Collaborative Annotation of 3D Crystallographic Models

Abstract

This paper describes the AnnoCryst systema 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.

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

“…Todor132 surveys a range of use cases in his presentation: ‘Semantic Linked Data Integration for Chemical eScience’. Hunter et al133 have focused on the annotation of 3D crystallographic models, essentially a form of curation. The main tool they use for their AnnoCryst system is Annotea, which is a W3C Semantic Web project that uses RDF schema 134.…”

Resource description framework technologies in chemistry

“…Frey implemented a system which would now be referred to as an electronic lab notebook (ELN) [3]. The use of the SPARQL query language goes back to 2007 where it was used in a system to annotate crystal structures [4]. …”

Supporting Multiple Perspectives on 3D Museum Artefacts through Interoperable Annotations

“…Most prior work in the field of 3D annotations has focused on the annotation of discipline-specific objects -for example, architectural and engineering CAD drawings [7,8], 3D crystallography models [26] and 3D scenes [27]. All of these systems enable users to attach annotations to 3D models and to browse annotations added by others, asynchronously.…”