AA1: Crystallography Annotation Tool
Applying the semantic web to crystallographic research.
The Crystallography Annotation Tool was developed as part of the AA1 DART workpackage.
The main focus of this project is the development of a secure collaborative crystallography annotation system for collaborators within eResearch. An essential requirement for such a sector is the need to be able to authenticate the source of the annotation and to restrict access to a particular group of trusted colleagues - for reasons of privacy, confidentiality or protection of intellectual property. This is particularly important within eScience, where the annotation or interpretation of the raw document or data, is often more valuable than the target of the annotation. The Crystallography Annotation Tool extends protocols for annotating online resources such as web pages and multimedia content to support collaborative annotation and online discussion of 3D crystallographic models.
Features
Browse
Search and open 3D Models (CIF, XYZ, MOL, PDB) stored on the web, or in Fedora and SRB databases.
View
Using the embedded JMol browser, view and manipulate CIF, PDB and MOL files in 3D.
Annotate
Leave annotations with associated selections and viewpoints
Collaborate
Annotations are shared asynchronously and instantly.
Replies to existing annotations form conversation threads.
Compare
Make annotations that compare multiple models, selections and viewpoints
Secure
Secure your personal notes and share them with trusted colleagues through XACML policies through a Shibboleth Fedoration.
Semantic Search
Harness the semantic web to search on information stored beyond the immediate annotation, such as a user's workplace or academic resources related through free-form tags
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| Two model layout with sidebar (Win IE) | One model layout (Mac OS X, Firefox) |
System Architecture
Technologies
The Crystallography Annotation Tool combines and extends a number of existing open source technologies and open standards:
- Annotea: A web-based annotation server developed by the W3C as part of the Semantic Web initiative, which we have extended to support annotation of fine-grained contexts within 3D crystallographic models. (License: W3C)
- Semantic Web: Annotea links with FOAF, Creative Commons Licenses and Connotea bookmarks, in RDF.
- RSS feeds are discovered and made available through standard web browser techniques. Custom feeds can be specified in terms of a SPARQL query, allowing complex monitoring of annotated data.
- SPARQL: Query annotation database using the semantic search query language.
- Tags: By allowing free-form tags to be added on a per-annotation basis, we can draw automatic links into academic resources and websites stored in web services such as Connotea and del.icio.us.
- External Web APIs, such as Connotea and del.icio.us, are accessed to automatically discover relevant academic resources and websites. The link is made by allowing free-form tags to be specified on a per-annotation basis.
- Fedora and SRB repositories are accessed for the raw crystallographic data and 3D models. (Licenses: ECL, BSD)
- XSL stylesheets are used to transform raw Annotation RDF data into alternative, human browseable interfaces.
- DART Secure Annotea Server: allows end user control over who can create and access annotations, using XACML policies and Shibboleth.
- Secure Annotation Sidebar: A related project, DART AA2, has developed an Internet Explorer sidebar which we've made compatible with this application. Attach semantic annotations to geographical locations within the 3D model, and restrict access to them by specifying XACML policies.
- JMol (License: LGPL)
- Friend of a Friend (FOAF)
Annotations
Sample annotation created by the tool (described in RDF/XML)
The tool uses XSL stylesheets to transform annotations into three different views: a visual graph showing annotations and their replies; a tag cloud, showing frequency of tags added to annotations, and RSS feeds, for receiving notification of changes to annotations.
Annotation RSS Feed (viewed from NetNewsWire reader)
Software
To install the Crystallography Annotation Tool (cBrowser):
- Download the source code archive
- Unpack the archive, and copy the entire directory onto your PHP webserver
- Edit cBrowser/config.php.inc to update the URLs and relative local file paths. Instructions for modifying these paths are included as comments in the configuration file.
Demo
- View a step-through flash movie demo of the Crystallography Annotation Tool
- Login to the live demo system (requires username and password).