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!

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!

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!

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.

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!

In December we closed off our fifth edition of the DH Virtual Discussion Group, during which we heard from three different early career researchers in our community. The Discussion Group series was jointly organized this semester by Prof. Margherita Fantoli (KU Leuven Faculty of Arts), Dr. Sven Lieber (KBR), Prof. Julie M. Birkholz (KBR Digital Research Lab and Ghent CDH), and myself, Dr. Leah Budke (KU Leuven Libraries Artes). This semester’s edition was yet another engaging and inspiring series of talks and discussions centering on many different aspects of DH research.

In October, Paavo Van Der Eecken from the University of Antwerp introduced us to his PhD project and detailed the decisions that went into to developing the annotation methods for a large corpus of images from nineteenth century Children’s literature. For a recap of this session and to learn more about Paavo’s work, you can read the full recap blog post here.

November brought us an engaging presentation from Houda Lamqaddam on the concept of digital satellites. This was our largest group for the fall edition with an attendance of 27, which led to a dynamic Q&A moment at the end of the meeting. Houda’s presentation took us behind the scenes of her work on Project Cornelia. This project is a hybrid research engine which focuses on bridging art history and computer science. As such, it uses and develops datasets and develops data retrieval and visualization tools to use with seventeenth-century Flemish tapestry and paintings.

From this starting point, Houda’s presentation raised some important questions about the creation and long-term preservation of digital tools. As Houda explained, questions of maintenance and sustainability are at the heart of digital humanities research, especially when it comes to the development of new digital research tools.

To conceptualize the relationship between digital research tools and their role in specific research projects and beyond, Houda introduced the concept of “digital satellites” to us. There are three defining characteristics to this concept: digital satellites are (1) “built to support a specific goal including communication, exploration or analysis, (2) they are artificial in nature, i.e. they exist in highly non-digital spaces, and (3) they orbit around more grounded research material.”[1] Houda also emphasized the importance of the end of the satellite’s life, likening this phase to a type of “space debris.” This phase also deserves thought and preparation; according to Houda, we should be asking ourselves how digital research tools can be useful for us during this phase as well. Some of the steps that Houda defines to support long-term function of satellites include (1) archiving the design, (2) archiving process and requirements, (3) making code available in open access, and (4) considering removing tools that no longer function.[2]

Houda’s presentation sparked much thought and interesting discussion. While we often see how new tools are developed or how existing tools are integrated into various research projects during the DH Virtual Discussion Group presentations, Houda’s presentation encouraged us to think more critically about the long lifecycle of these tools. This is of particular importance when we think of digital scholarship as a concept that also encompasses research data management and scholarly publishing. Documentation and extensive archiving of research output, in this case in the form of digital research tools, is of key importance. Moreover, publishing code in open access has the benefit of not only allowing more access but also creating transparency and giving insight into the research process and development of specific tools.

During our final session in December, we heard from Laura Soffiantini about her research on the extraction of formulae from ancient Latin funerary inscriptions. As Laura explained during her presentation, the funerary inscriptions are typically written or carved into stone pottery or metal. This is a vast amount of material, but Laura’s corpus for this project was narrowed to texts written on tombstones. The pieces that Laura is particularly interested in in these texts—the formulae—are multi-word sentence(s) in semi-fixed or fully-fixed form(s) which are used as stock expressions. Links exist between these words and removing a word in the phrase cannot be done without altering the meaning of the phrase.

Laura was particularly interested in applying computational methods to this large corpus of textual data to test whether or not these methods hold any potential for the recognition and extraction of formulae. She relied on two approaches to test this: (1) a rule-based approach with a manually annotated dataset of funerary formulae and (2) a frequency-based analysis and extraction determined by word combinations.

Laura’s research gave us some insight into the application of different computational methods with a specific linguistic focus. The comparison showed that both methods hold potential for future application, but that neither was fail proof 100% of the time. As a result, Laura’s analysis is a great example of the importance of methods-based research. In addition to presenting us interesting research, it also helped our group to think about the digital methods we apply in humanities research and the way that we justify these decisions in our work.

On behalf of the organizers, I would like to thank all of our presenters from the fall 2022 edition as well as all of those who attended the sessions. We enjoyed learning more about these projects, catching up with and learning from others in our community, and welcoming new people into our DH circle! If you would like to join us for the spring 2023 edition of the Discussion Group, you can join our mailing list here. When we have the spring program finalized, we will also publish the details here on Scholarly Tales.

[1] Houda Lamqaddam, “In Search of Meaning: Thinking Information Visualization within Art History Research” (2022), 93.

[2] Lamqaddam, 98–99.

Recap Zotero workshop

On the 16^th of June the Artes Research team joined forces with the research support services from the Faculty of Law to help PhD researchers get started with Zotero, a free online reference manager. The session was a success with an attendance of around 30 researchers, who were all eager to dive into the world of reference management.

*Please note, these materials were created based on version 6 of the Zotero software; the interface received a major update with version 7. While the interface looks different, Zotero 7 still has the same features as previous versions, however, some plug-ins may no longer be supported.

We kicked off the workshop with an introduction to the basic functionalities of Zotero. Nele Noppe of the Artes Research team shared her knowledge on the various ways to gather references to a personal Zotero library, gave an in-depth explanation on how to organize a library with tags, folders and collections and zoomed in on several topics such as the integration of Zotero in Word which allows you to create in-text citations, footnotes and bibliographies among other things. Of particular interest was the analysis of Zotero plugins.  Zotero has a very wide range of plugins that add extra functionality and connect Zotero with other software and platforms. As there are numerous plugins, we have made a list of plugin recommendations with a short explanation of their use, which we have included in this post (see below).

This was followed by an introduction to Juris-M by Patrick Allo from the Faculty of Law. Juris-M is a Zotero offshoot with extra features for law research and multilingual bibliographies.

During the next part, the participants had the chance to bring this new information into practice.  Everyone was assigned to a breakout room with a group leader. During the next hour Leah Budke, Nele Noppe, Patrick Allo and Rebecca Burke guided their group through some basic exercises in Zotero.  In preparation for this workshop, the researchers had been asked to gather a few sources to experiment with. These sources were used to test out the functionalities of Zotero, including how to import a reference with the Zotero browser plugin, how to create a bibliography, and more.

If you weren’t able to attend the workshop, you can still consult the documentation provided by Nele Noppe. Her presentation is available on Zenodo here. We also have a few blogposts on how to get started with Zotero. Here you can find part 1 and part 2. Keep an eye out on the blog for future Zotero workshops or check out the Kubic classroom sessions.

Plugin recommendations

Plugin recommendations from Nele Noppe and Patrick Allo 

• For everyone: ZotFile, which adds all sorts of handy PDF functionality to Zotero. If you notice that a PDF-related feature described in the presentation linked above doesn’t seem to appear in your Zotero, it’s probably because you don’t have ZotFile installed yet. 
• For those who work with a lot of PDFs that are not searchable because the PDF pages are just images, not text you can select: Zotero OCR, which performs optical character recognition on PDFs to make them searchable. Setup has a number of technical steps, but the instructions are very clear. 
• If you do your writing in a program that isn’t Microsoft Word: Zotero word processor plugins to cite Zotero items from a range of other programs.  
• If your writing program isn’t covered by a plugin: First, double-check the list of plugins to make sure there’s nothing that covers your situation. If there’s nothing, you can still use the plugin RTF/ODF Scan for Zotero to create a workaround and connect your favorite writing program with your Zotero library. 
• For those who currently have a big library of PDFs in a manual folder-based system and want to switch to Zotero: Zotero Folder Import 
• To quickly start bringing order to a Zotero library: Zotero Storage Scanner looks for missing attachments and duplicate items. 
• For people who want to use Zotero for note-taking: Better Notes has useful functionality for organizing your notes and visualizing connections between them.
• For those who want to apply simple but inspiring data visualizations to their Zotero library: Zotero Voyant Export connects Zotero with the Voyant visualization software. 
• If you work in LaTeX: Better BibTex for Zotero is for you. The plugin also enables integration with some additional writing programs, though we haven’t tested this.  

The first meeting of the spring 2022 edition of the DH Virtual Discussion Group for ECRs in Belgium kicked off on Monday 21 March with a presentation from Gianluca Valenti (University of Liège). We had a total of twenty attendees—some new faces and some familiar ones—who all contributed to an engaging conversation about digital humanities. 

This session followed our standard format, which opens with a greeting from the organizers, Julie M. Birkholz (KBR and Ghent University), Margherita Fantoli (KU Leuven), and Leah Budke (KU Leuven). This is followed by our networking session where new and returning attendees can introduce themselves in a small group, tell about their interests and experiences in DH, and get to know others in the community. This networking moment also allows those of us who already know each other to catch up and enjoy a coffee or tea before the main presentation starts and to welcome new members into our community. After the networking moment, the group comes back together to share any upcoming DH events or opportunities. The main event follows, when a member of our community gives us a behind-the-scenes look at a digital project, workflow, or tool. 

Gianluca’s “under-the-hood” presentation was titled “Modern Letters and Text Analysis: The ‘EpistolarITA’ Project” and discussed the importance of epistolary texts in historical research. As Gianluca explained, today there is a wealth of correspondence available to researchers, but we are still lacking adequate tools to engage with these materials to the fullest extent. The EpistolarITA project aims to fill this gap and to contribute to scholarly efforts to exploit historical epistolary texts through the development of the EpistolarITA database. The database brings together fifteenth through seventeenth century Italian letters and allows users to perform statistical analysis on this corpus. As Gianluca explained in his presentation, the database allows readers to compare a target text to the texts in the corpus. The database then has the capability to return similar texts, ranking them in order of their similarity. In order to be able to accomplish this, the algorithm uses a number of different techniques including TF-IDF, Word2Vec, and Named-Entity-Recognition. The advantage of using the database, as Gianluca demonstrated, is that it allows users to draw connections or to see patterns that they might not otherwise see. While the full text of letters is not made available due to copyright restrictions, users are still able to perform text analysis on these materials and to return results that they would otherwise not be able to achieve without many visits to the archives and the additional work that goes into creating the infrastructure which allows this type of text analysis.  

The EpistolarITA database is still in the process of being populated, but the official publication is expected this spring. For now, the project site and database is entirely in Italian, but they hope to make an English translation available in the future. 

If a look behind the scenes of a digital project sounds interesting to you, we would be delighted to have you join us for our next DH Virtual Discussion Group meeting on Monday 25 April from 15h-16h30 CEST! In this session, Montaine Denys from the Flanders Heritage Libraries will take us behind the scenes of the Flanders Heritage Libraries’ digitization projects. Montaine’s talk, titled “Managing the Evaluation of OCR Quality in Flemish Newspaper Collections,” will include a discussion of the project workflow, the creation of a “ground truth” dataset, interpreting results, and the specific challenges they have faced and the lessons they have learned while undertaking this project.  

To join us for this session or any future sessions all you need to do is register for our mailing list. Once registered, you will receive all future emails, including the links to the Zoom meetings. These links are distributed via email the morning of the event. 

The DH Virtual Discussion Group is designed to be a low-threshold way for researchers, particularly early career researchers, to come together and learn about digital humanities. Everyone is welcome to attend and absolutely no DH expertise is required. To see a full overview of this spring’s sessions, click here. If there is a session that seems of interest to you, please do join us!