[Obi-instrument-branch] inconsistent comet assay

[Alan Ruttenberg]

utilizes_instrument gel_tank
but gel_tank is a device, not an instrument, and range of
utilizes_instrument is, surprisingly, instrument.

possible resolutions:
1) use has_participant, instead of utilizes_instrument
2) decide that gel_tank is an instrument
3) rename utilizes_instrument to utilizes_device and change the
range to device

-Alan

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[Alan Ruttenberg]

In the interest of having a consistent file, I've implemented (1)
below, until this is resolved.
-Alan

[Philippe]

Thanks Alan for looking into this.
When I created those assays (PCR-SSCP and Comet assay), my intent was
essentially to see how thing would work.
I did not pay too much attention to the range of the relation
'utilizes_instrument'. but you are right on this.
Now that I have a closer look at the instrument branch ,I guess the
decision of creating a specific relation 'utilizes_device', which would
be refined by a 'utilizes_instruments' rests on the definition of
'mechanical function' or 'electronic function' that would eventually
allow for distinguishing an instrument from a device univocally.
This is obviously a cross branch exercice. The virtue of trying to
represent protocol applications and assays (a process that we will
intensify) is that it allows precisely to identify caveats/problems
(well, provided AR is inspecting OBI using LSW).

Cheers

Philippe

Alan Ruttenberg wrote:

> Noting below, saying utilitize_instrument some device in the
> definition of protocol application is misleading. It can only be an
> instrument by the domain of the property. Might change
> utilizes_instrument min 1 instead, unless the domain of the property
> changes.
> -Alan
>
>
> Begin forwarded message:
>
>> *From: *Alan Ruttenberg <alanrut...@gmail.com
>> <mailto:alanrut...@gmail.com>>
>> *Date: *May 9, 2008 6:40:19 PM EDT
>> *To: *obi-instru...@lists.sourceforge.net
>> <mailto:obi-instru...@lists.sourceforge.net>
>> *Cc: *Melanie Courtot <cou...@ebi.ac.uk <mailto:cou...@ebi.ac.uk>>
>> *Subject: **inconsistent comet assay*

>>
>> utilizes_instrument gel_tank
>> but gel_tank is a device, not an instrument, and range of
>> utilizes_instrument is, surprisingly, instrument.
>>
>> possible resolutions:
>> 1) use has_participant, instead of utilizes_instrument
>> 2) decide that gel_tank is an instrument
>> 3) rename utilizes_instrument to utilizes_device and change the
>> range to device
>>
>> -Alan
>>
>
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[frank gibson]

Hi,

I would have favoured the third option :)

We have touched upon some of these issues during the function
discussion. All devices by definition have a function. A function must
be realised via a process, therefore the utilises_instrument should be
renamed utilises_device with the domain changing to device.
If I can draw parallels from what we have done in the past, the RU
instrument, is more likely to end up being a defined class, very
similar to the biomaterial example.

Cheers

Frank

--
Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
Newcastle upon Tyne, NE1 7RU
United Kingdom
Telephone: +44-191-246-4933
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