Re: Functions. Re: suggest instrument terms.
Frank Gibson
My apologies for the slow reply- some comments in line. - In general
we want to try and avoid where possible creating named functions for a
device just be adding the suffix function to the device name. We want
to try and break it down into generic actions performed by the device.
Submitting a function folllows the same principle as submitting any
other term for OBI in that as far as possible it should be accompanied
by a defintion in the for of " A "term" is a "parent term"
that/which.... An example is always helpful as well. In this regard I
dont actually know what some of the devices do.
On Thu, Feb 26, 2009 at 1:50 PM, Yongqun He <yong...@med.umich.edu> wrote:
> Hi Frank,
>
> Here is another try. Let me know what you think. Please let me know when you
> like to make a call. Thanks.
>
> Here I propose more functions in order to finish the work:
> 'centrifugation function' (propose to put this one under ‘separation
> function’)
Why will separation funtion not suffice?
> 'transport function'
I am assuming this is synounymous with transfer?
> 'particle delivery function'
this is more specific, the transfer of particles. You will have to
define here what you mean by "particle" to distinguish it from general
materials
> 'electroporation function'
Probably need a bit more of a definition for this
> 'biolistic particle delivery function’
Again a defintion would help to determine if this is different from
"particle delivery"
>
> Here is another definition for the functions of these 11 devices I proposed:
As far as the devices go, we already have the class centrifuge in OBI.
Would it be possible for you to look at how we have described this and
then propose definitions for each device below, in addition to the
more generic functions as described above. Really we need class
definitions to really understand the devices and functions,
Again, apologies for my delatyed reply. I hope this makes things
clearer, please feel free to ask any more questions
Cheers
Frank
>
> 1. 1. electroporator
> Function:
> has_function some 'electroporation function'
> (NOTE: this is a new function I propose.)
>
> 2. pipettor
> Function:
> has_function some 'transport function'
> (NOTE: this is a new function I propose)
>
> 3. 'gene gun'
> Function:
> has_function some 'biolistic particle delivery function'
> (NOTE: this is a new function I propose)
>
> under centrifuge, add
> 4. 'microcentrifuge',
> Function:
> has_function some 'centrifugation function'
> (NOTE: this is a new function I propose)
>
> 5. 'ultracentrifuge',
> Function:
> has_function some 'centrifugation function'
> (NOTE: this is a new function I propose. Alternatively, we can use the
> existing function ‘separation function’)
>
> 6. 'high speed centrifuge'
> Function:
> has_function some 'centrifugation function'
> (NOTE: this is a new function I propose)
>
> under microscope, add
> 7. 'fluorescence microscope',
> Function:
> has_function some ‘magnify function’
>
> 8. 'electron microscope',
> Function:
> has_function some ‘magnify function’
>
> 9. 'light microscope'
> Function:
> has_function some ‘magnify function’
>
> under 'DNA microarray', add
> 10. 'Affymetrix DNA microarray',
> Function:
> has_function some 'transcription analysis function'
>
> 11. 'Agilent DNA microarray'
> Function:
> has_function some 'transcription analysis function'
>
>
>>>> Frank Gibson <fgi...@gmail.com> 2/23/2009 4:44 AM >>>
> Hi Oliver,
>
> I appreciate alot of this is new to you, and some of the function
> classes that are there may be confusing, and the documentation is not
> really available at the moment to describe this further. We are trying
> to avoid a situation where we have micorarray_device has
> micorarary_function and mass_spec has mass_spec function. These
> definitions are circular and dont really describe what the device
> actually does. If you try and think of a function as a type of action
> verb. So some of the devices you list may have a measure function, a
> transfer function, a perterbation function, etc. Would you be able to
> have another go like this. Then we can arrange a call and go through
> them in more detail
>
> Cheers
>
> Frank
>
> On Fri, Feb 20, 2009 at 7:49 PM, Yongqun He <yong...@med.umich.edu> wrote:
>> Hi Frank,
>>
>> I have added functions to the instrument terms I suggested. Please see the
>> function assignments after each term in the end of the email. Since I
>> cannot
>> find many functions I need from OBI for many instruments, I suggest to
>> add the following functions under "instrument_function":
>>
>> 'centrifuge function'
>> 'transport function'
>> 'particle delivery function'
>> 'electroporation function'
>> 'gene gun function'
>>
>> See if it works. Thanks.
>>
>> Oliver
>>
>>
>>>>> Frank Gibson <fgi...@gmail.com> 2/19/2009 8:13 AM >>>
>> Hi Oliver,
>>
>> Would it be possible for you to try and indentify the functions of
>> these? There are some functions allreadi in obi so it would be helpful
>> if you could match these up or suggest new ones.
>>
>> Cheers
>>
>> Frank
>>
>>
>> ---------- Forwarded message ----------
>> From: Yongqun He <yong...@med.umich.edu>
>> Date: Wed, Feb 18, 2009 at 6:31 AM
>> Subject: Re: suggest terms. Re: [Obi-instrument-branch]
>> Obi-instrument-branch Digest, Vol 25, Issue 2
>> To: Frank Gibson <fgi...@gmail.com>
>> Cc: obi-instru...@lists.sourceforge.net
>>
>>
>> Hi Frank,
>>
>> Here is my descriptions of the terms I proposed to the Instrument
>> branch based on the minimal metadata:
>>
>> 1. electroporator
>> Definition:
>> electroporator is a device that is used for conduct electroporation.
>> Electroporation is a prcoess that involves in significant increases
>> in the electrical conductivity and permeability of the cell plasma
>> membrane caused by an externally applied electrical field. It is
>> usually used in molecular biology as a way of introducing some
>> substance into a cell, such as loading it with a piece of coding DNA.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Electroporation
>> Function:
>> has_function some 'electroporation function'
>> (NOTE: this is a new function I propose)
>> 2. pipettor
>> Definition:
>> pipettor is a laboratory instrument used to transport a measured
>> volume of liquid.
>> Synonyms:
>> pipette, pipet, pipeter, chemical dropper.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Pipette
>> Function:
>> has_function some 'transport function'
>> (NOTE: this is a new function I propose)
>> 3. 'gene gun'
>> Definition: The gene gun is a device for injecting cells with genetic
>> information.
>> Synonym: Biolistic Particle Delivery System
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Gene_gun
>> Function:
>> has_function some 'gene gun function'
>> (NOTE: this is a new function I propose)
>> under centrifuge, add
>> 4. 'microcentrifuge',
>> Definition:
>> A microcentrifuge is a small size centrifuge that uses microcentrifuge
>> tube or microfuge tube. Microcentrifuge tubes or microfuge tubes are
>> small, cylindrical plastic containers with conical bottoms, typically
>> with an integral snap cap. They are used in molecular biology and
>> biochemistry to store and centrifuge small amounts of liquid.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Microcentrifuge
>> Function:
>> has_function some 'centrifuge function'
>> (NOTE: this is a new function I propose)
>> 5. 'ultracentrifuge',
>> Definition:
>> The ultracentrifuge is a centrifuge optimized for spinning a rotor at
>> very high speeds, capable of generating acceleration as high as
>> 1,000,000 g (9,800 km/s²). There are two kinds of ultracentrifuges,
>> the preparative and the analytical ultracentrifuge.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Ultracentrifuge
>> Function:
>> has_function some 'centrifuge function'
>> (NOTE: this is a new function I propose)
>> 6. 'high speed centrifuge'
>> Definition:
>> A high speed centrifuge is a centrifuge optimized for spinning a rotor
>> at high speeds
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Centrifuge
>> Function:
>> has_function some 'centrifuge function'
>> (NOTE: this is a new function I propose)
>> under microscope, add
>> 7. 'fluorescence microscope',
>> Definition:
>> A fluorescence microscope is a light microscope used to study
>> properties of organic or inorganic substances using the phenomena of
>> fluorescence and phosphorescence instead of, or in addition to,
>> reflection and absorption.
>> Synonym:
>> epifluorescent microscope
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Fluorescence_microscope
>> Function:
>> has_function some 'microscope function'
>> 8. 'electron microscope',
>> Definition:
>> An electron microscope is a type of microscope that uses electrons to
>> illuminate a specimen and create an enlarged image. Electron
>> microscopes have much greater resolving power than light microscopes
>> and can obtain much higher magnifications.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Electron_microscope
>> Function:
>> has_function some 'microscope function'
>> 9. 'light microscope'
>> Definition:
>> The light microscope is a microscope that uses visible light and a
>> system of lenses to magnify images of small samples. Optical
>> microscopes are the oldest and simplest of the microscopes.
>> Synonym: optical microscope
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Optical_microscope
>> Function:
>> has_function some 'microscope function'
>> under 'DNA microarray', add
>> 10. 'Affymetrix DNA microarray',
>> Definition:
>> Affymetrix DNA microarray is a DNA microarray format that is
>> manufactured by Affymetrix. These chips are collectively called
>> GeneChips. Affymetrix DNA microarray is one color (or one channel)
>> microarray and uses short 25-mer probes.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/Affymetrix
>> http://en.wikipedia.org/wiki/DNA_microarray
>> Function:
>> has_function some 'transcription analysis function'
>> 11. 'Agilent DNA microarray'
>> Definition:
>> Agilent DNA microarray is a DNA microarray that is manufactured by
>> Agilent. Agilent DNA microarray uses long 60-mer probes.
>> Defintion Source:
>> http://en.wikipedia.org/wiki/DNA_microarray
>> Please let me know if you need more information. Thanks!
>> Function:
>> has_function some 'transcription analysis function'
>> Oliver
>> Yongqun "Oliver" He, DVM, PhD
>> Assistant Professor
>> Unit for Laboratory Animal Medicine
>> Department of Microbiology and Immunology
>> and Center for Computational Medicine and Biology
>> University of Michigan Medical School
>> Office: Room 105, Animal Research Facility (ARF)
>> Mailing: 018 ARF, 1150 W. Medical Center Dr.
>> Ann Arbor, MI 48109
>> Email: yong...@umich.edu
>> Tel: 734-615-8231 (O); 734-615-2455 (L)
>> Fax: 734-936-3235
>> http://www.ulam.umich.edu/academic/he.htm
>> http://www.med.umich.edu/microbio/bio/he.htm
>> http://www.hegroup.org/
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not
>> be
>> used for urgent or sensitive issues
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/