A.nnotate and Pliny

Learning, study and research tools for the digital age

By Robyn O. Berland

Annotating a page with A.nnotate.

Annotating a page with A.nnotate.

This article is the first in a series that looks at digital tools that have been designed to facilitate scholarship by helping us navigate, study, organize, derive meaning from and share the massive and ever-increasing amount of digital content — primary and secondary source materials — that is distributed via the Internet, bringing together digital content with non-digital content through the process of digitization. It’s about managing information, but also about staying digital and being green, since by reducing our need to print, we reduce printing costs and the impact printing has on the environment.

Paper or Digital?

Students routinely search masses of scholarly content now digitized for distribution on the Internet, and download course materials through NYU’s learning management systems. The Gutenberg Project (gutenberg.org) alone currently offers approximately 30,000 book titles and — with Gutenberg partners, affiliates, and sister projects — a total of 100,000 public domain books for download, free of charge. The NYU Libraries provides a digital portal to thousands of article databases, e-journals, e-books, documents, and more. And the NYU Bookstores now offer e-textbooks and plan to expand their digital inventory.

The genre of technologies for education known as Learning Management Systems (LMS), such as Blackboard and ALEX, have made access to course materials — presentations, articles, images, e-books, etc. — just as easy. For those materials licensed by NYU, the linking service (library.nyu.edu/services/reserves_faculty.html) is a convenient way to post links to materials to students who are enrolled in NYU courses. Where NYU does not hold the copyright and does not license the material, the NYU bookstore partners with vendors and publishers to provide resources in electronic format to students (www.bookstores.nyu.edu/faculty.services/course.packs.html). Where faculty own the copyright to materials or they are in the public domain, they may choose to post it online in the LMS. Each student decides whether to read and study a document on his or her computer or mobile device, or convert it to a paper format where appropriate.

Many of us convert digital documents to paper because paper allows us to interact with the content: we highlight, write comments and notes in the margins, bend the corners to bookmark locations, and share our notes with others. This is a comfortable and active way to read, analyze, and derive meaning from the content. Maryanne Wolf, a developmental psychologist at Tufts University, believes we are how we read. She worries that in the “Google universe…when information is given almost simultaneously, as it is in digital presentations, is there either sufficient time or sufficient motivation to process the information more inferentially, analytically, and critically?”1 The deep reading required for interpreting textual content relies on focused and active engagement.

Can technology provide tools to facilitate this physical and cognitive process, even if it cannot replace, in the short term, the comfort of working with a non-reflective, bendable sheet of paper? Collaborative annotation and digital annotation tools are in their early stages of development. Some tools are delivered as desktop applications, others through the Web, and still others are hybrids using a desktop application with a web-based component. Textbooks are just beginning to be offered in digitized forms by publishers who in some cases are bundling their e-textbooks with collaborative annotation tools.

The tools described in this series are freely available and can be downloaded from the web. Some are more fully developed than others, some focus on individual scholarship, while others provide simple annotation and collaboration tools. Many are cross-platform. This is a rapidly changing domain, and I hope to continue writing about these tools as they become available and as existing tools mature. The current article will focus on A.nnotate and Pliny.


The A.nnotate Home index page.

The A.nnotate Home index page.

A.nnotate (a.nnotate.com) is a web-based annotation and collaboration service. A.nnotate runs in your web browser — “in the cloud,” as Internet-delivered, remote-server-based services are sometimes described. Supported web browsers are Firefox and IE 6, 7, and 8 for Windows; Firefox and Safari for Mac OS X; and Firefox for Linux. In all cases, Javascript and cookies must be enabled.

The benefit of working “in the cloud” is that your work is available to you from wherever you are. You simply need a networked device to access A.nnotate. The downside is that your productivity will be affected should you happen to be working from a location where bandwidth is poor or you don’t have Internet access, or if for some reason the A.nnotate server is unavailable.

The annotation tools in A.nnotate can increase your engagement with the research and course materials you are studying, by allowing you to markup the material as you would with a paper-based equivalent. Of equal, if not greater utility, is that A.nnotate has built-in collaboration tools that enable a shared work environment. Email notifications keep everyone in the group in the loop about the latest modifications to a document and/or a shared folder.

Before using A.nnotate, you must set up an individual account. The free-service-level account allows you to upload approximately 30 pages per month. Once documents have been uploaded, they can be shared. A.nnotate promises that your email address and the documents you upload will be kept private. Once you enter your email address and click the “Login or Register” button, A.nnotate confirms your identity by sending a confirmation email to the email address you entered. For a fee, A.nnotate supports group accounts and an enterprise installation of the service.

The Dashboard

When you log in to A.nnotate, you see the blog-like Home index page. It is an overview of your current activities, as well as those of your collaborators. It contains a list of any collaboration invitations that require a response, the latest notes and documents that you and others have added, as well as notifications of changes to documents that you and your team have made. You will notice the “Email Notifications are off” message on the top left portion of the page. Make sure you’ve turned this feature on if you want to be notified of changes.

Document Management

A.nnotate's Documents index page.

A.nnotate’s Documents index page.

You must upload your documents to the A.nnotate server before you can apply annotations or share the document with others. All your files are stored on the A.nnotate remote server. A.nnotate recognizes PDF, MS Word (.doc, .docx), MS Excel (.xls, .xlsx), Powerpoint (.ppt, .pptx), OpenOffice documents and spreadsheets (odt, odp), Rich Text Format (.rtf), and Image (.jpg, .gif, .png) files. Web pages can be captured for annotation using a built-in snapshot function, which can be added to your web browser’s Bookmarks toolbar for quick and easy web page capture. All uploaded files are converted to a proprietary format that supports online annotation.

The Documents index page provides document management and organization tools. To upload a new document or to take a snapshot of a web page click the Upload… or Snapshot buttons, respectively. Files can also be uploaded to the A.nnotate server by attaching the document to an email addressed to cc@nnotate.com from the email address you registered. This tells A.nnotate which account owns the document. Documents may be organized into a typical hierarchical folder system. It is possible to view a detailed list of folders and subfolders or view the documents as thumbnails. You can apply Tags to documents and notes to provide enhanced organization and search capabilities. Tags can be used to establish a standard nomenclature for individual or group use. Clicking any one of your documents in the Documents index view will open the document in annotation mode.

You can download your documents as PDF files with or without annotations. Doing so is a good backup strategy.

Annotation Tools

Your notes are attached to selected text. You can highlight, strike through, insert text, or add a live URL reference to the selected text. Each note contains the name of the author, the date, and the time it was created. Images can be annotated with rectangular and dotted oval regions. Annotations can be color-coded to connote specific meaning. The controls in the upper-right-hand corner allow you to navigate among notes, change the way notes are displayed (floating above the selected text, placed in the right hand margins of the document, or inserted as a footnote), see a list of notes, or send email invitations to collaborators. To upload a document and allow several people to collaborate, simply email the document as an attachment and send the message to cc@nnotate.com. A.nnotate will store the document in your account and send an email to each recipient with a personalized link.

Notes Management

The Notes index page is a list of notes that have been attached to documents you own or those on which you are collaborating. Each note contains a reference to the location of the note. You may search across documents by the type of note or document, by tags associated with the note, and by other parameters, as well. Notes can be listed by date, subject, tag, or document. Each note in the list can be opened to display the note’s context and content. The list of notes can be exported as a CSV file and imported into a spreadsheet application.


The Pliny interface

The Pliny interface

Pliny (pliny.cch.kcl.ac.uk) is a cross-platform study and research tool designed to facilitate your note taking as you read through both digital and non-digital research and course materials. Although part of a larger Open Source project of the same name that aims to promote the development of tools that support scholarship in the Humanities, Pliny is useful across the range of disciplines. The project takes its name from Pliny the Elder (23 – 79 AD), a Roman historian and notorious note taker.

Pliny is a discrete desktop application; that is, the software runs on your computer, and all the notes and annotations you make using Pliny are stored on your computer’s hard drive. One of the advantages of using a desktop application, rather than a web-based tool, is that you can associate your notes with collections of digital and analog source materials that are both web-based and locally stored. Images, web pages, PDFs, and non-digital readings can all be annotated and then organized within Pliny. Pliny helps you manage your collection of notes and organize them into a coherent interpretative model, using several different paradigms to build a visual presentation in a two dimensional space, allowing categories and their associations to emerge. What follows is a basic overview of Pliny’s functionality. I encourage you to visit the Pliny website, download and install the desktop application, and try it out. The documentation and tutorials are well developed, if not perfect. Pliny’s system requirements are Macintosh OS X, with a Java Runtime Environment 1.5 or higher; or all Windows OS versions with Java 1.4.2 or higher installed (java.com). Links to the appropriate Java software are also available on the Pliny site.

Note-Taking with Web-Based Materials

The power of Pliny is that it integrates your notes with the web-based materials you are studying. Pliny’s embedded web browser navigates to and displays web pages using a browser already installed on your computer (Safari, Firefox, Internet Explorer).

Web Browser & Reference Area

Launch Pliny, and click the Browser icon on Pliny’s Main Toolbar to start Pliny’s embedded web browser. The browser works as any conventional browser does. You can key in URLs or drag-and-drop them from another browser’s Location field; active links can be used to navigate through the material; you can move forward and backward through the web pages, and so on.

Pliny’s Reference Area is linked to the web page that the embedded browser is displaying. Any notes that you place in the Reference Area are permanently linked to the web page that is being displayed, so that each time you return to the web page, these linked notes will show up in your Reference area. This is very similar to the way in which we use the margins of a printed document to record notes. But the Reference Area is also a two-dimensional expandable space that allows notes to be positioned and repositioned, based on their associations with and significance to other notes that you take over the course of your study. This provides a far more dynamic note-taking space than the margins of a book.

Creating Notes

Use Bookmarking in Pliny's Resource Explorerto create a quick reference of all PDFs one-learning you have read

Use Bookmarking in Pliny’s Resource Explorer
to create a quick reference of all PDFs on
e-learning you have read

To create a note, click the New Note icon in the Reference Toolbar and place your cursor in the Reference Area. The cursor will transform into a new note icon. You may place the note anywhere in the reference area. Hold your mouse button down, and drag the mouse to define a small area from top left to bottom right until the area is the desired size. This creates a note reference object, which has two pieces of information associated with it: a title and textual content. By default, Pliny creates a note title based on the title of the current web page, but you can replace it with a meaningful title, which may prove useful later in the study process, when you are organizing your notes to develop your understanding of the text.

The textual content can be anything you feel is relevant — references to other readings or a portion of the text itself, for example.

Unfortunately, Pliny cannot markup a web page in the traditional sense; since its web browser does not tell Pliny where the text is located on the screen, reference objects cannot be attached to specific text. To compensate, you can capture text from the web page by selecting it and then dragging the selected area into the Reference Pane, which will create a new note that contains the selected text. Drag and drop works from any application on your computer that supports this function. Text from Microsoft Word documents, for example, can be dragged and dropped into the Reference Pane, creating a new note.

Managing Notes

Managing notes is a relatively easy process. Each note is called a reference object and is modifiable. For example, to change the title and content areas of a note, you simply double-click the Note title bar and the Content area, respectively, and type in the desired text. In addition, notes and other reference objects can be:

  • Resized by dragging any of the eight handles on the bounding box.
  • Minimized by clicking the Minimize/Maximize icon on the Note title bar.
  • Moved by placing your cursor on the Note title bar and dragging the object to the desired location to create relationships between notes.
  • Deleted by selecting the note(s) and choosing Delete from the Edit menu.
  • Connected to other reference objects to indicate immediate associations by drawing a line between the objects. To connect two objects click the Connection icon, then place the cursor inside one reference object and drag the cursor (mouse down) to the other object releasing the mouse button. In addition, use the Type Manager tool to establish color codes for different sets of notes and connectors.

Resource Explorer

The Resource Explorer keeps track of all the resources Pliny can display. These are organized by resource type in a hierarchical folder structure: Notes, Web Pages, Images, PDF/Acrobat, and My Bookmarks.

When you create a note associated with a web page in the Reference Area, Pliny creates two resource folders: one for the note and the other for the web page that contains it. The Resource Explorer displays a note’s title, not its content (which is one reason why using meaningful titles can be helpful). Resource folders are listed alphabetically, based on the title of the note(s), along with a number indicating how many notes it contains. Figure 7 illustrates the alphabetical organization of resources and the numeric note counter. The Resource Explorer is a live reference and navigation tool, and notes and web pages referenced within it can be viewed and managed. As you add notes to the Reference Pane, they are simultaneously added to the Resource Explorer.

Annotating PDF Files

Pliny contains an embedded Annotation tool that works with PDF documents. To annotate PDFs, you must first import them into Pliny and associate the Annotation tool with the document. Pliny treats each page of a PDF as an image. The PDF is stored on your computer and opened with Pliny’s embedded PDF viewer.

Importing a PDF

There are three ways you can import a PDF.

  • If the PDF file is on your computer, drag its icon to the PDF/Acrobat folder in Pliny’s Resource Explorer, or open the file in your web browser and drag the URL to the Pliny’s PDF/Acrobat folder.
  • To import a PDF file that you are viewing in an external Web Browser, drag the URL to Pliny’s PDF/Acrobat folder.
  • To import a PDF file you are viewing in Pliny’s embedded web browser, drag the Source Object to Pliny’s PDF/Acrobat folder.

Your PDF is now an available resource within the Resource Explorer. Pliny uses the filename for the name of the resource. You can modify the name to reflect the title of the document. In Figure 7 the “Heiland Gothic Monsters” document has been renamed “UncannyMontersMaryShelly.”

The PDF Viewer

When the PDF Viewer launches, it modifies Pliny’s interface to include the PDF Viewer’s annotation and navigation tools (Figure 8).

The PDF Viewer has two toolbars. The Navigation Toolbar helps you navigate through the PDF pages, much as you would a CD player. You can view a PDF one page at a time, move forward or back, jump to the first page or the last, or skip through the document ten pages at a time. The Annotation Toolbar (see Figure 8) includes annotation and note-making tools. To add an annotation, click the New Annotation tool. Drag your cursor over the area in the PDF you wish to annotate. You have created an annotation with a note. The annotation and note are recorded in Pliny’s Resource Explorer and can be used to navigate to the annotated text. Use the New Anchor tool to outline a block of text.

You can create a quick reference list of the PDFs you have read and annotated by creating a Readings note folder in the Resource Explorer, and then dragging the source object tool to the Readings folder for each page you want referenced. These newly created references are active and can be used to navigate to each of the referenced pages.

Annotating Images

Importing an image and its meta data from a web page into Pliny

Importing an image from a web page into Pliny

As with web pages and PDF files, images must be imported into Pliny and stored on your computer’s hard drive before they can be annotated. The three methods used to import images into Pliny mirror those used to import PDFs and web pages. When importing images from a web page, Pliny will actually import all the images it finds on the page. Images you do not want can be deleted using Pliny’s Resource Explorer.

Pliny creates an Image resource for each of the imported images (Figure 10). Pliny uses the title of the web page in naming the image resource. Two other resources associated with the image are created, a green-bannered note that contains all the text found on the html page and a blue-bannered reference to the original web page from which the image was imported. The note and banner can be deleted or repositioned, and the note’s text modified. Even the name of the resource can be modified.

In addition to the image resource, Pliny creates two other associated resources: a web page resource that refers to the source page of the image and a note resource that contains the text of the html page (green-bannered note). Both can be edited.

Annotating an Image

The Annotation Toolbar is the same toolbar used to annotate PDFs. To add an annotation, click the New Annotation button. Drag your cursor over the area in the image you wish to annotate. You have created an annotation with a note. The annotation and note are recorded in Pliny’s Resource Explorer and can be used to navigate back to the annotation. Use the New Anchor and New Note tools to associate additional annotations with the image.

Managing Images

The Resource Explorer can be used to manage image resources. In the usual sense, image resources can be edited, deleted, and used as a navigation tool. Creating a meaningful organization of images may be helpful as your collection grows.

The following illustrates how one might use Pliny to organize images – in this example, images of art objects depicting battle scenes. To begin, create a new note using the New Note button in Pliny’s Resource Explorer. Name the Note “My Images.” Now create a category “Battle Scenes” that will hold all references to images that depict battle scenes. Open the Battle Scenes note and drag the Image reference of the “Battle of Carthage …” to the Battle Scenes note. You have now created a folder to hold your readings and another to hold your images. You can continue to use Pliny to organize your collection of materials. The power of this tool is in its flexibility to organize material in multiple ways that reflect your growing mastery of the material.

Pliny’s current use as an individual research tool does not exclude the possibility that a collaborative suite of tools will be developed and integrated into Pliny. The Pliny project and its associated Eclipse platform are built on a plug-in model, and a plug-in that adds collaboration tools to Pliny may be on some programmer’s radar. John Bradley, a Senior Analyst for Humanities Computing at King’s College London, is the developer of Pliny, the Pliny Project, and the Eclipse Platform.

To learn more about Pliny, or to contact its developer, go to pliny.cch.kcl.ac.uk/index.html

In future articles, I plan to write about CaféScribe, an eTextBook distribution service used by the NYU Bookstores, which offers a hybrid environment combining a desktop application with web-based tools. I also plan to cover Zotaro and Reformit, both of which are Firefox plug-ins, as well as other “green” study and collaboration tools that may appear on the horizon.

(For an overview of another tool that might help you organize your digital scholarly notes and materials, see Atlas.ti: Using QDA software to manage & analyze your research materials, also in this issue of Connect.)


  1. Maryanne Wolf. Proust and the Squid: The Story and Science of the Reading Brain. Harper Perennial, 2007, p. 16. Maryanne Wolf is a Professor in the Eliot-Pearson Department of Child Development at Tufts University, where she holds the Hohn DiBiaggio Chair in Citizenship and Public Service and is the Director of the Center for Reading and Language Reasearch.