Techriti

First prototype !

Well a lot of things have happened since the last post.

I started with setting up a local server for Wikipathways on my laptop. That took roughly a week with all those attempts to debug those error messages in the Pathvisio applet n having to study the documentation for Ant and Apache derby which are required for setting up the Pathvisio applet and the synonym database respectively....

Then another milestone was coding a REST client for accessing the REST API of BioPortal for fetching n traversing the Ontologies. The backend considered of a proxy script which interacts with BioPortal and is also required for an AJAX interface. The frontend s of a treeview for taversing the ontology and an complete text box for searching. It was implemented using YUI Javascript framework. I opted for YUI instead of going for other frameworks like DoJo or JQuery just because of the vast amount of documentation available. It provides most of the widgets you will ever need out of the box. JQuery was another option but I believe it has a steeper learning curve and you will have to customize the existing widgets available to some extent.

We ( me, Alex n Mr. Nigam) had our Skype Conference on 26th for discussing BioPortal n how we can use it for my project. One important thing we discussed was using the BioPortal Annotater Service for automated anotation of pathways using the pathway titles. I believe we can start working on it by the end of this month ...after the plugin has been completed !

The next step was to integrate the 'REST Client' with the MediaWiki engine. That I had begun some 4 days back. The first step was to go through the documentation of Mediawiki. You will have to understand some rather complicated concepts like Hooks etc. before you can start writing your own extensions. However, studying other extensions available proved to be more helpfule than the documentation... I have come up with a basic extensions which has the AJAX based autocomplete - Search box . It allows you to tag the pathways. However the tags are not permanent and are store using Cookies. I believe storing the tags in the GPML still requires some work n discussion with Alex !

You can find my first Weekly Report along with the first version of the REST Client here .

Labels: GSOC, meeting, prototype, Wikipathways

posted by Chetan @ 7:16 PM