One of the key skills in any research project is good organisation. This is especially true for a PhD research project, lasting as they do over three years of full-time study, or up to seven years part-time. Students start off with two or three seminal articles relating to their research topic, but the field of reference will grow dramatically within the first six months, and citations will continue to be added to the reference list right up until the dissertation is submitted. Even then, the external examiner(s) might insist at the viva that the student needs to consider further a certain area of the research which will require further reading. Without a careful system, it does not take long for this growing pile of references to become unmanageable!
Some researchers swear by the old “traditional” system of individual index cards, alphabetically filed for each reference. This has the advantage of being able to add notes, summaries, questions etc., and also it is not dependent on technology, so does not require electricity or a battery. On the other hand, a file of cards is not very portable, can be a bit clumsy to sort, and not being digital, is less flexible to re-purpose. There are number of software packages, both free and commercial, that allow you to store and sort references on a computer. A product called Refworks provides an online database to manage bibliographic data, and this has numerous advantages, including being able to manipulate the data to display in different academic styles, create bibliographies for different publications, and also to access the data from different devices and locations. The university may subscribe to this product or some comparable service. Personally, I use a simple word processed file. This does not have the flexibility of customised bibliographic management software, but it has the advantage of being easy to create and use without specialised training. To create a bibliography for a new article I simply cut-and-paste from my master list (not forgetting to keep back-up copies of the master-list in other locations!)
In addition, Mendeley https://www.mendeley.com/ is a free manager for references and pdf documents which can be used to annotate articles and share online with students and other colleagues. It’s easy to use, see https://youtu.be/qRiAIaqdAOg and allows storage and access to a personalised library collection from any internet location. So, for example, a researcher could import an identified article, store it in a personalised online space, add comments and questions to the file, then share with an online social network which could include a research team, supervisors, or a cohort of students. Whatever filing system for research articles is used by a PhD student, it needs to be able to store, display and allow easy retrieval of anything that has been read over the duration of the study, which is not a simple task when this means five or six hundred individual references.