[Obi-devel] Is supernatant a role?

[Alan Ruttenberg]

Definition from wikipedia:

Supernatant refers to the often clear liquid above non-soluble
solids. These solids may reach the bottom of a container by means of
settling, precipitation, or centrifugation.

Since supernatant can be any of a variety of mixtures of
biomaterials, would it be proper to call supernatant a role?

-Alan

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[Fostel, Jennifer (NIH/NIEHS) [C]]

supernatant is the outcome of a separation process

[Fostel, Jennifer (NIH/NIEHS) [C]]

sorry -- hit the send key
outcomes are roles, so at the moment, supernatant would be a role

[Susanna]

> outcomes are roles

However if we follow this rule, other terms can be seen as result/outcome of certain processes, e.g. 'mixing process'. In this case: 
- lysate (def: A mixture (collection) of cell components created by rupturing of the cell wall)
- emulsion (def: A mixture of immiscible (unblendable) substances, that are finely....ect)
will be role. But this are in the Biomaterial branch at the moment.

Susanna

-- 
Susanna-Assunta Sansone, PhD

NET Project - Coordinator

www.ebi.ac.uk/net-project
	
The European Bioinformatics Institute   email:  san...@ebi.ac.uk
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[frank gibson]

As Alan suggests and for the reasons he describes supernatant is a role

- lysate (def: A mixture (collection) of cell components created by rupturing of the cell wall)

This is probably a role  although is a bit more complex.

- emulsion (def: A mixture of immiscible (unblendable) substances, that are finely....ect)

emulsion is a state or arrangement of form, so in this sense would not be a role, maybe a quality.

Frank
 

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[Fostel, Jennifer (NIH/NIEHS) [C]]

yes, but this is not an issue as long as we clearly define what we mean and use different terms.

 

the original MAGE model converted one biomaterial into another when a process was applied, but some experimental designs are less well-served by this, and have the idea of using one biomaterial undergoing several process but remaining the same animal or specimen.

 

we have not added supernatant to roles, and are happy to work with folks to make things consistent and unambiguous

---

From: Susanna [mailto:san...@ebi.ac.uk]
Sent: Thursday, November 01, 2007 1:05 PM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: Alan Ruttenberg; OBI_DEV Listserv (E-mail); Barry Smith

[Daniel Schober]

Difficult question, but yes, role seems fine for 'supernatant'.
In any case the discussion should take into account the definitions of 'role' and its superclass 'realizable continuant'.
According to the role.owl  and BFO.owl definitions,'role' inherits the following definition/characteristics from its 'realizable entity' parent:
"A specifically dependent continuant that inheres in continuant entities and that is not exhibited in full at every time. Its exhibition or actualization is a particular manifestation, functioning or process that occurs under certain circumstances."
The current definition for 'role' states that its a "manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is, but that can be served or participated in by that continuant in some kinds of natural, social or institutional contexts.
So in short a 'role' is a particular manifestation that occurs only under certain circumstances (natural, social or institutional contexts (Wittgensteins 'state of affairs' I believe) and at certain times (is not exhibited in full in the corresponding continuant at every time).
To me the word 'role' indicates that the continuant that is manifested by the role is temporarily used in/occurs in some context that lies outside of its inherent characteristics and is so to speak something extrinsically asserted.
Cheers,
    Daniel Schober.


PS: For the pure fun of it, I would like to cite from Wittgensteins Tractatus logico-philosophicus ;-) :

[...]

2.011 It is essential to things that they should be possible constituents
of states of affairs.

2.012 In logic nothing is accidental: if a thing can occur in a state of
affairs, the possibility of the state of affairs must be written into the
thing itself.

2.0121 It would seem to be a sort of accident, if it turned out that a
situation would fit a thing that could already exist entirely on its own.
If things can occur in states of affairs, this possibility must be in them
from the beginning. (Nothing in the province of logic can be merely
possible. Logic deals with every possibility and all possibilities are its
facts.) Just as we are quite unable to imagine spatial objects outside
space or temporal objects outside time, so too there is no object that we
can imagine excluded from the possibility of combining with others. If I
can imagine objects combined in states of affairs, I cannot imagine them
excluded from the possibility of such combinations.

2.0122 Things are independent in so far as they can occur in all possible
situations, but this form of independence is a form of connexion with
states of affairs, a form of dependence. (It is impossible for words to
appear in two different roles: by themselves, and in propositions.)

2.0123 If I know an object I also know all its possible occurrences in
states of affairs. (Every one of these possibilities must be part of the
nature of the object.) A new possibility cannot be discovered later.

2.01231 If I am to know an object, thought I need not know its external
properties, I must know all its internal properties.

2.0124 If all objects are given, then at the same time all possible states
of affairs are also given.

2.013 Each thing is, as it were, in a space of possible states of affairs.
This space I can imagine empty, but I cannot imagine the thing without the
space.

2.0131 A spatial object must be situated in infinite space. (A spatial
point is an argument-place.) A speck in the visual field, thought it
need not be red, must have some colour: it is, so to speak, surrounded
by colour-space. Notes must have some pitch, objects of the sense of
touch some degree of hardness, and so on.

2.014 Objects contain the possibility of all situations.

2.0141 The possibility of its occurring in states of affairs is the form of
an object.

[...]

6.53 The correct method in philosophy would really be the following: to say
nothing except what can be said, i.e. propositions of natural science--i.e.
something that has nothing to do with philosophy--and then, whenever
someone else wanted to say something metaphysical, to demonstrate to him
that he had failed to give a meaning to certain signs in his propositions.
Although it would not be satisfying to the other person--he would not have
the feeling that we were teaching him philosophy--this method would be the
only strictly correct one.

6.54 My propositions are elucidatory in this way: he who understands me
finally recognizes them as senseless, when he has climbed out through them,
on them, over them. (He must so to speak throw away the ladder, after he
has climbed up on it.) He must transcend these propositions, and then he
will see the world aright.

7. What we cannot speak about we must pass over in silence.

frank gibson wrote:

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-- 
__________________________________________________________________________________________

Dr. Daniel Schober

NET Project - Ontologist

The European Bioinformatics Institute   email:  sch...@ebi.ac.uk
EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
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[Matthew Pocock]

I think the acid test is if something being
a 'lysate', 'emulsion', 'supernatent', 'solvent' and so on are intrinsic to
the substance, or if they are about how it relates to the things arround it.
So - emulsion seems self-contained to me - it's an emulsion because it's a
mixture of a water-based liquid and an oil-based liquid, and the oil is
broken up into very small balls and distributed fairly evenly through the
water. Supernatent seems to require external things - it is a supernatent as
a result of being the bit at the top of a series of substances resulting from
seperating a mixture by a process like centrifugation.

It's as if we need role-like things describing how substances participate in
parts relations. A similar stuation arrises in the case of solvent, solute,
solution - these terms can mean the roles different substances play before or
after mixing, but solvent and solute can also mean the substances that are
currently mixed without appealing to the history of how the solution was
manufactured. So we need a role sense for solvent, and a role-like partonomy
sense for solvent.

Not sure this gets us anywhere :)

Matthew

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