Molecular Models

[Michel Dumontier]

On Mon, Aug 17, 2009 at 12:16 PM, Phillip Lord <philli...@newcastle.ac.uk> wrote:

Anyway, we are getting of the point here; we need to describe models,
independently of the thing that they represent; this includes an
ontology, and includes BFO.

Phil

Right!

 so next on the BFO shopping list is how to handle a molecular model.

 For instance, let's say i take that structure data (derived from a structure analysis of real molecules) and make an in-silico mutation that replaces one set of points with another set, and that generates another structure. Now this structure is arguably derived from (and not in the RO sense) the previous structure, but is an entire fabrication for which the aim is to create a model of and ultimately a represent for a structure of a class of molecules which do *not necessarily exist*.

 Moreover, the spatial coordinates no longer specify a position for a real object in a real space, these coordinate data dictate the position of points in a virtual space with a corresponding expectation in real space (but not always - 11 dimensional spacetime M-theory models comes to mind). We also perform computational experiments in molecular dynamics that represent the motion of particles and which generates structure data at various discrete simulation time intervals that represent intervals of real time. This now all becomes a mathematical playground. Do we need to add virtual space-time? Do we need to create a class of information entities that mirror real objects like proteins, as well as adds new imaginary ones?

What says BFO?

-=Michel=-

--
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com

[Colin Batchelor]

Michel Dumontier writes:

> so next on the BFO shopping list is how to handle a molecular model.

There is no need to expose the insides of your molecular modelling to the ontological description _unless_ you are somehow exposing the insides as RDF.

What do you intend to expose? If you don't intend to expose it, we can pass over it in silence.

Colin.

DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening.

[Larry Hunter]

On Aug 19, 2009, at 9:45 AM, Colin Batchelor wrote:

> What do you intend to expose? If you don't intend to expose it, we
> can pass over it in silence.

I won't speak for Michel, but it seems to me that molecular models are
part of the purview of OBI, since often they are sometimes the result
of, or an input to, biomedical investigations. I believe that they
are information artifacts, so we need to handle them in IAO as well.
Therefore BFO needs to provide the fundamentals for talking about them
in an ontologically sound way. I also suspect that other sorts of
models (e.g. the neuron models in ModelDB, http://senselab.med.yale.edu/ModelDB/default.asp
) need to be represented as separate from the underlying reality
that they are proposed to model.

I would expect that a model would be an information artifact about a
real entity that is intended (by someone) to accurately describe
(only) some specific aspects of that entity. it might be useful to try
to capture what aspects of reality the model is intended to capture
(or those which it does *not* intend to capture). We have more or less
punted on what a hypothesis is (now just a statement or proposition,
but see, e.g. http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/b0825584009fb768
and point 12 of https://wiki.cbil.upenn.edu/obiwiki/index.php/Day_4_Thursday_12_July
) which is a related problem. It would be great if the BFO folk
could shed some light on how best to handle "models"

Larry

[Michel Dumontier]

On Wed, Aug 19, 2009 at 11:45 AM, Colin Batchelor <Batch...@rsc.org> wrote:

Michel Dumontier writes:

> so next on the BFO shopping list is how to handle a molecular model.

There is no need to expose the insides of your molecular modelling to the ontological description _unless_ you are somehow exposing the insides as RDF.

What do you intend to expose? If you don't intend to expose it, we can pass over it in silence.

Various databases expose everything from the methodology, experimental system, the raw and refined output data, with corresponding annotations relating to biological process, function and material entities.  People (like us) are in the process of building semantic web services in which we desire BFO-grounded descriptions for the processing of data and assignment of newly discovered relations. It is of clear and present need to address any and all parts of that description (and much much more). 

-=Michel=-

 

Colin.

DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening.