AnnoConnotea

© Pierre Lindenbaum PhD 2005
This software was created with the help of Ben Lund from Nature Publishing Group.


Get AnnoConnotea *.war file

About AnnoConnotea

Annotea is a project from w3C used to create and share annotations on an 'annotea server'.
Annozilla is a Firefox extension called annozilla which looks in one or more annotea servers to search any already existing annotations about the site you are currenlty browsing.
Connotea is a free online reference management service. It allows you to save links to all your favourite articles, references, websites and other online resources with one click. Connotea is also a social bookmarking tool, so you can view other people's collections to discover new, interesting content.
AnnoConnotea acts as a bridge between Connotea and Annozilla allowing scientist to see and share comments about a web site/ a paper. It can also be used to send a new bookmark to Connotea

Forewords

I had the chance to test the Connotea API developped by Ben Lund & Al. and I decided to use Annozilla as a kind of proof-of-concept for this API (it works !... ). Nevertheless, I also discovered that annozilla does not use the parameters in an URL for security reasons. In other words if you want to share a comment about this paper:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11934909
then, the bookmark stored in connotea will only be
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi.
Hum... not really intersting :-(. I asked people of the annozilla-project to be able to turn on/off this feature and I hope AnnoConnotea could be a good reason to create this option.
Another point: at this time, the API doesn't allow to fetch the COMMENTS written by the connotea users.

Server Installation

You'll need an apache-tomcat web server. The WAR file is available [HERE]. This archive also contains the source code of the program. I'm not an expert of apache-tomcat but AFAIK, installing this archive in something like .../tomcat/base/webapps/ should be sufficient to run the servlet.

Client Installation

get Firefox 1.5 : Get Firefox!

Install Annozilla Extensions

In firefox: Tools -> Extension -> Annozilla -> Preferences -> Server Options -> Edit Server Options: Add the address of the tomcat-servlet where AnnoConnotea was installed. The login and the password MUST be the same as the one used on www.connotea.org.
In Viewing Option you can add your name and specify Automatically Load Annotation: always.


In firefox: use View->SideBar->Annozilla to show the annozilla panel.

Using AnnoConnotea

In this example: firefox opened the NCBI home page (right side). Once the page is loaded, annozilla fetches the bookmarks about NCBI from connotea (top left). Double clicking in the annotations makes annozilla download the body of those bookmarks (bottom left).

Adding Annotation: annotation are created by clicking the right button of your mouse. There is no use to add style (italic, bold) in your annotation.