Annotea shared bookmarks: connecting lifescience research

Marja-Riitta Koivunen, PhD


In the real world, annotations and bookmarks are familiar, commonly used labels for attaching information to objects. They suit well to be used as an easy metaphor for creating and presenting Semantic Web content as in Semantic Web users also attach information to objects with meaningful labels. Different types of annotation or bookmark labels can be easily included to the metaphor.

Annotea [1, 6] has already demonstrated the use of the Semantic Web based annotation labels that users can select to subcribe from one or more annotation servers. Annotea shared bookmarks, based on the same technology, demonstrate the use of Semantic Web based bookmark labels.

Annotea shared bookmarks supports tools that help users including students, librarians and researchers to easily organize Web information by using concepts or categories that they are familiar with, or just starting to explore while benefitting from the underlying Semantic Web technologies. With Annotea shared bookmarks users can easily make connections to concepts used by their collaborative peer groups or to concepts agreed on in standard ontologies.

Shared bookmarks are especially interesting in the multidisciplinary lifesciences area, where researchers are typically not experts in computer science. They can greatly enhance collaboration by enabling connections and easy sharing across research areas and selected groups [7].

When shared bookmarks become commonly used they can help to create a network effect leading to new discoveries. In addition to bookmark sharing applications we hope to be able to see applications using bookmark repositories, such as data mining applications, services with user profiles, search engines and applications organizing blog type information.

Selected examples of usage

This demonstrates the use of the new Annotea shared bookmarks user interface in Mozilla, which we currently also call Ubimarks. We also have a simple interface in Amaya 8.6 which is demonstrated in CML scenario [7].

Figure 1, shows the basic Annotea shared bookmarks toolbar in Mozilla. It consists of the pagemarks icon and text that can be clicked to see the bookmarks that recall the current page, the quick button for creating a default bookmark and a related menu, a configure menu for configuring the default bookmark stores, and the default topics to be used with the quick bookmark. The toolbar also has a reservation for a search field planned to be used for searching bookmarks according to their topics or other information.

Pagemarks are bookmarks that recall the current page. They let the user know that this page is bookmarked by one or more users in the bookmark servers or files that the user subcribes. The pagemark icon in Figure 1 tells the user that the current page is bookmarked by himself or by some other users that subscribe the same bookmark stores. Other possible pagemark icons are shown on the right side of the image. The user has clicked the pagemark icon and opened a window that shows a list of all the bookmarks on this page. In this case there is only one, which is done by user marja.

Annotea shared bookmarks toolbar and a pagemark icon and text for having pagemarks
icon and text for page not having bookmarks
icon and text for page not having bookmarks

Figure 1: The Annotea shared bookmarks toolbar, selected pagemark icon and resulting pagemarkview, and list of possible pagemark icons.

The user can click the bookmark in the pagemark window to further examine the bookmark properties. As a result a bookmark window opens up showing the properties of the bookmark (see Figure 2).

In this view it is possible not only to get information of the bookmark properties but also to open up information about the topics and follow the related links to find related topics or other interesting documents. If the user follows the links to another bookmark, topic, or a collection of topics and bookmarks, they could be presented in a bookmark or a topic view or a bookmark hierarchy. It is also possible to present list of other properties found in the datasource even if they were not included in the bookmark definitions.

window presenting bookmark properties

Figure 2: Properties of a bookmark presented in a Bookmark view.

The bookmarks can be viewed in a topic hierarchy. This looks very similar to looking at the bookmarks or favorites folders. The menu related to creating the quick bookmark can open a window for showing the bookmarks in a topic hierarchy. The Annotea schema supports bookmarks that belong to several topics, which is not always the case with the traditional hierarchies or even Semantic Web based shared libraries, such as DMOZ [3]. Clicking on the bookmark opens the recalled page and clicking on the property icon shows the properties of the bookmark. Clicking on the topic always shows the topic properties right now. Figure 3 presents a sample RDF bookmark file containing a collection of bookmark and topic metadata.

bookmarks in topic hierarchy

Figure 3: Presenting bookmarks in a topic hierarchy

In the topic hierarchy the user can click the bookmark title to open the recalled page, or the properties icon to see the bookmark properties. Similarly, he or she can also click the topic to see the topic properties. When the user want to create a new bookmark or a topic, he or she can use the toolbar menu operations presented in Figure 1. According to the selection a bookmark or a topic window opens showing the default properties of the bookmark or a topic. The window showing the properties is similar to the one presented in Figure 2.


Annotea bookmark architecture

Figure 4: Annotea shared bookmarks use the basic Annotea architecture

Annotea shared bookmarks [5] uses the basic Annotea architecture [4]that we have already demonstrated for Annotea annotations. Like annotations, bookmarks and topics are RDF metadata [2] and collections of them can be stored on local bookmarks files or published on the Web. The Annotea server has also been prepared for storing bookmark and topic collections.

Annotea shared bookmarks aims to be flexible and extensible. It works with existing services and applications that provide unambiguous URIs for their concepts and elements and return a useful presentation based on the URI.


We currently have two implementations that can be demoed: one in Amaya 8.6 and and another one in Mozilla that is exploring the possibilities of the user interface. We are also developing a libAnnotea library to Mozilla that will help in implementing Annotea hopefully in other platforms as well.


Annotea shared bookmarks already offers an easy way for lifescience researchers to start sharing, connecting and organizing data in different databases from their selected viewpoints.

In the next phase we need some exploration of the how far we can to use the current standards and what additional standardization would be beneficial. Possible targets for standardization are the basic shared bookmark schemas, mapping mechanisms from Annotea topics to different category systems, and a the query language. We also need to solve the problems in addressing the bookmarks and topics [8].

When we extend the basic annotations, bookmarks, and topics we have a need for a user interface definition language that would support the creation and presentations of new types of bookmarks and annotations. It could be related to XUL type template rules and the rules we experimented with Annotea and Isaviz.


[1] Annotea home page,

[2] Koivunen, M., Swick, R., Kahan, J., and Prud'hommeaux, E. (2003) An Annotea Bookmark Schema,

[3] DMOZ home page,

[4] Kahan, J., Koivunen, M., Prud'Hommeaux, E., and Swick, R. (2001) Annotea: An Open RDF Infrastructure for Shared Web Annotations. In Proc. of the WWW10 International Conference, Hong Kong, May 2001

[5] Koivunen, M., Swick, R., and Prud'hommeaux, E. (2003) Annotea shared bookmarks. KCAP 2003 Knowledge Markup and Semantic Annotation workshop.

[6] Koivunen, M., and Prud'hommeaux, E. (2003) Annotea Review slides.

[7] Koivunen, M., (2003) Scenario: Organizing CML cancer research knowledge by using Annotea shared bookmarks.

[8] Prudhommeaux, E., and Koivunen, M. (2004) Identifying local and global resources in Annotea.

[9] Shiraishi, N. (2004) The RDF Trust Model Using RDF Bookmark and it's Application. In WWW2004 Workshop on Content Labeling -Technical and Socio-Cultural Challenges and Solutions.