Re: playing with pil ontology

Hi Helena,

Thanks for this, I think that this is a good exercise and some of the 
point you mentioned relate to the conceptual model, not only the formal 
model.

On 11/08/2011 18:52, Deus, Helena wrote:
>
> Hi all,
>
> Reiterating a bit on what was addressed today  in the telco, I 
> downloaded the ontology from mercurial and tried to use it with my use 
> case.
>
> I am using the use cases published in [1] and demoed with SPARQL at 
> http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html
>
> Here is my input so far:
>
> 1.Agent could have dataProperty "label" and "description"; it would 
> help the implementer describe what type of agent does he/she intend to 
> describe. Is the ontology here being confused with the query model?
>
I think that there was previously a long thread discussion on agent and 
agent types, and whether the model should be prescriptive in this 
respect. One of the solutions that I think many people were happy with 
is to leave users choose their favorite model(ontology) for agent, which 
means that the agent class defined in the ontology acts as a place 
holder that can be specialized to include description, types, and 
whatever the application needs.
>
> 2.ProvenanceContainer is not useful, or its description is not clear; 
> what should be an instance of provenanceContainer?
>

At this stage, the description of this concept is not yet stable in the 
conceptual model as far as I know.
>
> 3.I want to create an instance of a "untransformed" entity (in my 
> case, a dataset) and a "transformed" entity. Is the model going to 
> give me that granularity/expressivity or do we expect each implementer 
> to come up with their own way of defining these?
>
Could you please clarify what you mean by transformed and untransformed 
entity?

> 4.ProcessExecution needs more expressivity, I think. Not sure how to 
> solve this in a domain independent way, but here's my problem:
>
> a.An investigator (agent) performs an experiment
>
> b.That experiment has several input parameters, some of which are 
> entities (e.g. samples), other are not (e.g. temperature).
>
> c.Resulting from the experiment are several output parameters (entities)
>

I think that the current model caters for the above need. If you are 
specifically trying to differentiate between different kinds of inputs 
(samples as opposed to temperature), then the notion of role can be 
helpful in this resepect.


Thanks, khalid
>
> Have not completed my "experiment" yet, but will provide more feedback 
> soon J
>
> Best Regards,
>
> Helena F. Deus
>
> Post-doctoral Researcher
> Digital Enterprise Research Institute
>
> National University of Ireland, Galway
>
> http://lenadeus.info
>