[Obi-instrument-branch] instrument branch '10 most wanted' representational units
Daniel Schober
here an initial draff for the '10 most wanted' in our branch. This was the outcome of this tuesdays instrument call, but I added some additional thoughts.
Please add and refine. When ready, I believe we should send it to Bjoern as well.
Best ,
Daniel Schober.
10 most ‘important’ representational units
from the obi Instrument branch
Most important classes:
Intrabranch classes:
device
instrument
plattform
artefact object
Interbranch classes:
device function
( canonical realisation of device function )
produce data function
information processor function
process
protocol
Most important relations: (using Manchester syntax)
For device:
material entity and
has function SOME function
is manufactured by SOME (organisation OR homo sapiens)
is device for SOME process (inverse: process utilizes device )
gets_energy_from SOME homo sapiens (just an idea to reflect that a device is usually more passive and handled by humans, whereas instruments are actively driving processes )
For instrument:
device and
has_parameter_settings SOME information artefact (how does this relate to has quality? Would has software be a subrelation here as well?)
gets_energy_from SOME power supply
has part min 5 (5 is quite arbitrary…, just an idea)
Interbranch requirements:
The process or its representation, the protocol needs to capture:
A. Material inputs and outputs of an instrument application
has material entity input material entity/biomaterial
has material entity output material entity/biomaterial
B. Data/parameter inputs and outputs of an instrument
application
has information artefact input information artefact
has information artefact output information artefact
Issues/Problems:
It’s hard to find a
formal differrentiae to distinguish
instrument from device. Humans tend to classify more in a probabilistic
and fuzzy
way. It is hard to discretely model phase transitions that are
continuous.
In general an instrument is regarded to be more complex as a
device. Complexity is hard to define. Can a certain amount of ‘has
part’ statements
(min cardinality) lead to an acceptable solution ? Are there approaches
to
model Entrophy? This also lead to the question if a distinction
between a device function and a instrument function is justified.
Do we need the device / instrument distinction at all? What do we gain
having this distinction? A simple device should not get all the
properties of an instrument. E.g. a 'tube' does not need to have
parameters, data outputs, software, ..that a 'flow
cytometer' instrument might have.
In short these are
our current issues:
1. What additional intrinsic characteristics (differrentiae) do
Instruments have ?
– Complexity
– Active-passive usage
– Electric, mechanic
– Facilitates more than one step in a process ?
– There is a protocol and settings for it
2. Can certain biomaterials be seen as device, E.g:
• Biomaterial
– Plasmid Vector
• Device
– molecular maschine
• Plasmid Vector
• Role
– molecular maschine
• Plasmid Vector
-- __________________________________________________________________________________________ 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/
Daniel Schober
\obi\trunk\docs\developer\Instrument branch docs
rather than in the email.
Cheers,
Daniel.
Daniel Schober wrote:
------------------------------------------------------------------------------ SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
_______________________________________________ Obi-instrument-branch mailing list Obi-instru...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch