Re: [Obi-protocol-application-branch] Action Item Assay

[Matthew P. <mat...@nc...>]

> It is implicit (and could be added as an axiom) that every Assay has
> a process part that includes an observation. This seems adequate -
> I'm not sure why one needs to state this explicitly.

It makes no difference to me if you explicitly introduce all of this manually 
or if the reasoner injects it. That's implementation detail. However, this is 
what happens so we should consider making room for it. It makes a difference 
because it is one of the places that error creeps in. Some classes of errors 
are specific to the way the observation is performed, independent of anything 
else.

> input:  cup of tea
> instrument: digital thermometer model xxx serial yyy
> output: data (temperature of tea as read off thermometer, units:
> Fahrenheit)

Surely the cup of tea exists afterwards? It is not gobbled up by the process 
of having its temperature taken, so it is an output. I could take the cup of 
tea after it has had its temperature taken and drink it, so the tea (in an 
altered state) is an output, albeit a booring one of the protocol. The tea 
changes is temperature in response to having it's temperature measured by 
thermometer due to the very nature of how thermometers work. I think its 
important to capture this, particularly if now when I drink that cup of tea 
it is tepid. Where would that go in your current model?

> My understanding of Assay as it currently exists is, effectively,
> protocol application with output that is data. (though I note that I
> don't see an english or format definition attached ...

As an asside, the current deffinition where it is a process with a material 
input and a data output doesn't sit easy with me. I have a philosophical 
problem with real physical processes having inputs or outputs that are 
anything other than real physical things. You can't pick up a lump of data 
and carry it across the room. If a process has physical inputs (a cup of 
tea), then I'd argue that it has physical outputs (some media that now bears 
a representation of the temperature of that tea) rather than a data output 
(the temperature reading itself).

Similarly, a 'process' that transforms one lot of data into another (e.g. 
xslt) has data inputs and data outputs that are data. This has a dual (and 
perhaps in the BFO sense, more real) process that is the physical enactment 
of this as electrons and stuff, that usually we don't care about, but which 
always exists.

Matthew