Every academic year, the HDYDI (How Do You Do It?) event on research data workflows signals the start of the Digital Scholarship Module. Through a series of sessions and (mini-)workshops, Artes Research aims to guide students through the complexities of scholarship in the digital age, from Open Science to Research Data Management and beyond. At the HDYDI kick-off event, three researchers from the Faculty of Arts lift the curtain on their own research workflow and offer a behind-the-scenes look at the ways in which they approach their research, the data they engage with, and the tools they use in doing so. The goal of this session is to provide examples of more advanced workflows for the first-year PhD researchers as they embark on their own research journey. Hopefully this recap of the session can spark some inspiration for you!

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Seb Verlinden – Using Obsidian as a note-taking tool for literature

The first speaker, Seb Verlinden, is a second-year PhD candidate in medieval history. Under the supervision of Maïka De Keyzer and Bart Vanmontfort, Seb is studying the long-term landscape changes – mainly in the form of gradual desertification – that characterize the Campine region, one of the driest areas in Belgium. Particular focus is on the impact of eighteenth-century drainage in the region.

Seb’s talk concerns an issue that all researchers can relate to, regardless of the relative complexity of their project – that of taking notes. It is true, as Seb highlights, that every researcher has their own unique workflow, often relying on a combination of tools that makes sense for them (in his case, QGIS, FileMaker Pro, MAXQDA, and spreadsheet software). But at the heart of any research process is the need to organize one’s thoughts, and this is where note-taking apps can make a real difference. So, what are some of the options out there?

Zotero is a possible solution – one we’ve already discussed elsewhere on this blog. As a reference manager first and foremost, Zotero has the potential to become a researcher’s living library, a knowledge base covering all relevant literature. It also has great capabilities for annotating PDFs, especially with its new 7.0 update. What you’re missing in the context of note-taking, however, is the big picture. Seb aptly points out that using Zotero to make notes is like putting post-its in books: you have no real overarching structure, and no way to easily link notes across books.

Other tools are likewise flawed. Lots of researchers use Microsoft Word to take notes, even though it is primarily tailored to mid-length longform text. As a result, it is easy to lose track of notes, unless you’re willing to navigate multiple files; and it tends to grow slow and cumbersome, since it is occupied with layout. It is, simply put, unintuitive for this purpose.

This is why Seb puts forward another solution, one that he believes to be faster, better automated, and easier to use: Obsidian. A widely supported and free tool, Obsidian does have its advantages: in contrast to both Microsoft Word and Zotero, it uses open-source file formats (.md or Markdown files, written in an accessible markup language) and it is full-text searchable and provides a structured overview of notes. Moreover, it offers a versatile workspace, allowing you to go as simple or as complex as you like – especially with the addition of supported plugins. One such plugin, in fact, allows your Obsidian environment to easily interoperate with your Zotero library (including references, bibliographies, and PDF annotations), which is particularly useful.

Seb ends his talk by highlighting another key benefit in using Obsidian. By introducing links in your notes, it is possible to cross-reference other notes within your system with minimal user effort; and through the use of tags, you can generate another layer of structure. Obsidian then uses this information to visualize the relations between your different notes, automatically creating a network of clusters that correspond to certain topics of interest. This way, it expands the possibilities of the data without the need for the researcher to make any real effort – a great reason to think about using Obsidian for your own note-taking needs!

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Laura Soffiantini – Managing linguistic and historical data. A PhD workflow using FileMaker

Laura Soffiantini is the second speaker: as a PhD researcher at the Cultural Studies Research Group, she is currently analyzing the geographical representation of Greece in Pliny the Elder’s Naturalis Historia. With the help of her supervisor Margherita Fantoli, Laura intends to shed new light on the way in which Greece was perceived in Flavian-era Rome. In order to do so, she has to manage a varied mix of linked data – textual, linguistic, and historical – as part of her daily routine.

Grappling with 37 books of a classical encyclopedia, and dealing with data in different formats and with different qualities (actual text, numeric coordinates, symbols, etc.), Laura realized the importance of proper Research Data Management. It enables aggregating, manipulating, analyzing, and comparing your data more efficiently throughout – and even beyond – the research process. Indeed, a challenge faced by many researchers is the retrieval of data collected or processed at an earlier time, with the aim of relating it to “new” data. In this context, Laura provides a look at her own research workflow.

The primary strategy in managing your data, she remarks, is to structure it. By adding structure to your data, you can parse it more easily and return to it without issues, even in later phases of your project. Software like Obsidian is indispensable for this purpose, but it’s also good to think about using tabular formats like .csv (an open plain text format) as a way to organize your data. A useful tool put forward here is pandas, a Python library designed to help manage and analyze data derived from such .csv files. That might sound technical, but Laura ensures us that – even if you have no background in programming – pandas is a very accessible and convenient tool in handling tabular files.

Having thought about what data she worked with (an essential step for every researcher), Laura adopted an initial workflow in three parts. She first started out with .json files containing Pliny’s text, which she converted into tabular .csv files, adding data related to the lemmatization of the corpus, part-of-speech tagging, and references to book and chapter positions. Subsequently, she thought about grouping this data into different categories, which she assigned to different columns – such that there is a column titled “book_chapter”, one titled “lemma”, and so on. Finally, Laura assigned identifiers to the information contained in these files; she explains she wasn’t aware of the importance of such identifiers at the start of the project, but now realizes they form a crucial part of keeping tabular data.

As a result, Laura ended up with multiple .csv files, which she then related to each other using FileMaker (with the expert assistance of Mark Depauw and Tom Gheldof). One table, for instance, contains a list of all the Latin words used (the tokens, e.g. urbs) alongside their identifier, book number, lemma, and possible identifier linked to the Trismegistos database of ancient texts. Another contains the lemma along with its part-of-speech tag (e.g. proper noun) and meaning (e.g. “city”). By linking the different files through the use of identifiers – the keys to the data – Laura made a relational database easily managed and organized through FileMaker. The resulting dataset is at the core of her research project.

The main takeaway Laura wants to leave us with is that it is important to create an environment in which you can efficiently collect, store, manipulate, and analyze your data. This should not come at the cost of traditional approaches and methodologies – in fact, you can add to them to create a better workflow as a whole!

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Zakaria El Houbba – Obsidian as part of the research workflow

The third and final speaker is Zakaria El Houbba, third-year PhD candidate in Arabic Studies. Zakaria’s project, supervised by Arjan Post, focuses on the pre-modern relation between Islamic jurisprudence and Sufism, and in particular on the way in which these two strands are united in the figure of Aḥmad Zarrūq. In doing so, the research aims to come to a theory of applied legal epistemology in Zarrūq’s Sufism.

By discussing his own workflow in detail, Zakaria intends to highlight a number of key takeaways revolving around the idea of the “second brain”. Because we are so deeply involved with knowledge gathering on a daily basis, and constantly receive input from various sources (whether academic or not), we run the risk of being overwhelmed by a flood of information. When you use software to carry that burden for you, you can save your own brainpower for actual critical thinking rather than secondary tasks like categorizing information. This way, you’re effectively constructing what’s referred to as a second brain.

In this context, Zakaria also makes use of Obsidian, though he approaches it from a very different angle than Seb. Zakaria doesn’t actually enter all of his notes into Obsidian – he first uses an app like Microsoft OneNote as a “vault” to record random, non-processed thoughts, which he periodically goes through to think about how they fit in his project. He then sorts these thoughts and puts them in corresponding folders (relating to certain projects, classes, issues, etc.) in order to process them properly in Obsidian. Zakaria emphasizes that it’s fine to keep it simple and take it slow, focusing on what you specifically need from the note-taking environment so as not to get overwhelmed by all the options and information.

There are more tools Zakaria uses in his workflow – in fact, he says, there is a constant conversation between himself, Obsidian, Zotero, and ChatGPT. He uses Zotero to make notes and highlight text when reading articles, which he imports into Obsidian and categorizes using tags. Afterwards, he copies those highlights from Obsidian into ChatGPT, asking it to take up the role of copy editor and summarize the text. The resulting summary, which he critically revises, is then given a place in Obsidian once again.

Next to the powerful visualization capabilities discussed by Seb, Zakaria explains that Obsidian can also be used to create subpages within notes to explain terms and concepts, provide brief biographies of important figures, and so on. These “subnotes” can be linked back to in other notes as well, resulting in a kind of personalized Wikipedia for your research topic. This can also be helpful when you’re following classes on a certain topic or revising your own teaching material!

Finally, speaking of teaching material, Zakaria points us to a couple of helpful AI tools that can be used to process video files, such as recorded lectures or talks – whether you attended them or gave them yourself. One such tool is NoteGPT, which essentially functions as a transcriber and summarizer of recordings. You can revise and copy the resulting transcriptions and summaries into Obsidian as well, further expanding the scope of your second brain. Brisk Teaching serves a similar purpose as NoteGPT, but can also be used to turn a video into a PowerPoint presentation, which can be very convenient and time-saving. By thus constructing a workflow, gradually accumulating relevant information through different tools, it becomes much easier to manage your research.

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The workflows of the presenters reveal both similarities and differences, but there’s one thing all three can agree on – what’s important is to find a workflow that works for you. To that end, take inspiration from some of the tools and processes described here, but always make sure they support your specific research methods. This was emphasized in the questions as well: don’t feel pressured to adopt a tool like Obsidian, but try it out and see if it accommodates your needs. Who knows, you might uncover a more efficient workflow or see your data from a new perspective.

Happy holidays from the Artes Research team, and may your data be blessed in the year to come!