Whether you are researching a paper or attending a business meeting, note-taking programs help you collect digital information in one page. EndNote, from Thompson Rueters, is useful for managing research, references and bibliographies and is targeted to the research professional and student. OneNote, from Microsoft, is geared for personal, student and business use. The best option for you depends on the type of research you are doing.
Organization
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EndNote is about conducting research and organizing references. From within EndNote, you can search online databases and import articles as PDFs. You can then group those PDFs and add notes to them. You can also attach up to 45 files to a single reference, gathering all your information about a subject in one place. EndNote supports searching through your whole library so you can quickly find references. It integrates with Microsoft Word so you can build your citations as you write your paper.
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OneNote is based on the idea of a paper notebook. You can create several notebooks that contain sections; each section contains pages. Your notes appear on the pages. You can collect Web clippings, write notes and embed documents. To help you navigate your notebooks, you can create links on a page that take you to another notebook's page.
Web Clipping
EndNote can pull reference information from an online page and import it into one of your EndNote groups. However, you can't clip sections of a Web page and have them appear in your reference. You need to capture a screenshot of the page and then attach that file to the reference.
When you are using OneNote and you see something on a Web page you like, you can select the portion of the Web page you want to add to your notebook and select the notebook and page on which you want it to appear. Add a OneNote extension to your browser to capture entire Web pages.
Synchronization and Sharing
With EndNote, you can share your references and groups with others by giving them permissions to read and write your files or by emailing a reference and its attachments. EndNote syncs your content online, on your desktop and on your iPad.
Using OneDrive, Microsoft's cloud storage service, OneNote syncs your notes to your desktop, phone, tablet and the Web. You can invite others, even people who don't use OneNote, to view and modify your notebook pages. Several people can work on the same page simultaneously.
Cost
EndNote offers student and regular versions. The student version ships to you for $114; the regular version of EndNote ships to you for $300 or you can download it for $250 (as of June 2014). EndNote can be installed on three computers, but only the license holder can use it.
OneNote is free for anyone. If you purchase Office 365 Home or Office 365 Personal, OneNote is upgraded to the premium version. The premium version gives you increased security with password protection and enhanced functionality -- you can make notes from audio and video recordings, sync to OneDrive for Business and create notebooks on your computer.