Re: [Obi-function-branch] [Obi-instrument-branch] flow cytometer functions

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Hi Ryan,

Excelent question and example. For my money, you describe what the flow cytometer actually does, not how we use it. They do stuff with particles suspended in a fluid, including sorting and counting. Unless the instrument itself does different things to cells vs other particles, it's probably not that useful to say much more. I think that's the function.

Then there are a load of 'typical' processes describing how you use it. E.g. in a cell-counting process, there would be inputs including an instrument flow_cytometer and a sample containing cells in suspension, and the outputs including a count of the cells, or those cells sorted into different fractions by size or whatever.

I guess we have a more general class of processes that involve a flow cytometer - it must have an instrument input flow cytometer, and a sample input 'suspension of microscopic particles'.

Related question - can we define things like 'suspension of microscopic particles' in the biomaterials branch yet? There's a bunch of great definitions and names for these guys reachable from wikipedia http://en.wikipedia.org/wiki/Suspension_(chemistry) . I'm guessing that materials are linked into these mixtures by roles - since we use words like solvent, slute, and so on. The reason I sudgest modelling this that it gives us loads of extra constraints to validate experimental protocols via. For example, if someone claims to have feed a flow cytometer a solid lump of wood as the sample, and also know that the sample must be a liquid, then we can discover that something is up.

Matthew

On Tuesday 03 July 2007, Ryan Brinkman wrote:
> What sort of granularity for instrument  function hierarchy do you
> envisage?
>
>
>
> For example, at the highest level flow cytometers can be used to analyze
> particles suspended in a fluid (and the subtype of flow cytometer
> sorters can put them into tubes based on their characteristics).
> Particles are usually cells, but can be microorganisms. At a more
> granular level the function of a flow cytometer can be to examine many
> cellular parameters on live or fixed cells including surface,
> cytoplasmic and nuclear proteins, DNA, RNA, reactive oxygen species,
> intracellular pH and calcium flux. Measurement of the expression of
> cellular activation markers, intracellular cytokines, immunological
> signaling, cytoplasmic and nuclear cell cycle and transcription factors
> can also be readily performed. In the tissue-engineering field, FCM can
> analyze cell proliferation and other critical biological and functional
> properties of cells. Clinically, FCM is used to analyze a wide array of
> immunological parameters in disease. Following treatment, FCM can be
> used to study the humoral and cellular response to vaccines and a
> variety of other clinically relevant cellular data. Major clinical uses
> that require multiple samples per patient include the diagnosis and
> monitoring of leukemia and lymphoma patients, the evaluation of
> peripheral blood hematopoietic stem cell grafts, and the quantitation of
> CD4+ vs. CD8+ T lymphocytes in blood to monitor HIV infection and assess
> the performance of treatment. FCM is also commonly used for measuring
> the total DNA content per cell in biopsy specimens from tumors for
> clinical cancer diagnosis and prognosis. Cytometers can also function to
> determine particle size and shape.
>
>
>
>
>
> Cheers,
>
> Ryan
>
>
>
>
>
>
>
>
>
> From: Daniel Schober [mailto:sc...@eb...]
> Sent: Tuesday, July 03, 2007 7:26 AM
> To: frank gibson
> Cc: Ryan Brinkman; obi...@li...;
> obi...@li...
> Subject: Re: [Obi-instrument-branch] flow cytometer functions
>
>
>
> Hi,
> I think the functions should not be sorted according to the instruments
> that perform them. This should be 'inferable' via a has_function
> relation. However the inheritance of this has_function relation and its
> values needs to be discussed. Of cause we will run into problems as long
> as we have is_a and part_of mixed Hierarchies, e.g. currently we have
> sample_fluid is_a fluidic_subsystem is_a instrument, which is wrong...
> and would clearly prevent any function inheritance.
> Cheers, Daniel.
>
> frank gibson wrote:
>
>
>
>
> 			I know this branch is one of the more recent
> ones, although, a question for the branch. is it going to be common
> practice to create a hierarchy based on the object that inheres the
> function rather that what the function is?
>
> 		Yes, that is what we need the application use case for.
> Depending on the usage, e.g. for a simple CV/taxonomy RAs we would
> capture Instrument_function classes or for DL RAs moldel these through
> other RUs, e.g. relations...
> 		Cheers, Daniel.
>
>
> 	I was referring to the function heirachy rather than the
> instrument hierarchy. I know we need to assign funtions to devices.
> However, because an instrument has the function does not mean another
> object can not have the same function. Although the current hierarchy in
> the function branch enforces this.
>
>
> 		Frank
>
>
>
>
>
>
>
>
> 				Frank
>
> 				On 7/3/07, Ryan Brinkman
> <rbr...@bc... <mailto:rbr...@bc...> > wrote:
>
> 				As I understood it, during the last
> instrument call I was asked  to provide a list of functions(?) of flow
> cytometers. I'm a bit stuck. Part of my confusion relates to the
> granularity of the requested terms, and how the requested terms would
> differ from what we already sent to the function branch. Many of the
> properties a flow cytometer can measure are proxies for biological
> properties, but they are numerous and I didn't grok how these other
> functions help classify a flow cytometer at the moment.
>
>
>
> 				Any help would be very much appreciated.
>
>
>
> 				Cheers,
>
> 				Ryan
>
>
>
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> ________________________________________________________________________
> __________________
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> 			Dr. Daniel Schober
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> 		--
> 		Frank Gibson
> 		Research Associate
> 		Room 2.19, Devonshire Building
> 		School of Computing Science,
> 		University of Newcastle upon Tyne,
> 		Newcastle upon Tyne, NE1 7RU
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> 	--
> 	Frank Gibson
> 	Research Associate
> 	Room 2.19, Devonshire Building
> 	School of Computing Science,
> 	University of Newcastle upon Tyne,
> 	Newcastle upon Tyne, NE1 7RU
> 	United Kingdom
> 	Telephone: +44-191-246-4933
> 	Fax: +44-191-246-4905