Annotation Tutorial 1: Using Zotero Version 7

Two Crucial Academic Workflow Challenges

As an academic researcher, scholar, or student, you likely find yourself in a similar academic workflow. You collect, read, and annotate scholarly articles, research papers, and books as part of your daily routine. You then elaborate on this material in personal notes either during the annotation process or immediately afterward.

The next step in the academic workflow involves:

• Refine and structure the rough text passages.
• Incorporating feedback from peers or supervisors.
• Formatting them according to the publication guidelines.

These tasks can be undertaken individually or as part of a collaborative effort.

In this chain of timely delayed tasks, one always had to meet at least two challenges:

1. While reading and annotating, how do you know which passages would later be necessary for the final publication?
2. Are the annotations and notes sufficient to remember the context even after a long time?

These insecurities were still more cumbersome when one did not always have immediate access to the original material, such as when you lent a book from a library or the danger that the webpage could always disappear.

One counter strategy to meet these challenges is to be safe and collect as much material as possible. This includes saving all relevant resources, making detailed annotations, and systematically organizing them. But even then, finding the exact position of the text passage I was looking for took time and effort.

In response to these challenges, I will introduce a solution that significantly improves the efficiency of your academic workflow, particularly when you always have access to the PDF resource.

Annotations in Zotero

I started using Zotero on December 30, 2007—yes, during the holidays! I always use the holidays to learn new apps and try things out. My Zotero database currently holds 5872 items created during more than 15 years of research. Until last year, I mainly used Zotero to produce correct formatted citations for publication. However, these changed when I learned new note-taking possibilities emerged with Zotero 6 (March 2022). It took me over a year to transform my workflow. Old habits die hard.

Note 1: Zotero 7 update

This article focuses on the integration between Zotero and Obsidian. However, I will summarize some aspects of Zotero’s annotation process relevant to the export/import process to Obsidian.

During the planning & writing of this post Zotero 7, the most significant update in Zotero’s 18-year history was released. Almost finished with the article on August 18, I had utterly to revise the article to include the new features of version 7. Whenever it is sensible in explanations, I will either add the addition “(V7)” in parenthesis to emphasize the new features of Zotero 7 or write another note like this one for a more extended text passage.

---

Book recommendation

For those of you that are interested to learn more about the philosophy and theory of annotation, I recommend the book-length treatment “Annotation” by Remi Kalir & Antero Garcia (2021).

There is also a website were you not only can you read the book for free, but you can also see how annotations features are used for an open peer review process of the book (R. Kalir and Garcia 2020).

Definition 1

Here, I will understand under the term “annotation” every addition anchored to the text and reinforces it. Annotations are a kind of paratext, produced outside the text but constantly referring and tied to it.

Figure 1: Book cover of Annotation by Remi Kalir & Antero Garcia

---

Eight types of annotations in Zotero

Zotero 7 has eight different types of annotations: highlighted text, underlined text (V7), “sticky” notes, adding text (V7), screenshots, drawing, resp. Ink annotation (V7), comments and tags.

Figure 2: Six of the (eight) Zotero annotation types are selected with the menu in the horizontal bar of the middle pane visible whenever a PDF, EPUB-eBook or snapshot website is open

Note 2: Annotations for PDF, EPUBs, and Webpage Snapshots

With Zotero version 7, the following explanations are not only valid for PDFs but also for eBooks in EPUB format and for snapshots of web pages!

1. Highlighting

Figure 3: Zotero has eight colors for highlight and underline annotations

To highlight text, click the symbol with the letter ‘A’ surrounded by a box at the top toolbar. You have eight colors for highlights at your disposal: yellow, red, green, blue, purple, magenta, orange, and gray. You can set your preferred color as the default color, which is, in my case, yellow.

2. Underlining (V7)

Note 3: Underlining as a new annotation type

Version 7 of Zotero supports underlining text with the eight colors mentioned in Figure 3.

Zotero treats highlighting and underlining as being very similar to highlights. Therefore, I refer to both annotation types whenever I talk about highlighting.

It is crucial to design a consistent system when to use each color. This will allow you to organize your annotations in Obsidian.

Some people have developed a system of argumentation types to distinguish the different highlighting colors. Below are two examples to give you a flair for the idea.

Table 1: Two examples of color classifications for text highlights

Color	mgmeyers	My own system
Yellow	Relevant / important	Running text
Red	Disagree	Important: Concept, Definition,
Orange	Question / confusion	ToDo
Green	Agree	Resources: article/book/package/URL
Blue	Relevant to current task	(R) Code; Example
Magenta	TODO / follow up	Section
Purple	Definitions / concepts	Chapter
Gray	Interesting but not relevant	Figure / table title

Both examples stem from times before Zotero 7. Therefore, there is no difference, and both annotation types will translate to the same meaning. I will explain more about the purpose of an appropriate classification system when we talk about Obsidian templates for the import of the Zotero annotations.

3. “Sticky” notes

To add a “sticky” note, click on the piece of paper symbol with the earmark. Then, you can click on a place in the PDF to generate the note. A “sticky” note symbol appears on the page, and on the left bar, a note box open for writing comments. You can move the “sticky” note around inside the page, but you can’t move it to another page (therefore “sticky”).

The primary purpose of “sticky” notes is to add a text annotation that relates to the text but not to a specific passage of the text. This can be, for instance, a comment on the structure of the text, a comment related to several paragraphs, a recurring argument, etc.

4. Text (V7)

With version 7, you can also write text directly into the document as an overlay. Zotero treats this as a comment, e.g., add tags or change the note text. But this annotation type is eye-catching, and you can move it around, but only on the same page.

5. Snapshots

By clicking on the black box surrounded by a rectangular selection, you can drag with the cursor to select the area of the screen to capture. You can add comments and tags as in the other annotation types, but you can also copy the picture or save it as a PNG file to your disk.

6. Drawings (V7)

Your pointing device (mouse, stylus, touchscreen) will be converted to a drawing device by clicking the ink button (with the drawing symbol). Selected the appropriate color, you can now create drawings overlaying the document.

7. Comments

You can add additional text to all types of annotations mentioned so far. Zotero will treat this additional text as your comment.

Warning 1: Changing highlighted text via the note?

Strange enough, You can also edit the highlighted text stored as annotation. Frankly, I do not know appropriate use cases because, with these changes, you would temper the original quote.

8. Tags

Another way to annotate a document is to add tags to highlighted text, “sticky” notes, screenshots, or comments.

You can select all annotations with the same tag inside the document (e.g., whenever the document is open and visible in the middle pane). Colors work as a tag, too. Hence, you can select all highlighted text in the same color. You can also combine different tags. For instance, two text tags with two colors will select all annotations that have one of these text tags or one of the chosen colors.

Outside the document, the tag works as a standard document tag in the tag pane at the bottom of the left column. Although the tags are attached to specific annotations outside the PDF (e.g., in the tag pane), they will select only the Zotero item with the document where the tag was used and not the appropriate annotations. But if you use the same tag for annotation in different documents, Zotero will open all items where these tags were applied.

We will see that after the export to Obsidian, these annotated tags gain power as the work across all Obsidian documents!

Summary

The Zotero documentation is not yet up-to-date, so detailed information is still lacking or incorrect. For instance, is The Zotero PDF Reader and Note Editor talking only about the PDF reader (version 6). The best page so far is the announcement page Zotero 7: Zotero, redesigned. However, many YouTube tutorials will explain the details of Zotero version 7 in several weeks.

In the meantime, the following annotated screenshot may be helpful. It recapitulates graphically the above textual description.

Figure 4: Screenshot of Zotero Reader and Note Editor with explanations of the graphical user interface (GUI). Click on the image to enlarge it.

References

Kalir, Remi H., and Antero Garcia. 2021. Annotation. Annotated Edition. Cambridge, Massachusetts: The MIT Press.

Kalir, Remi, and Antero Garcia. 2020. “Annotation [Annoted Website].” https://mitpressonpubpub.mitpress.mit.edu/annotation.