RE: BioRDF [Telcon]: slides for the UMLS presentation

Hi Marco,

I'm hopeful of putting together a usecase for how the annotation of
MAGE-ML documents with ontology terms makes sense for the semantic
web--I usually end by saying that once the ontology information is
loaded into the local data store, knowledge based tools can be used on
them.

It looks like that's where you pick up the ball.  I'm hopeful that Bill
will help round out the use case but I believe your ideas will be
valuable also. 

> - I think that converting the whole MAGE or FUGE into RDF is hard in 
> practice and maybe not so useful. The problems are:

One other issue is that the actual objects in a microarray experiment
are for the most part one offs--i.e. a chip is a chip, it is only
hybridized once, the current investigation is only performed once with a
set of chips and so on.  Even the genes that are being investigated,
nothing new is being added to them except the interpretation of the data
from the investigation.

But as you say, it is, however, useful to annotate these one off objects
with where they fit into the larger world.

cheers,
Michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Marco Brandizi
> Sent: Friday, June 09, 2006 8:39 AM
> To: public-semweb-lifesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
> 
> 
> 
> Hi all,
> 
> some notes on the discussion of MAGE/FUGE/FUGO and RDF.
> 
> - I think that converting the whole MAGE or FUGE into RDF is hard in 
> practice and maybe not so useful. The problems are:
> 
>    - FUGE and MAGE are object models and should be reviewd in 
> order to 
> provide an OWL modelling. For instance the use of OntologyEntry as a 
> pointer to an ontology term doesn't make much sense in OWL.
> 
>    - FUGE/MAGE are used to represent huge quantities of data 
> (an average 
> MAGE-ML file is sized some hundreds MBs) and I am not sure 
> that current 
> technologies would support such requirement.
> 
> - Maybe only some aspects of a Functional Genomics models are really 
> needed in the context of Semantic Web. For instance telling 
> in RDF that 
> an experiment has been performed to study a given disease would be 
> useful, telling to the whole web the concentration value of the 
> application of an extraction protocol maybe is more 
> implementation specific.
> 
> 
> 
> 
> - I am modelling something about microarrays, although my 
> intent is not 
> to convert MAGE and to face its degree of details. I am more 
> interested 
> in a less detailed knowledge representation about Microarrays, and in 
> the management of the knowledge that is achieved from the 
> study of Gene 
> Expression.
> 
> Here an introduction about that:
> http://gca.btbs.unimib.it/brandizi/mysite/phdintro
> 
> My latest version of the ontology (very draft actually), plus 
> some notes 
> about the user interface I am developing:
> 
>    http://gca.btbs.unimib.it/brandizi/mysite/phdv1
> 
> 
> Cheers.
> 
> -- 
> 
> ==============================================================
> =================
> Marco Brandizi <brandizi@ebi.ac.uk>
> http://gca.btbs.unimib.it/brandizi
> 
> 
> 
>

Received on Friday, 9 June 2006 20:37:15 UTC