[Obi-protocol-application-branch] plan cleanup: question about material transformation objective

[Philippe Rocca-Serra]

Hi,

currently, processes such as (animal care, acclimatization, maintaining
cell culture) are sibling of material processing and assay.
I could add a restriction to achieves_planned_objective some 'material
transformation objective' so those classes classify under material
processing.

Checking the definition of the 'material transformation objective',
which is pretty lose, I presume that 'maintenance' or 'care' can be
viewed as some kind of 'invariant' transformation.
maintaining cell culture obviously aims to ensure cell retain their
phenotype, at minima keep cells alive.

If OK with everyone, I will perform the change. If not, then make a case
for an additional objective to cover those cases.

cheers

Philippe

--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute email: ro...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
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[Helen Parkinson]

Invariant transformation sounds like an oxymoron. I think these are
material processing by the current definition. The other option would be
to come up with a specific objective for these, I don't have strong
feelings about either option. I had this issue on my list, just hadn't
added it to the tracker yet,

thanks

Helen

Philippe Rocca-Serra wrote:
> Hi,
>
> currently, processes such as (animal care, acclimatization, maintaining
> cell culture) are sibling of material processing and assay.
> I could add a restriction to achieves_planned_objective some 'material
> transformation objective' so those classes classify under material
> processing.
>
> Checking the definition of the 'material transformation objective',
> which is pretty lose, I presume that 'maintenance' or 'care' can be
> viewed as some kind of 'invariant' transformation.
> maintaining cell culture obviously aims to ensure cell retain their
> phenotype, at minima keep cells alive.
>
> If OK with everyone, I will perform the change. If not, then make a case
> for an additional objective to cover those cases.
>
> cheers
>
> Philippe
>
>

--
Helen Parkinson, PhD
ArrayExpress Production Coordinator,
Microarray Informatics Team,
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi

[Philippe Rocca-Serra]

Hi,

currently, processes such as (animal care, acclimatization, maintaining
cell culture) are sibling of material processing and assay.
I could add a restriction to achieves_planned_objective some 'material
transformation objective' so those classes classify under material
processing.

Checking the definition of the 'material transformation objective',
which is pretty lose, I presume that 'maintenance' or 'care' can be
viewed as some kind of invariant transformation.
maintaining cell culture obviously aims to ensure cell retain their

phenotype, at minima stay alive.

If OK with everyone, I will perform the change. If not, then make a case
for an additional objective to cover those cases.

cheers

Philippe

--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute email: ro...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
--

[James Malone]

Hi Philippe,

I'm not sure about animal care. Is the objective of animal care to simply
maintain the animal in a 'normal' state, i.e. within some acceptable
living conditions, or is the objective to actually change the animal, such
as starvation? I'm not clear from the definition of animal care. I
understand Frank's early example of 'feeding' where he gave the example of
'fatter animal' as output, in which case there is a material
transformation as the objective there appears to be make a larger animal.
If it is just to maintain the animal within normal bounds then I would
think this is not a material transformation objective or at least not in
the spirit of what I think the class material transformation objective
should be intended for.

Cheers,

James

--
EMBL Outstation - Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD,
United Kingdom
Fax: + 44 (0) 1223 492 468

[Philippe Rocca-Serra]

I have the same feeling but invariant exist in math so provided we
accepted this case, it was good enough.

but of course, this is biology so may be we need 'care objective' which
may be handy considering the timely post by Christian (congratulations
for the award!)

I initially thought of 'maintenance objective' but then it would have
been quite restrictive.

Cheers

P

--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute email: ro...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
--

[Philippe Rocca-Serra]

hi James,

well 'animal care' has definitely something to do with compliance with
ethical standards. So we could need to incorporate this kind of constraints.

Even if you dose your animals with deadly compounds, there is still some
'animal caring ', to do and this could cover humane termination.

As I said, and jsut like you are pointing out, having a 'maintenance
objective' might be too restrictive unless we understand 'maintain
within some limits'

Again, we might want to revisit the 'material transfromation objective'
and clarify it

Cheers

P

[Bjoern Peters]

This is a tricky issue. Once we assert that the objective is to transform material, animals that have been fed will classify as 'processsed material'. It wasn't clear if that is what we want, which is why that assertion was not made before.

My take:
- We don't need to have superclasses for all of these beyond 'planned process', so I would be fine in leaving as is for now until we have a good overview of what we have left
- I would be against using 'material transformation objective;
- I would be okay with experimneting with an 'material maintenance objective', which is realized in processes that are designed to specifically maintain one or more characteristics of a material. 'storage' could also fall under this.

[Philippe Rocca-Serra]

Ok, I think this it is wise to leave at it is for now and revisit as need

I have continued the cleanup of the branch (see svn commits) and then
created a defined class of 'laboratory animal care' in order to make
sure that rodent care would classify under it.
The resulting classification (though not perfect) now shows the following:

laboratory animal care
-administering substnace in vivo
-animal feedning
-clinical diagnosis
-killing (I know some will complain about killing and care, well in
practice it is part of the case when dealing with animals.)
-weigth assessment
-taking sample from organism

contentious classification
-viral RNA extraction
-survival assessment (well humans are not really lab animal..)
-DNA transduction

Again, work is needed but this encouraging and looking better

Philippe

PS: classification takes longer, so optimization will be required.