[Obi-instrument-branch] not completely defined classes

[Alan Ruttenberg]

The classes:

flow cytometer
device and has_part some 'flow cell'
and has_part some 'light source'
and has_part some 'optical filter'
and has_part some photodetector

This reads: Anything that has a flow cell, light source, optical
filter, and photodetector as parts is a flow cytometer.
It's easy to imagine things that have these parts (for instance not
arranged correctly) that are not flow cytometers.

Same issue:
mass spectrometer
device and has_part some 'mass analyzer'
and has_part some 'ion source'
and has_part some 'ion detector'
hybridization station

Same issue:
cytometer
device and has_part some 'light source'
and has_part some 'optical filter'
and has_part some photodetector

I have move the conditions to be necessary but not sufficient for the
moment. This also resolves an issue we are having with the reasoner.
I believe the definitions above can be repaired by addition of a
condition that the instrument has the appropriate function.

I haven't moved these from _defined_material pending resolution.

-Alan

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Obi-instrument-branch mailing list
Obi-instru...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch

[Daniel Schober]

Hi Alan.

Alan Ruttenberg wrote:

>The classes:
>
>flow cytometer
>device and has_part some 'flow cell'
> and has_part some 'light source'
> and has_part some 'optical filter'
> and has_part some photodetector
>
>This reads: Anything that has a flow cell, light source, optical
>filter, and photodetector as parts is a flow cytometer.
>It's easy to imagine things that have these parts (for instance not
>arranged correctly) that are not flow cytometers.
>
>
>

I think this should be fine for what we want given that later we add the
flow cytometers Function as part of the axiom (then this excludes the
example of a non-sensically constructed device just having the parts).
Besides, we are not likely to have a phantasy device like the one you
mentioned annotated and queried for. So I think when the flow cytometer
function is added this definition is fine.

>Same issue:
>mass spectrometer
>device and has_part some 'mass analyzer'
> and has_part some 'ion source'
> and has_part some 'ion detector'
> hybridization station
>
>
>

same as above.

>Same issue:
>cytometer
>device and has_part some 'light source'
> and has_part some 'optical filter'
> and has_part some photodetector
>
>I have move the conditions to be necessary but not sufficient for the
>moment.
>

Yes, the only N&S cond is the device functions which we add later.

>This also resolves an issue we are having with the reasoner.
>I believe the definitions above can be repaired by addition of a
>condition that the instrument has the appropriate function.
>
>

Yes, exactly.

>I haven't moved these from _defined_material pending resolution.
>
>

Why are they not under instrument or device ?
Cheers, Daniel.

>-Alan
>
>
>
>-------------------------------------------------------------------------
>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>Build the coolest Linux based applications with Moblin SDK & win great prizes
>Grand prize is a trip for two to an Open Source event anywhere in the world
>http://moblin-contest.org/redirect.php?banner_id=100&url=/
>_______________________________________________
>Obi-instrument-branch mailing list
>Obi-instru...@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>

--
__________________________________________________________________________________________

Dr. Daniel Schober

NET Project - Ontologist

The European Bioinformatics Institute email: sch...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 494410
Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK Room: A3-141 (extension building)

Project page: www.ebi.ac.uk/net-project

Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/

[Ryan Brinkman]

Agreed. I think things like instruments with lasers where flow cells are supposed to go isn't something we should probably worry about. Adding the function  should clear up any misunderstanding, including by reasoners.

[frank gibson]

Hi,

On Tue, Sep 9, 2008 at 10:28 AM, Daniel Schober <sch...@ebi.ac.uk> wrote:
> Hi Alan.
>
> Alan Ruttenberg wrote:
>

>>The classes:
>>
>>flow cytometer
>>device and has_part some 'flow cell'
>> and has_part some 'light source'
>> and has_part some 'optical filter'
>> and has_part some photodetector
>>
>>This reads: Anything that has a flow cell, light source, optical
>>filter, and photodetector as parts is a flow cytometer.
>>It's easy to imagine things that have these parts (for instance not
>>arranged correctly) that are not flow cytometers.

I don't really care what you can imagine. Only when, and only if
something is added to the ontology that has these three parts, and we
determine that is is not a flow cytometer, should we change this -
this is all part of iterative development. Can you give an example of
your imagination?

>>
>>
>>
> I think this should be fine for what we want given that later we add the
> flow cytometers Function as part of the axiom (then this excludes the
> example of a non-sensically constructed device just having the parts).
> Besides, we are not likely to have a phantasy device like the one you
> mentioned annotated and queried for. So I think when the flow cytometer
> function is added this definition is fine.

What function does a flow cytometer have other than the function of its parts?

>
>>Same issue:
>>mass spectrometer
>>device and has_part some 'mass analyzer'
>> and has_part some 'ion source'
>> and has_part some 'ion detector'
>> hybridization station
>>
>>
>>

What is the issue here? - hybridization station is not a mass
spectrometer and it does not classify as such

> same as above.

>
>>Same issue:
>>cytometer
>>device and has_part some 'light source'
>> and has_part some 'optical filter'
>> and has_part some photodetector
>>
>>I have move the conditions to be necessary but not sufficient for the
>>moment.
>>

> Yes, the only N&S cond is the device functions which we add later.

We have device functions. What do you mean here?

>
>>This also resolves an issue we are having with the reasoner.
>>I believe the definitions above can be repaired by addition of a
>>condition that the instrument has the appropriate function.
>>
>>

> Yes, exactly.

>
>>I haven't moved these from _defined_material pending resolution.
>>
>>

> Why are they not under instrument or device ?

These are the defined classes, they are in the defined classes bin
_defined_material so they dont get disjoints added to them upon
release.

> Cheers, Daniel.

>
>>-Alan
>>
>>
>>
>>-------------------------------------------------------------------------
>>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>>Build the coolest Linux based applications with Moblin SDK & win great prizes
>>Grand prize is a trip for two to an Open Source event anywhere in the world
>>http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>_______________________________________________
>>Obi-instrument-branch mailing list
>>Obi-instru...@lists.sourceforge.net
>>https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>>
>>
>

> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>
>
>

> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Obi-instrument-branch mailing list
> Obi-instru...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>

--
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
Fax: +44-191-246-4905
https://homepages.cs.ncl.ac.uk/frank.gibson

[Daniel Schober]

Hi Frank,
(see inline)

frank gibson wrote:

Hi,

On Tue, Sep 9, 2008 at 10:28 AM, Daniel Schober <sch...@ebi.ac.uk> wrote:
  

Hi Alan.

Alan Ruttenberg wrote:

    

The classes:

flow cytometer
device and has_part some 'flow cell'
  and has_part some 'light source'
  and has_part some 'optical filter'
  and has_part some photodetector

This reads:  Anything that has a flow cell, light source, optical
filter, and photodetector as parts is a flow cytometer.
It's easy to imagine things that have these parts (for instance not
arranged correctly) that are not flow cytometers.
      

I don't really care what you can imagine. Only when, and only if
something is added to the ontology that has these three parts, and we
determine that is is not a flow cytometer, should we change this -
this is all part of iterative development. Can you give an example of
your imagination?



  

Alan and me have already discussed this in the previous mails. I think they are fine and don't have a problem modeling the parts as long as the function is the n&s part of the definition.

I think this should be fine for what we want given that later we add the
flow cytometers Function as part of the axiom (then this excludes the
example of a non-sensically constructed device just having the parts).
Besides, we are not likely to have a phantasy device like the one you
mentioned annotated and queried for. So I think when the flow cytometer
function is added this definition is fine.
    

What function does a flow cytometer have other than the function of its parts?
  

Have you ever heared of synergetics and non-deterministic 'emergent' properties? In most cases, when complex systems are tackled, like instruments and all homeostatic organisations like living things, the whole is more than the simple sum of its parts and the function of the whole is more than the sum/list of its parts functions. To answer your question simply:
Cell count
Cell identification
Cell sorting
are all higher level functions that require an orchestrated interplay of the parts and function parts of the flow cytometer. The flow cytometer is more than the sum of its parts/function.

Same issue:
mass spectrometer
device and has_part some 'mass analyzer'
  and has_part some 'ion source'
  and has_part some 'ion detector'
  hybridization station



      

What is the issue here? - hybridization station is not a mass
spectrometer and it does not classify as such
  

don't know where this 'hybridization station' came from.

same as above.

    

Same issue:
cytometer
device and has_part some 'light source'
   and has_part some 'optical filter'
   and has_part some photodetector

I have move the conditions to be necessary but not sufficient for the
moment.

      

Yes, the only N&S cond is the device functions which we add later.
    

We have device functions. What do you mean here?
  

To cover the emergent but essential function we will add a flow cytometer function as N&S axion once this is ready.
Cheers,
    Daniel.

[frank gibson]

[snip]

> Have you ever heared of synergetics and non-deterministic 'emergent'
> properties? In most cases, when complex systems are tackled, like
> instruments and all homeostatic organisations like living things, the whole
> is more than the simple sum of its parts and the function of the whole is
> more than the sum/list of its parts functions. To answer your question
> simply:
> Cell count
> Cell identification
> Cell sorting
> are all higher level functions that require an orchestrated interplay of the
> parts and function parts of the flow cytometer. The flow cytometer is more
> than the sum of its parts/function.

The reverse is also true - and entity can be the sum of its parts -
this is one issue I have. The mass spec is an example of this where a
mass specs function is the function of its parts. The cell examples
you give are not a clear example, cell count and cell identification
are the same - an instrument measure a characteristic of a cell in
order to relay the information of count and identification, sorting we
have already identified as a measure and then a compartmentalisation -
sticking it in a tube.

Anyway - for the short term, I will concede that the restrictions of
parts should be moved to neccessary. The issue is that we may have to
restate the functions of the parts as a function of the instrument as
opposed to inferring it.

Frank

>
>
>
>
> Same issue:
> mass spectrometer
> device and has_part some 'mass analyzer'
> and has_part some 'ion source'
> and has_part some 'ion detector'
> hybridization station
>
>
>
>
>
> What is the issue here? - hybridization station is not a mass
> spectrometer and it does not classify as such
>
>

> don't know where this 'hybridization station' came from.
>
>
>

> same as above.
>
>
>
> Same issue:
> cytometer
> device and has_part some 'light source'
> and has_part some 'optical filter'
> and has_part some photodetector
>
> I have move the conditions to be necessary but not sufficient for the
> moment.
>
>
>
> Yes, the only N&S cond is the device functions which we add later.
>
>
> We have device functions. What do you mean here?
>
>

> To cover the emergent but essential function we will add a flow cytometer
> function as N&S axion once this is ready.
> Cheers,
> Daniel.
>
>
>
>