Re: [Obi-instrument-branch] Obi-instrument-branch Digest, Vol 25, Issue 2

[Yongqun He]

Hi Frank and Melanie,

 

I would like to help edit the instrument branch. I am still new to OBI and would like to contribute more. As a junior faculty here in Michigan, I still have flexible time to do some research I enjoy doing. 

 

When is the instrument branch call time?

 

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/  

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Today's Topics:

   1. Re: instrument calls (Alan Ruttenberg)
   2. Re: instrument calls (Frank Gibson)
   3. Re: instrument calls (Trish Whetzel)


----------------------------------------------------------------------

Message: 1
Date: Tue, 10 Feb 2009 04:31:29 -0500
From: Alan Ruttenberg <alanrut...@gmail.com>
Subject: Re: [Obi-instrument-branch] instrument calls
To: Trish Whetzel <plwh...@gmail.com>
Cc: obi-instru...@lists.sourceforge.net
Message-ID:
<29af5e2d0902100131m364...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Another question forgot to ask. How does it interact with imports? We need
the imports to reason correctly (and because parts are defined in different
branches). We also need to be able to control to which branch edits are
made.
Finally, if we do try this it needs to be done in a way that supports our
version management - after some session of work, either collaborative or
individual, the branch that is edited needs to be checked in.

-Alan

On Mon, Feb 9, 2009 at 9:10 PM, Trish Whetzel <plwh...@gmail.com> wrote:

> Since it sounds like you will need to intersperse conversations with
> changes to the owl file, would use of Collaborative Protege be helpful?
>
> Here are answers to questions brought up at the OBI workshop:
> 1) Can it do reasoning?
> Yes.
>
> 2) Can it save all versions?
> The edits are simultaneous in Collaborative Protege. There isn't really the
> concept of versions. Whatever change a user makes, all other users will see
> immediately. The ontology can be saved at any time in an OWL format and can
> be submitted to a SVN, if needed.
>
> 3) Can changes be rolled back?
> No. It is dangerous to do that with simultaneous editing. New version based
> on Protege 4 has that in plan.
>
> 4) Is the OWL file accessible in case there are special edits that need to
> be done offline that cannot be performed in Prot?g??
> Yes.
>
> 5) Can the file be locked similar to a svn lock so that if offline work is
> needed, the file will be the same when added back to the server?
> No. Edits are simultaneous, so there are no versions. This "locking"
> feature is planned for the next version.
>
> 6) Is this an active project?
> Definitely.
>
>
> Trish
>
>
>
> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mcou...@gmail.com>wrote:
>
>> Hi all,
>>
>> Due to lots of things happening for all the OBI instrumenters, the
>> recent calls were attended by Daniel, Frank and myself.
>>
>> Daniel has now left the EBI, Frank started working for a private
>> company so won't have as much time as before to dedicate to OBI, and I
>> won't be able to attend future instruments call either.
>>
>> We therefore propose to cancel those, unless other editors are willing
>> to take on.
>>
>> Frank and myself had a chat during the OBI meeting last week: the
>> instrument branch is in need of clean up, and in order to try and move
>> forward with what we think would be the most efficient process we
>> propose to try and coordinate via emails between the both of us.
>>
>> Obviously and for the reasons mentioned above this will be a slow
>> process, so if you have any other suggestion or comment please let us
>> know :)
>>
>> Melanie
>>
>>
>> ---
>> M?lanie Courtot
>> TFL- BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Create and Deploy Rich Internet Apps outside the browser with
>> Adobe(R)AIR(TM)
>> software. With Adobe AIR, Ajax developers can use existing skills and code
>> to
>> build responsive, highly engaging applications that combine the power of
>> local
>> resources and data with the reach of the web. Download the Adobe AIR SDK
>> and
>> Ajax docs to start building applications today-
>> http://p.sf.net/sfu/adobe-com
>> _______________________________________________
>> Obi-instrument-branch mailing list
>> Obi-instru...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>>
>
>
>
> ------------------------------------------------------------------------------
> Create and Deploy Rich Internet Apps outside the browser with
> Adobe(R)AIR(TM)
> software. With Adobe AIR, Ajax developers can use existing skills and code
> to
> build responsive, highly engaging applications that combine the power of
> local
> resources and data with the reach of the web. Download the Adobe AIR SDK
> and
> Ajax docs to start building applications today-
> http://p.sf.net/sfu/adobe-com
> _______________________________________________
> Obi-instrument-branch mailing list
> Obi-instru...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>
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------------------------------

Message: 2
Date: Tue, 10 Feb 2009 09:37:24 +0000
From: Frank Gibson <fgi...@gmail.com>
Subject: Re: [Obi-instrument-branch] instrument calls
To: a.l.l...@newcastle.ac.uk
Cc: obi-instru...@lists.sourceforge.net
Message-ID:
<65a299a90902100137q79c...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

I think in this case, using collaborative protege may be overkill. I
have used it before and I do think using collaborative protege should
be the direction we should be heading in. However, in this case the
editing required is minimal and is really just curating the terms with
the new relations we have and fixing all the imported MSI terms, this
can be handled offline with very little communication.

For anyone that wants to edit the instrument branch the idea is to
review everything under device, add missing funtions, has_supplier and
device_setting  and the other device relations and assert the classses
under material entity rather than device.

I will remove the instrument calls from the calendar unless anyone steps up

Frank

On Tue, Feb 10, 2009 at 9:08 AM, Allyson Lister
<allyson...@googlemail.com> wrote:
> Hi all,
>
> The idea of trying out collaborative protege sounds good. And, while I don't
> have much time for TCs right now, doing a little work here and there on the
> ontology might be something I can make time for, especially since the
> instrument group is dropping in numbers. So, please include me on whatever
> next steps you take!
>
> :) Allyson
>
> 2009/2/10 Trish Whetzel <plwh...@gmail.com>
>>
>> Since it sounds like you will need to intersperse conversations with
>> changes to the owl file, would use of Collaborative Protege be helpful?
>>
>> Here are answers to questions brought up at the OBI workshop:
>> 1) Can it do reasoning?
>> Yes.
>>
>> 2) Can it save all versions?
>> The edits are simultaneous in Collaborative Protege. There isn't really
>> the concept of versions. Whatever change a user makes, all other users will
>> see immediately. The ontology can be saved at any time in an OWL format and
>> can be submitted to a SVN, if needed.
>>
>> 3) Can changes be rolled back?
>> No. It is dangerous to do that with simultaneous editing. New version
>> based on Protege 4 has that in plan.
>>
>> 4) Is the OWL file accessible in case there are special edits that need to
>> be done offline that cannot be performed in Prot?g??
>> Yes.
>>
>> 5) Can the file be locked similar to a svn lock so that if offline work is
>> needed, the file will be the same when added back to the server?
>> No. Edits are simultaneous, so there are no versions. This "locking"
>> feature is planned for the next version.
>>
>> 6) Is this an active project?
>> Definitely.
>>
>>
>> Trish
>>
>>
>> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mcou...@gmail.com>
>> wrote:
>>>
>>> Hi all,
>>>
>>> Due to lots of things happening for all the OBI instrumenters, the
>>> recent calls were attended by Daniel, Frank and myself.
>>>
>>> Daniel has now left the EBI, Frank started working for a private
>>> company so won't have as much time as before to dedicate to OBI, and I
>>> won't be able to attend future instruments call either.
>>>
>>> We therefore propose to cancel those, unless other editors are willing
>>> to take on.
>>>
>>> Frank and myself had a chat during the OBI meeting last week: the
>>> instrument branch is in need of clean up, and in order to try and move
>>> forward with what we think would be the most efficient process we
>>> propose to try and coordinate via emails between the both of us.
>>>
>>> Obviously and for the reasons mentioned above this will be a slow
>>> process, so if you have any other suggestion or comment please let us
>>> know :)
>>>
>>> Melanie
>>>
>>>
>>> ---
>>> M?lanie Courtot
>>> TFL- BCCRC
>>> 675 West 10th Avenue
>>> Vancouver, BC
>>> V5Z 1L3, Canada
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Create and Deploy Rich Internet Apps outside the browser with
>>> Adobe(R)AIR(TM)
>>> software. With Adobe AIR, Ajax developers can use existing skills and
>>> code to
>>> build responsive, highly engaging applications that combine the power of
>>> local
>>> resources and data with the reach of the web. Download the Adobe AIR SDK
>>> and
>>> Ajax docs to start building applications
>>> today-http://p.sf.net/sfu/adobe-com
>>> _______________________________________________
>>> Obi-instrument-branch mailing list
>>> Obi-instru...@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Create and Deploy Rich Internet Apps outside the browser with
>> Adobe(R)AIR(TM)
>> software. With Adobe AIR, Ajax developers can use existing skills and code
>> to
>> build responsive, highly engaging applications that combine the power of
>> local
>> resources and data with the reach of the web. Download the Adobe AIR SDK
>> and
>> Ajax docs to start building applications
>> today-http://p.sf.net/sfu/adobe-com
>> _______________________________________________
>> Obi-instrument-branch mailing list
>> Obi-instru...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>>
>
>
>
> --
>
> Allyson Lister
> http://lurena.vox.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
>
> ------------------------------------------------------------------------------
> Create and Deploy Rich Internet Apps outside the browser with
> Adobe(R)AIR(TM)
> software. With Adobe AIR, Ajax developers can use existing skills and code
> to
> build responsive, highly engaging applications that combine the power of
> local
> resources and data with the reach of the web. Download the Adobe AIR SDK and
> Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com
> _______________________________________________
> Obi-instrument-branch mailing list
> Obi-instru...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>



--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/



------------------------------

Message: 3
Date: Wed, 11 Feb 2009 23:33:53 -0800
From: Trish Whetzel <plwh...@gmail.com>
Subject: Re: [Obi-instrument-branch] instrument calls
To: Frank Gibson <fgi...@gmail.com>
Cc: obi-instru...@lists.sourceforge.net
Message-ID:
<139835960902112333n1d6...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Got it, less discussions and decision-making, but more hands-on editing
needed.

Trish


On Tue, Feb 10, 2009 at 1:37 AM, Frank Gibson <fgi...@gmail.com> wrote:

> Hi,
>
> I think in this case, using collaborative protege may be overkill. I
> have used it before and I do think using collaborative protege should
> be the direction we should be heading in. However, in this case the
> editing required is minimal and is really just curating the terms with
> the new relations we have and fixing all the imported MSI terms, this
> can be handled offline with very little communication.
>
> For anyone that wants to edit the instrument branch the idea is to
> review everything under device, add missing funtions, has_supplier and
> device_setting  and the other device relations and assert the classses
> under material entity rather than device.
>
> I will remove the instrument calls from the calendar unless anyone steps up
>
> Frank
>
> On Tue, Feb 10, 2009 at 9:08 AM, Allyson Lister
> <allyson...@googlemail.com> wrote:
> > Hi all,
> >
> > The idea of trying out collaborative protege sounds good. And, while I
> don't
> > have much time for TCs right now, doing a little work here and there on
> the
> > ontology might be something I can make time for, especially since the
> > instrument group is dropping in numbers. So, please include me on
> whatever
> > next steps you take!
> >
> > :) Allyson
> >
> > 2009/2/10 Trish Whetzel <plwh...@gmail.com>
> >>
> >> Since it sounds like you will need to intersperse conversations with
> >> changes to the owl file, would use of Collaborative Protege be helpful?
> >>
> >> Here are answers to questions brought up at the OBI workshop:
> >> 1) Can it do reasoning?
> >> Yes.
> >>
> >> 2) Can it save all versions?
> >> The edits are simultaneous in Collaborative Protege. There isn't really
> >> the concept of versions. Whatever change a user makes, all other users
> will
> >> see immediately. The ontology can be saved at any time in an OWL format
> and
> >> can be submitted to a SVN, if needed.
> >>
> >> 3) Can changes be rolled back?
> >> No. It is dangerous to do that with simultaneous editing. New version
> >> based on Protege 4 has that in plan.
> >>
> >> 4) Is the OWL file accessible in case there are special edits that need
> to
> >> be done offline that cannot be performed in Prot?g??
> >> Yes.
> >>
> >> 5) Can the file be locked similar to a svn lock so that if offline work
> is
> >> needed, the file will be the same when added back to the server?
> >> No. Edits are simultaneous, so there are no versions. This "locking"
> >> feature is planned for the next version.
> >>
> >> 6) Is this an active project?
> >> Definitely.
> >>
> >>
> >> Trish
> >>
> >>
> >> On Mon, Feb 9, 2009 at 5:05 PM, Melanie Courtot <mcou...@gmail.com>
> >> wrote:
> >>>
> >>> Hi all,
> >>>
> >>> Due to lots of things happening for all the OBI instrumenters, the
> >>> recent calls were attended by Daniel, Frank and myself.
> >>>
> >>> Daniel has now left the EBI, Frank started working for a private
> >>> company so won't have as much time as before to dedicate to OBI, and I
> >>> won't be able to attend future instruments call either.
> >>>
> >>> We therefore propose to cancel those, unless other editors are willing
> >>> to take on.
> >>>
> >>> Frank and myself had a chat during the OBI meeting last week: the
> >>> instrument branch is in need of clean up, and in order to try and move
> >>> forward with what we think would be the most efficient process we
> >>> propose to try and coordinate via emails between the both of us.
> >>>
> >>> Obviously and for the reasons mentioned above this will be a slow
> >>> process, so if you have any other suggestion or comment please let us
> >>> know :)
> >>>
> >>> Melanie
> >>>
> >>>
> >>> ---
> >>> M?lanie Courtot
> >>> TFL- BCCRC
> >>> 675 West 10th Avenue
> >>> Vancouver, BC
> >>> V5Z 1L3, Canada
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Create and Deploy Rich Internet Apps outside the browser with
> >>> Adobe(R)AIR(TM)
> >>> software. With Adobe AIR, Ajax developers can use existing skills and
> >>> code to
> >>> build responsive, highly engaging applications that combine the power
> of
> >>> local
> >>> resources and data with the reach of the web. Download the Adobe AIR
> SDK
> >>> and
> >>> Ajax docs to start building applications
> >>> today-http://p.sf.net/sfu/adobe-com
> >>> _______________________________________________
> >>> Obi-instrument-branch mailing list
> >>> Obi-instru...@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Create and Deploy Rich Internet Apps outside the browser with
> >> Adobe(R)AIR(TM)
> >> software. With Adobe AIR, Ajax developers can use existing skills and
> code
> >> to
> >> build responsive, highly engaging applications that combine the power of
> >> local
> >> resources and data with the reach of the web. Download the Adobe AIR SDK
> >> and
> >> Ajax docs to start building applications
> >> today-http://p.sf.net/sfu/adobe-com
> >> _______________________________________________
> >> Obi-instrument-branch mailing list
> >> Obi-instru...@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
> >>
> >
> >
> >
> > --
> >
> > Allyson Lister
> > http://lurena.vox.com
> >
> > CISBAN, http://www.cisban.ac.uk
> > Newcastle University
> >
> >
> ------------------------------------------------------------------------------
> > Create and Deploy Rich Internet Apps outside the browser with
> > Adobe(R)AIR(TM)
> > software. With Adobe AIR, Ajax developers can use existing skills and
> code
> > to
> > build responsive, highly engaging applications that combine the power of
> > local
> > resources and data with the reach of the web. Download the Adobe AIR SDK
> and
> > Ajax docs to start building applications today-
> http://p.sf.net/sfu/adobe-com
> > _______________________________________________
> > Obi-instrument-branch mailing list
> > Obi-instru...@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
> >
> >
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
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Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com

------------------------------

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End of Obi-instrument-branch Digest, Vol 25, Issue 2
****************************************************

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[Frank Gibson]

Hi Oliver,

We have currently suspended the instrument calls at the moment as we
have no branch leader and Melanie and I cant devote as much time as we
used to. We are currently editing the branch in are own time based the
current definintion of device. Are there specific instrument terms you
require for inclusion within OBI?

Thanks

Frank

[Philippe Rocca-Serra]

Hi Oliver,

as we discussed on the coord call yesterday, it is likely that monthly
called will be held instead of weekly calls.
We 'll have to agree on time slot and date: I guess we could retain the
current time slot and set the call 2 weeks before the release dates
(which are usually end of months)
How does it sound ?
All issues could be discussed on the list. Unresolved issues pushed to
the call.
Term submission could be made following the guidelines James pointed to
in his recent post.
(Note: there is a perl script written by Jay to parse those term
templates into OWL classes, in the right location if a parent class is
provided).

Cheers

Philippe

[Yongqun He]

Hi Frank,

 

I looked the terms under device and instrument classes. The list is long and pretty good. It has covered most of the device and instruments my lab uses every day. Here I want to add a few more:

 

-----------------

1. electroporator
2. pipeter
3. 'gene gun'
under centrifuge, add

4. 'microcentrifuge',

5. 'ultracentrifuge',

6. 'high speed centrifuge'
under microscope, add

7. 'fluorenscence microscope',

8. 'electron microscope',

9. 'light microscope'
under 'DNA microarray', add

10. 'Affymetrix DNA microarray',

11. 'Agilent DNA microarray'

---------------

 

Do you want me to define these terms for you? The term 'gene gun' is very specific for vaccine delivery. The other terms are more broadly used in biomedical investigations.

 

I will also see if I can provide more terms to you later.

 

Thanks.

 

Oliver 
 

>>> Frank Gibson <fgi...@gmail.com> 2/12/2009 7:28 AM >>>

[Frank Gibson]

Hi Oliver,

Thats great, as James and Phillipe highlighted, if you could prepare
the terms according to the minimum metadata and according to how
device is described (i,e function) this would be a great start.

Cheers

Frank

------------------------------------------------------------------------------
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-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

[Yongqun He]

Hi Frank,

Sure. I will provide you the metadata early next week.

Best,

--Oliver

>>> Frank Gibson <fgi...@gmail.com> 2/13/2009 04:05 >>>

[Yongqun He]

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

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

 

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

 

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

 

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

 

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

 

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

 

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

 

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

 

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

 

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!

 

Oliver

 

>>> Frank Gibson <fgi...@gmail.com> 2/13/2009 04:05 >>>

[Frank Gibson]

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

Hi Frank,

Oliver

Cheers

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

------------------------------------------------------------------------------

Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

[Yongqun He]

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 >>>

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/