded metadata Yes, quality varies, can extract citation without embedded metadata Yes, quality varies, can extract citation without embedded metadata
Browser plugin to extract citation from web pages Yes, quality varies Yes, quality varies Yes, can save snapshots of web pages Yes, can save snapshots of web pages
PDF Annotation and highlighting No Yes No Yes
Searching PDFs and annotations No Yes Yes for PDFs and notes; not for annotations in PDFs Yes
Collaboration Private groups Private groups Private and public groups Private and public groups; Free version with up to 25 people in a group and 5 private groups max. 
Open Web API No No Yes Yes