W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > July 2006

Re: ontology specs for self-publishing experiment

From: chris mungall <cjm@fruitfly.org>
Date: Fri, 7 Jul 2006 16:09:06 -0700
Message-Id: <DD2E447D-7623-4C04-A60A-195C7E64B081@fruitfly.org>
Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>


On Jul 7, 2006, at 3:35 AM, Phillip Lord wrote:

>
>>>>>> "TW" == Trish Whetzel <whetzel@pcbi.upenn.edu> writes:
>
>   TW> Hi all,
>
>   TW> As a terribly simple question, is it possible to take the actual
>   TW> FuGE-ML that is generated on a per instance reporting of an
>   TW> experiment/study/investigation and then convert than to RDF for
>   TW> use with semantic web technologies?
>
>
> Converting between one syntax and another is fairly simple, and there
> are some reasonably tools for it. XSLT would work for converting XML
> into RDF. I wouldn't like to use it for converting the other way
> (actually I wouldn't like to use it at all, but this is personal
> prejudice!).
>
> This is assuming, however, that the semantics of the two
> representations are compatible. To give an example, syntactically it
> is possible to convert between the GO DAG and an OWL representation of
> GO. However, the GO part-of relationship doesn't distinguish
> universal and existential, while OWL forces you to make this
> distinction; you can't sit on the fence.

Hi Phillip

Actually GO uses the definition of part_of from the OBO relation  
ontology
http://obo.sourceforge.net/relationship/#OBO_REL:part_of

You can see from the definition that the use of this relation  
suggests an existential relation. The GO OWL transform encodes this,  
so you don't need to sit on the fence, the decision has been made for  
you.

That aside, I completely agree with what you're saying. Coming up  
with various syntactic translations of XML to RDF is trivial but  
capturing the intended semantics can be difficult, unless the  
semantics of the source is specified both formally and in a way that  
is commensurable with the semantics of the target formalism. There  
are definitely some issues here in using the defined OBO relations  
(which involve time) to OWL (which has no explicit account of time)

> So, the simple answer to a simple question is: it depends. I wouldn't
> assume that FuGE-ML will be convertible into a given
> ontology or representation in RDF, unless a reasonable amount of care
> is taken in the design of FuGE-ML or the ontology to ensure that it
> can happen.
>
> Course, you could always hack it with some rules and a bit of human
> intervention. That works as well.
>
> Cheers
>
> Phil
>
>
>
Received on Friday, 7 July 2006 23:10:41 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:44 GMT