Productive Scholar: Ben Johnston on New Annotation Tools for Scholars

A small pad of Post-It notes.

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This session looked at current and future methods of annotating and analyzing text and multimedia materials for scholarly work.  From the bookmarking and annotation of webpages, to commenting Word documents for review, and the marking up of XML versions of manuscripts, annotation can take many different forms and be used in many different ways.

Reflecting on experiences of a pilot project undertaken as part of an NEH grant proposal working with a very large 19th Century manuscript, Ben Johnston presented a survey of tools available for annotation including Microsoft Word, Zotero, Pliny, blogs, wikis and also looked work currently being done through a group called Open Annotation Collaboration to standardize and explore the use of annotation in scholarly practice.

What is annotation?

Ben Johnston believes that scholarly annotation should go beyond post-its and marginal notation. In his Productive Scholar talk, Johnston said that physical ink-on-paper note-taking is traditionally the most common way that annotation is done. Post-its, those little multicolored sticky notes, are portable, stable, and  work well for one book and one person. New digital tools extend the scope and capability of annotation. Johnston asked “what if I want to use a single note in multiple books” or “move it to other places and other contexts?” In this case, he argues, post-its are limited in their capability. Newer tools such as mind-mapping applications, wikis, and shared databases, for instance, connect different ideas, often with contextual notes on those connections..

Johnston began to define what annotation is, and the ways in which it can be more or less effective. Twitter posts about Hamlet or Macbeth, for example, may be annotation on those topics, but they might not offer constructive or beneficial content adding to the scholarly discussion. More traditional methods, such as writing a scholarly journal article, is often an  extended form of annotation. An article that describes central themes in Macbeth and categorically compares them to themes in a contemporary story is an example of this. Annotation can also simply be the end-notes, footnotes and comments that you add to a document in Microsoft Word or Open Office. Johnston explained that deep reading, in which one writes notes in and adds comments to a textbook in order to record personal understanding and interpretation, is a very common form of annotation for students, but potentially compacts the experience for the next scholar reading (and annotating) that book. All of these methods are able to be done electronically, but can still fail on some key scholarly activities, such as sharing and allowing for continued discussion.

Scholarly skill sets

People who research and define the important skill sets for scholarly work often find annotation in the short list of those skills. In May of 2000, John Unsworth (University of Illinois, Urbana-Champaign) proposed the idea of Scholarly Primitives, eight basic functions common to scholarly activity across disciplines. They are discovering, comparing, sampling, representing, annotation, referring, and illustrating. He chose them as a way of assessing the common threads of scholarly activity in the humanities, and how scholarly tools might be best used to focus on these primitives. Tools or workflows that allow scholars to achieve more of these tasks in a streamlined, cohesive way are potentially more useful than those that do not. (

Other groups have discovered a more condensed toolset and have included annotation (ideologically) within other terms. Project Bamboo is:

“a multi-institutional, interdisciplinary effort that brings together humanities scholars, librarians, and information technologists to tackle the question: ’How can we advance arts and humanities research through the development of shared technology services?’” (
They have developed some slightly different primitives. Scholars now discover, gather, create, and share. Gathering and creation is primarily where annotation happens in their framework, though discovery supports it and sharing extends it. Notably, create and share are missing from Unsworth’s ideas, possibly because the increased ability to share has become more common in the last ten years due to web 2.0, social media and other technology platforms. Project Bamboo works to solve problems that have emerged along with these new capabilities. They ask the questions “How do we most effectively facilitate and discuss the scholarly process in the contemporary digital style”” and ”how do we get faculty members, scholars, and  IT people to work together to provide platforms to discuss what happens in scholarly practice?” New tools for scholarly annotation begin to answer these questions.

New tools

Some of the digital tools that help scholars to discover, gather, create, and share with annotation are much more than simply virtual post-it notes, but others are just that.

Fleck was an example of a service that allowed you to create post-its on web sites and share them with others. It is no longer in business as an annotation service, but now develops games about battling zombies. (

Annotate it ( allows you to use a bookmarklet (a small javascript that you keep in your bookmarks) to save annotations about sites that you are visiting. It saves annotations using a centralized server, which can be locally installed, or hosted by the developer. You can highlight some portion of a page and create an annotation, and you can tag it with metadata. Then, other AnnotateIt users get to see your notes and tags and (hopefully) benefit from them.

You can use Google Earth to overlay historical images on top of a particular area, then add notes and pins to denote metadata about specific locations. You might use it in order to dissect the progression of a famous battle or talk about urban sprawl over time.

Video annotation tools are coming, but are still fairly immature., for example, allows for annotations, but those annotations are neither listable nor searchable, and you must own the video in order to annotate it. You also can not use the annotations in order to navigate the video. In VideoANT, a project from the University of Minnesota, you can import your video, then pause and annotate it. You can then share those annotations with students or peers.

Professor Herbert Ginsburg at Teachers College in collaboration with the Columbia Center for New Media Teaching and Learnin (CCNMTL) helped to create a system called Video Interactions for Teaching and Learning (VITAL), which is described as follows:

VITAL comprises tools for editing and annotating video and for writing “multimedia essays” with text and video, embedded in an online course syllabus, and housed within a community space where instructors and peers can review work published within the system and build up a personal repository of video and written content. Students who use VITAL learn to observe closely, interpret what they see, and develop arguments using cited video content as evidence. (
DigressIt, which used to be known as CommentPress, is a plugin for the open source content management system (CMS) called WordPress. It allows you to create a post, and break the text up into paragraphs, then select the paragraph to add comments per paragraph. Typically you could comment on the site itself, or on an individual post, but this tool adds a level of granularity that makes commenting potentially useful for scholars.

Johnston says that Microsoft Word, Scrivener, Open Office, Adobe Acrobat, and Google Docs all allow you to annotate and discover commentary, but that the trouble lies with searching the comments, footnotes, endnotes, references, and so on. For deep reading, and pulling text apart in order to discover deep connections, these are limited tools for the job.


New tools have been created to help you to more effectively gather (one of the Bamboo Project’s key scholarly activities) and annotate the gathered data. Zotero, for instance, is a browser plugin and local database that quickly provides references, citations, PDFs, and more from online newspapers, journals and databases that provide that metadata. You can then create relevant collections of those sources. It allows for annotation and commenting, and creates a snapshot of the content so that you can use it even if the online source disappears. A central server allows for sharing collections with colleagues and students.

Endnote is a citation management database with a long list of fields you can populate, and you can leave metadata tags on your notes. However, Johnston notes that Endnote is not as powerful for sharing data as Zotero is.

Johnston describes Mendeley as iTunes for PDF documents. It extracts information such as  author, title, and date from PDFs, which you can then sort and filter. It allows you to open, highlight, comment, and search comments in a PDF. Johnston says Qiqqa is just like Mendeley, though he really likes the name and the developer’s interest in improving your productivity. According to the developer, the application “makes you work qiqqa”.


One definition of a wiki is that it is an ecosystem of related documents. Wikis can be collections and interconnections of anything, including annotations. OneNote, which comes with the Microsoft Office suite, is a note taking tool, but also a kind of wiki. In OneNote, You can create a note, link it to other notes, and you can end up with a forest of interrelated notes.

Tomboy, an open source, cross-platform desktop wiki, allows you to create notes, highlight text within notes, link notes to other notes. It allows you to search for those items, as well as create a note that follows certain terms that you denote, such as names of characters in stories you are dissecting. Johnston said that Tomboy is a powerful tool to follow specific terms and content throughout a highly complex set of notes. You can even categorize the notes with folders. Simplicity is Tomboy’s best benefit for scholars, says Johnston.

Nvivo is an example of especially useful software for use in the social sciences for transcribing interviews, and coding responses. It comes at a price of $700, which could be a barrier, but makes codes (akin to tags) applicable to any part of the text.

Pliny, a java based desktop wiki developed at Oxford, allows you to import images, PDFs, text, and create notes about their content. It includes a web browser to create notes about web content. You can highlight a section of text on a page, and make an associated note. Then you can bring those notes up in an interconnected mind-map view, and name associations between notes.

New directions in annotation

The University of Illinois at Urbana Champaign has an Open Annotation Collaboration project ( that is working on expanding the idea of annotation on the web. The group believes that when you create an annotation, it should be available for others to use to create a semantic web, or an interconnected, openly accessible, searchable, navigable group of organized content.  In order to do this, every bit of information, rather than entire pages or sites, should have its own finite location, such as a Universal Resource Locator (URL), on the web. They feel that bits of information should cross boundaries, and be connected, searchable and available. They are focused on the goal of sharing annotation, using open and common web standards, such as RDF and URLs, creating this semantic web.

The Open Annotation Collaboration project has a specific definition of what an annotation should contain, including fields for event, title, author, expression, target, and time. They also feel that annotations can and should be of any media type, and support multiple targets and structured relationships. Annotations should also be searchable and discoverable, according to the group.


Johnston shared his understanding of what annotation is and is not, and talked about the limitations of traditional methods such as note-taking as compared to new methods that allow for centralization, sharing, and collaborative editing. His problem with the post-it is not in its simplicity or stability, but in its physical limits, keeping a single note from being shared in two articles, for example. A short review of scholarly activities shows the importance of annotation, but also the importance of the discovery, gathering and sharing aspects of scholarly work.  Tools like Zotero, Mendelay, and wikis allow you to quickly collect annotation data, craft omnimedia bibliographic entries in your expertise, and share those collections with others in just a few clicks. Very often the same kind of work is being done with more traditional methods. With newer tools, which potentially increase scholarly productivity, more attention can be paid to the beneficial outcomes of good annotation: understanding, teaching, learning, and sharing knowledge.

The presentation from this presentation is available here.


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