Hi Mummi,
hope you doing well.
We have not enhanced the ontology look up and still using the
old-styler.
The project you referred to, just had a quick scan on its architecture.
It relies on TOMCAT server. The AJAX requests are sent, I guess from
SMDService.js to
url = "http://smd.stanford.edu/smd/ontology/SubmitService";;
where it expects to have server returning the response.
You have to hack this code (provided its not under any anti-hack license
or something) to get it to work with Apache Web Server and then think
about getting this into BioMart. If I were to do this, I wont go after
hacking the project there which in this case, as per our requirements
offers just a treeView using AJAX. The important question is to fit it
into BioMart architecture. We are already redesigning the system which
will probably change a lot of things related to configuration of
MartView, so may be by the time your work is finished, the system will
changed after some time. I really dont know how to go about this, may be
you need to calculate the amount of effort you plan to spend into this.
We do intend to make an AJAX driven tree for such ontology look ups in
near future as a part of new development and configuration system.
Cheers
Syed
On Mon, 2007-12-10 at 17:27 +0000, Gudmundur A. Thorisson wrote:
> Hey guys on BioMart team: did anybody get around to tackle one of the
> 'leftover' tasks from when I worked on Martview, namely the directed-
> graph/hierarchical browser, for ontologies and such? We are working
> with phenotype ontologies over here in our group in Leicester and are
> setting up some datasets with genotype and phenotype data. If nobody
> has done anything on this, we may be interested in doing it for our
> site, and contributing back to the project. Any rough ideas on how
> this might be accomplished (Ajax/widget libraries etc.).
> BTW There's a recent paper on this subject: http://
> www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2080642, maybe
> some ideas to grab here:
>
> Catherine C Beauheim, Farrell Wymore2, Michael Nitzberg2,
> ZachariahKZachariah2, HengJin2, JH PateSkene3, CatherineABall2 and
> GavinSherlock*1. BMC Bioinformatics. 2007.
> OntologyWidget – a reusable, embeddable widget for easily
> locating ontology terms
>
>
> Mummi
>
>
> -----------------------------------------------------------
> Gudmundur A. Thorisson, PhD student, Brookes lab
> Department of Genetics
> University of Leicester
> University Road
> Leicester, LE1 7RH, UK
> E-mail: [EMAIL PROTECTED]
> Tel: +44 (0)116 252-3453
>
>
>
>
