Training scholarly information handling for geoscience faculty & PhDs: 3. Reference management

Using the boxes on the right, you can get a quick start in registering/installing and configuring your favorite reference management tool and try out some basic operations. It takes 45-75 minutes. 

The boxes on the right are to get you started. In our full LibGuide on Reference Management you'll find much more information, also on how the tools compare and how to choose a tool for reference management.

There are dozens of dedicated reference management tools. The best known and most widely used are:

• Mendeley, a free tool primarily built around a full text workflow, with good synchronisation between the desktop application and web interface, with a built-in PDF-reader and strong social functions.
• Zotero, a free, independent and open source tool, with very good ability to recognise and capture bibliographical data on webpages.
• RefWorks, a complete tool, licensed by Utrecht University, supported by many search engines and databases with fast and reliable direct export options, but, being a pure web service, sometimes a bit slower and without a good full text workflow.
• EndNote, also very complete and professional, licensed by the Utrecht University, very suitable for processing large numbers of references and with good sharing options.

The are many ways of keeping track of what you read:

1. Printing/copying and storing the prints
2. Downloading PDF's and other documents and storing them in folders on your hard drive, pen drive or cloud drive
3. Storing simple webadresses using your browser favorites
4. Making your own simple lists in using text editors, spreadsheets or general database software

But if you read a lot, and write many papers citing lots of publications it may save time to use a dedicated tool that supports citing in documents your are preparing and that supports citation styles required by journals and publishers. The most widely used are:

1. RefWorks or EndNote, the standard product at the university
2. Endnote or Reference Manager ( the second not installed in the UU), available in the UMCU
3. Free tools such as Zotero or Mendeley

A) Setting up:

1. Go to Zotero, click download now and download and install Zotero Standalone
2. Go back to the Zotero download page, scroll to the bottom and install the bookmarklet in your browser; make sure to make your favourites toolbar visible in your browser; this bookmarklet supports easy importing of bibliographical data
3. From the same download page install the plugin for Microsoft Word (this supports citing while you write your paper)
4. Start Zotero Stand Alone, go to options|preferences and then to 'advanced', then to the files tab to select a folder on your hard drive where you store/save your PDFs
5. Also in options|preferences on the 'search' tab, activate PDF indexing to be able to search the full text of your PDF files
6. To activate  the library lookup functionality (=UBUlink) please enter the Utrecht University OpenURL-resolver address (with question mark included but without the quotes):https://utrechtuniversity.on.worldcat.org/atoztitles/link" under tools|preferences|advanced|openurl

B) Getting some stuff in:

1. Go to Google Scholar, perform a search and import bibliographical data with the bookmarklet  ('save to Zotero') on your favourites toolbar; go to your Zotero desktop application and synchronize (green icon top right) to see the reference
2. Go to Scopus, perform a search and import bibliographical data with the bookmarklet on your favourites toolbar
3. Go to WorldCat, perform a search and import bibliographical data with the bookmarklet on your favourites toolbar
4. From a new Scopus search go to the full text of a paper and download that text as PDF in the folder on your hard disk that you set as linked (watch) folder; then, in Zotero add a new reference with the green +icon, select link to file and select the file on your hard disk; now you can add the metadata of that file by right-clicking the reference in your library and select the option to get the metadata
5. Find out how you could add a reference completely manually (although you hope to avoid that of course)

C) Organising, reading, annotating

1. Have a look at your library to see what you have imported/downloaded so far; right-click My Library top left to make a folder and start sorting if you wish
2. Select a reference in your library using the right-hand pane add a tag/label
3. Double click an item in your library with full text to read it in your PDF reader; you can also use the annotation options of the reader.

D) Citing:

1. Start Word
2. Make a fake sentence and put your cursor halfway and save your document
3. Using the Zotero functionality on the add-inns page, cite one publication from your Zotero database (you need to search for an author or title word, but you can also get a list by clicking the Z-icon in the dialog and select classic view)
4. Put your cursor on the in-text citation and click the edit citation button to add a page number
5. Create the bibliography with the bibliography icon
6. Switch to another style (e.g. to APA or Chicago Style) and reformat the paper with that style; you can do this with the "set Zotero doc prefs" icon

Support from Zotero itself: https://www.zotero.org/support/

A) Setting up:

1. Go to RefWorks (link for UU-members only) and make an account
2. (On your own computer:) once logged in to RefWorks go to the tools menu and select Write-n-Cite, then download Write-n-Cite 4. This is the add on for Word that allows you to cite items from your RefWorks library while writing your paper. N.B. On university computers Write-n-Cite has been pre-installed already.

B) Getting some stuff in:

1. Go to Google Scholar, dive into the settings and make sure that RefWorks is selected under bibliography manager; then perform a search and import bibliographical data of a few papers by clicking import into RefWorks under each of them
2. Go to Scopus, perform a search, tick a few relevant papers and click export; under choose information to export select citation and abstracts and then click RefWorks direct export.
3. Go to WorldCat, perform a search, and after that filter on books (including e-books) using the menu on the left; click through to the full details of a single book, then click cite/export and select export to RefWorks.
4. Find out how you could add a reference completely manually through the menu references|add new (although you hope to avoid that of course)

C) Organising, reading

1. Have a look at your library to see what you have imported/downloaded so far; please note that everything you import is first imported into the last imported folder, but replaced when you import something new; however you can always see all references by selecting view|all references from the menu
2. From the list of all references tick one and put that in a seperate folder by clicking the small yellow folder icon and making a new folder
3. Under one or two of the references click the red UBUlink icon to check whether the library has the full text or hardcopy available for you

D) Citing:

1. Start Word
2. Make a fake sentence and put your cursor halfway and save your document
3. Go to RefWorks tab you created in Word (which may be called ProQuest when you are not logged in yet), log in to your RefWorks account on that Word-tab
4. Use insert citation|insert new to cite a publication from your RefWorks database
5. Use bibliography options|insert bibliography
6. Switch to another style (e.g. to APA or Chicago Style) and see how the paper is reformatted with that style
7. Put your cursor on the in-text citation and double click to see the menu edit the citation; look at the options and use the suffix option to add a page number if necessary

Support from RefWorks itself: https://www.refworks.com/refworks2/help/RefWorks2.htm