Collaborative Annotation of 3D Crystallographic Models J. Hunter,* M. Henderson, and I. Khan The University of Queensland, St. Lucia, Queensland, Australia 4072 Received May 22, 2007 This paper describes the AnnoCryst systemsa tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues. INTRODUCTION Annotations have long been used as a tool to facilitate collaborative scholarly discourse. They enable users to attach additional information (such as comments, notes, queries, assessments, tags, and references) to electronic resources such as documents, images, or data sets and to share this information within their community. When applied to digital resources shared via the Web, they provide a very powerful collaborative toolsenabling the easy capture and wide dissemination of individual and group opinions of particular digital resources. The main focus of the work described in this paper is the development of an annotation system for 3D crystallographic and structural models for chemical compounds. The aim is to enable geographically distributed teams of crystallogra- phers and chemists to collaboratively discuss, compare, assess, and make comments on macromolecular crystal structuresseither before or after they have been published in public online databases. The long-term storage of this commentary on an annotation server provides a method for capturing group or peer knowledge and enabling its sharing and reuse. Such a framework is of significant interest to many communities (including protein crystallography and func- tional nanomaterials) in which uncertainty and debate exist over the precise 3D structure of a complex protein or compound or where there is significant interest in the ensuing biological implications of such structures. Critical to the adoption of such a system within a scientific community is the ability to authenticate the source of the annotation and to restrict access to a particular group of trusted colleagues. This is especially important in eScience 1 to protect intellectual property or maintain research com- petitiveness if the structure or functional description has not yet been published. In many cases, the annotation or interpretation of the 3D structure(s) may be more valuable than the target of the annotation. Our aim was to avoid reinventing the wheel by identifying existing relevant technologies and integrating, extending, and refining them in order to satisfy the requirements of this particular application. By building a prototype that works in a standard desktop Web browser and employs tools already in common use, we will lower the barrier to entry and ensure maximum usability and add value to the current infrastruc- ture. Hence, our implementation combines and extends the following existing open-source technologies which are based on open standards: • Jmol 2 - an open-source 3D crystallography model browser • Annotea 3 - a Web-based annotation server developed by the W3C as part of the Semantic Web initiative, which we have extended to support the annotation of structural features within crystallographic models • FOAF 4 - Semantic Web initiative for describing people and their network of relationships • Shibboleth 5 - an Internet2 middleware initiative that enables identity management and secure access to Web resources shared among a federation of organizations • XACML (eXtensible Access Control Markup Language) 6 - XML-based language for defining and enforcing access control policies This paper begins by describing the background of this work and identifying previous related efforts. We then describe an example scenario that illustrates how we envisage the system will be used. Following the example scenario, we describe the system’s architecture, implementation details, and user interface. Next, we present the results of the usability testing and system evaluation. Finally, we identify areas where further work is required and present our conclusions. * Corresponding author e-mail: j.hunter@uq.edu.au. 2475 J. Chem. Inf. Model. 2007, 47, 2475-2484 10.1021/ci700173y CCC: $37.00 © 2007 American Chemical Society Published on Web 09/28/2007