Managing references and notes

Managing references and notes is a continual challenge for graduate research students, mainly because there are many ways of doing it. Practices vary based on subject discipline, individual practice and preference.

Reference management is the practice of storing, organising and retrieving your research material. Reference management software is designed to assist with this, as well as helping you to correctly cite your sources and create reference lists or bibliographies.

During your doctoral studies it is essential to keep notes on what you have read. Recording your comments helps you to develop your ideas and start the writing process as you learn more about the research in your field. As you continue to collect sources you will need an efficient system to manage both references and notes.

Reference management

For your doctoral studies, you will need to read a wide range of literature. You will need to develop a system to keep track of what you have read and what you have cited in your writing.

Making the time to create and manage such a system early in your doctoral studies will greatly assist your writing as you write larger documents such as your thesis.


What can reference management software do for you?

Software packages are designed to build local libraries that can then be used to organise, sort, and reference sources when writing.

Three popular programs are EndNote (Monash supported), Zotero, and Mendeley. When deciding which program is most suitable for your needs, pay careful attention to the features offered by each one, as well as the support available.

The following case studies demonstrate how different doctoral researchers have used EndNote, Zotero, and Mendeley. This will give you an idea of the ways in which you can use reference management software to organise your sources.

Case study 1: EndNote

I use EndNote to manage my references. I add everything I read to my EndNote library, whether I intend to include it in my thesis or not (see image 1). This helps me avoid rereading irrelevant work. Because EndNote connects directly to Word, I can easily incorporate any of my sources as I write. I also use Group sets, like Primary sources, with Groups, like Ovid, to sort my references according to the themes and organisation of ideas in my thesis (see image 2).

In order to reference the texts as I need for my field, I have edited the Output style so that only the “Short Title” appears for ancient texts – these Short Titles are then filled with the accepted abbreviation for these authors (see image 3).

Case study 2: Zotero

I use Zotero to collect and save references automatically from library databases or websites. The best thing about Zotero is the “web–scraping” feature, where it can collect metadata from most references and save them with just one click. It has saved me a lot of time. Zotero is also free and easy to use. It took less than 5 minutes to install and didn’t take long until I fully understood how it worked. I work using multiple computers (at home and work) and so far I haven’t had any problems syncing my library across my different devices. Another important feature of Zotero is the word processor plugins which have helped me to automatically generate bibliographies, as well as in–text citations and footnotes. It has been a real lifesaver because even though I still need to understand the basic rules of the citation style I am using, it takes away the painstaking task of typing all the bibliographic information manually, (see image).

Case study 3: Mendeley

I save all my references in Mendeley and I organise them into folders. Mendeley has a folder, “Unsorted” so I can easily find references that I haven’t categorised. I try to put them into folders as soon as I upload the reference and PDF to Mendeley so that I remember why I thought the article or book would be useful. These folders form a library of material on different topics and I use them as the starting point for writing. I also use search in Mendeley to find material on a topic (see image).

I don’t use the notes tab in Mendeley but I do annotate and make notes on the PDFs. I sync my desktop to my iPad app and use this as my travelling library.

Managing Notes

As you read you should be making notes — more material that needs to be stored and managed, to allow you to make good use of your sources in your writing.


What can note–taking software do for you?

Note–taking software applications can help you to record, store, organise, and retrieve your notes. It might be possible to sign up for a free trial of the software prior to purchasing it. There are several programs available to help you manage your notes. Most reference management software (including EndNote, Zotero and Mendeley) allow you to store notes related to your references. Other popular programs, such as OneNote, and Evernote offer many possibilities for managing notes as part of a writing project. You can find more information about programs for notes in the Monash Software catalogue.

The following case studies demonstrate how different doctoral researchers have used OneNote and Evernote to organise their notes. This will give you an idea of the ways in which you can use different programs to organise your notes.

Case study 1: OneNote

OneNote works well in several ways, in my experience. It functions, in a way, as one’s office. It can be used for multiple purposes..

– for example,

  • as a template for writing reading notes, and a database in which to store them and in which to cross–reference
  • as a ‘filing cabinet’ in which to collate materials, store references, resource directories, contacts
  • as a notebook in which to write ideas, comments
  • as an archive in which to build focused collections of materials on specific themes, these collections can include PDFs, images, maps

My OneNote Notebook has grown like topsy, and I recognise that I have been a little undisciplined with my use of it. I notice that its subdivisions in part reflect the early stages of my project and perhaps I need to set aside a week to revisit its organisation and to ‘clean out’ the filing cabinet. I think also that I should have a firmer protocol for how I use it — it can become a too easily available ‘basket’ in which to drop things. But, it is invaluable.

OneNote offers other attractions to a researcher – for example,

  • it is searchable, so that content can be located through conventional search terms
  • a OneNote app for Google allows clipping from websites directly to your OneNote account
  • hyperlinks referenced in one’s Notebook are ‘live’
  • there is a library of tags limited/colours/typefaces to allow for helpful formatting
  • it offers the facility of creating sections, pages, sub–pages
  • a page can be enlarged or diminished, for viewing purposes

I use OneNote in conjunction with Zotero, which I access similarly via an app on the Google toolbar. I access both OneNote and Zotero on various platforms – on my laptop, on a desktop at home, and at Monash, and on my mobile. I have not had any problems with either application so far, but I make sure that I am careful! I never leave one platform to go to another without closing the application. In addition, I back–up OneNote (there are clear instructions available if you are not willing to rely just on your Microsoft Cloud account).

Both OneNote and Zotero are free, but there are limits to the storage offered without charge. Since I signed up to OneNote via my personal account, I have had to pay for further storage. At present, I am considering adding a further application to my toolbox: Tropy, which is a free, open–source software for organising and describing photos (see image). I am beginning to see the usefulness of developing a separate image library, particularly one that allows for the sometimes extended ways images require cataloguing.

Case study 2: Evernote

I use Evernote to take notes from both primary and secondary sources. I tend to have a PDF or e–book open on one side of my screen and Evernote open on the other (see image).

I use Evernote to embed images and whole PDFs into my notes — I use a lot of images of objects, so this function allows me to keep everything together in one spot. ‘I have also noticed that you can embed audio and video files straight into notes.

Within Evernote, I have created ‘notebooks’ for the different themes of my thesis (see image). When it comes to writing chapters, I sometimes go through these themed notebooks and copy the relevant notes into a new ‘notebook’ for the chapter I am working on. That way, I can just open the ‘notebook’ for the chapter and all the notes will be there. Otherwise, I just scour through the themes for the relevant notes I need for writing chapters.

I use the ‘tags’ function in Evernote to keep track of different themes, ideas, and topics. It’s important to start tagging from the beginning, because if some notes are tagged and others aren’t, untagged ones will not be caught when conducting a search (see image).

Evernote automatically syncs to the Cloud on up to two devices for free (unlimited devices with the paid version). I know that my notes are safe, but I still periodically download the files in an HTML format as extra back–up.

File and document management

It is recommended that you document and store your data so that you, and others, can find and use it into the future. As a researcher it is in your interest to make sure that you maintain sufficient documentation or metadata about your sources to enable it to be found, used, and managed. Documentation and metadata requirements will differ depending on the discipline and the nature of the research.

File naming conventions

It is important for you to name your folders, documents and records in a consistent and logical manner so they can be located, identified and retrieved as quickly and easily as possible.

You should develop file naming conventions early in a research project.

When you are deciding on digital file naming conventions, consider how you will access the files later. You can try to use names that are short and meaningful. You may want to have a version numbering system for your thesis drafts as well — this usually involves adding a number to the end of the file to indicate which version you have reached.

You can also check out the Library’s tips on Organising Data.