W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2007

Re: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

From: Marco Brandizi <brandizi@ebi.ac.uk>
Date: Fri, 17 Aug 2007 23:54:14 +0100
Message-ID: <46C62716.8020302@ebi.ac.uk>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
CC: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Helen Parkinson <parkinson@ebi.ac.uk>

Hi all,

sorry for late reply. I've been a bit busy.

thank you for the interesting replies. The Nigam tutorial, it is a
really good introduction to the world of BioOntologies.

In addition to that topics, I'd like to understand some further details
about the demo, and about how to put hands in it. For instance:

- How to expose RDF data to the demo? Via Joseki?
- Does the demo consist of code that have to be downloaded, changed and
run on my own server? Do I have to proceed like that if I want to extend
it with my own RDF data?

I guess some of the above questions may be answered by screening better
the Wiki and the mailing list. Help welcome anyway!

Alan Ruttenberg wrote:

> 
> 1) Representing the information about the samples, experiment, protocols 
> leading to the hybridization, technical aspects of the hybridization, etc.
> 2) Representing what the computed intensity of the spots on an array, as 
> well as how those were computed (e.g. MAS5, rma, d-chip, etc)
> 3) Representing which genes are thought to be relatively highly 
> expressed by interpreting the intensity of the spots as amount of 
> expression of certain genes.
> 

I am thinking to something quite simple: AE is able to show the
experiments and conditions under which a gene is expressed [1],
obviously according to stored microarray data. So it would be nice to
jump from genes to the conditions under which they're expressed, and
optionally show the expression levels.

Also I wonder how much complex would be attempting to expose only this
simple information. Certainly they're not enough, cause you would like
to add what supports the results, so things mentioned in 1) and 2). But
as a starting point...

I personally have worked in something similar in the past [2]. But
probably my work should be revised, and is not as simple as what I am
thinking of here.

Thanks a lot for replying.


[1]http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=nfkbia&species=&exp_query=leukemia
[2]http://gca.btbs.unimib.it/brandizi/mysite/phdv3

-- 

===============================================================================
Marco Brandizi <brandizi@ebi.ac.uk>

NET Project - Software Engineer
http://www.ebi.ac.uk/net-project

European Bioinformatics Institute
Hinxton, CB10 1SD, United Kingdom
Tel.: +44 (0)1223 49 2613
Fax: +44 (0)1223 49 4468

http://www.ebi.ac.uk/~brandizi
Received on Friday, 17 August 2007 22:54:31 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:49 GMT