Add instrument terms from BRO

[obi-bot]

These terms exist in BRO but not yet in OBI. I believe they should be in OBI. They are not yet defined, but I am indicating their proposed position within OBI. This is not really a step in resolving the "instrument" - "device" conundrum, but rather just a first attempt at integrating some of the relevant classes from BRO into OBI.

Thanks, Melissa

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Calorimeter name: Calorimeter namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000832 ! measurement device

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#CT\_Scanner name: CT Scanner namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000832 ! measurement device

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Electrode\_Puller name: Electrode Puller namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Faraday\_Cage name: Faraday Cage namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Micromanipulator name: Micromanipulator namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Electron\_Microscope name: Electron Microscope namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0400169 ! Microscope

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Light\_Microscope name: Light Microscope namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0400169 ! Microscope

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#MRI\_Scanner name: MRI Scanner namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000832 ! measurement device

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Oscilloscope name: Oscilloscope namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000832 ! measurement device

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#PCR\_Instrument name: PCR Instrument namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#PET\_Scanner name: PET Scanner namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000832 ! measurement device

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Vibration\_Isolation\_Table name: Vibration Isolation Table namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

[Term] id: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl\#Vibrotome name: Vibrotome namespace: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# is_a: OBI:0000047 ! processed material

Reported by: mellybelly

Original Ticket: obi/obi-terms/490

[obi-bot]

• assigned_to: nobody --> parkinso

Original comment by: helenp

[obi-bot]

Following are proposed definitions and synonyms for these terms, plus a couple of comments.

In cases where it isn't clear where the "genus" part of the definition would fit in OBI, it is enclosed in brackets. The issue of those parent terms will be pursued on tracker item http://sourceforge.net/tracker/?func=detail&aid=2894801&group\_id=177891&atid=886178

name: calorimeter 
is_a: OBI:0000832 ! measurement device def: A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. def xref: About.com Chemistry Glossary http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm syn: calorimetry instrument



name: CT scanner 
is_a: OBI:0000832 ! measurement device 
def: A measurement (or image acquisition) device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. def xref: Wikipedia http://en.wikipedia.org/wiki/X-ray\_computed\_tomography syn: computed tomography scanner; X-ray computed tomography scanner


name: electrode puller 
is_a: OBI:0000047 ! processed material 
def: A [preparation device], used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. def xref: Slish DF http://faculty.plattsburgh.edu/donald.slish/Puller1.html


name: Faraday cage 
is_a: OBI:0000047 ! processed material 
def: An [enclosure], formed by conducting material or by a mesh of such material, that blocks out external static electric fields. def xref: Wikipedia http://en.wikipedia.org/wiki/Faraday\_cage syn: Faraday shield


name: micromanipulator 
is_a: OBI:0000047 ! processed material 
def: A [device] that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. def xref: Wikipedia http://en.wikipedia.org/wiki/Micromanipulator


name: electron microscope
 is_a: OBI:0400169 ! microscope 
def: A microscope that produces an electronically-magnified image of a specimen for detailed observation. def xref: Wikipedia http://en.wikipedia.org/wiki/Electron\_microscope syn: EM


name: optical microscope 
is_a: OBI:0400169 ! microscope
 def: A microscope that uses visible light and a system of lenses to magnify images of small samples. def xref: Wikipedia http://en.wikipedia.org/wiki/Optical\_microscope syn: light microscope comment: BRO has Light Microscope, but I think "optical microscope" should be the preferred term. Might consider adding "digital microscope" as a type of microscope (http://en.wikipedia.org/wiki/Digital\_microscope)


name: MRI scanner 
is_a: OBI:0000832 ! measurement device
 def: A measurement (or image acquisition) device that visualizes detailed internal structure and limited function of the body, using a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body. def xref: Wikipedia http://en.wikipedia.org/wiki/Magnetic\_resonance\_imaging syn: magnetic resonance imaging scanner; nuclear magnetic resonance imaging scanner; NMRI scanner


name: oscilloscope 
is_a: OBI:0000832 ! measurement device
 def: A measurement device that allows signal voltages to be viewed, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). def xref: Wikipedia http://en.wikipedia.org/wiki/Oscilloscope


name: PCR instrument 
is_a: OBI:0000047 ! processed material def: An [instrument] that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. def xref: Wikipedia http://en.wikipedia.org/wiki/Polymerase\_chain\_reaction syn: thermocycler; PCR machine; DNA amplifier; polymerase chain reaction instrument comment: Same thing as thermal cycler (OBI:0400116)? OBI definition is broader than my proposed one. Are there such things as thermal cyclers that are not used for DNA amplification by PCR?


name: PET scanner
 is_a: OBI:0000832 ! measurement device 
def: A measurement (or image acquisition) device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. def xref: Wikipedia http://en.wikipedia.org/wiki/Positron\_emission\_tomography syn: positron emission tomography scanner


name: vibration isolation table 
is_a: OBI:0000047 ! processed material
 def: A [device] that supports an object such as a precision instrument while isolating the object from vibration that is transmitted from the floor. def xref: United States Patent 6877711


name: vibrotome 
is_a: OBI:0000047 ! processed material def: A [preparation device] that uses a vibrating razor blade to cut through tissue. def xref: Wikipedia http://en.wikipedia.org/wiki/Vibratome

Original comment by: seger

[obi-bot]

Probably PCR instrument should be a child of 'thermal cycler'. Also, PCR machine is a synonym of PCR instrument.

-melissa

Original comment by: mellybelly

[obi-bot]

Hi there, I noticed that these were had been imported from BRO, but now they seem gone. They could be added as terms in their own right with the above definitions, or if these definitions are added to BRO reimported.

Thanks, Melissa

Original comment by: mellybelly

[obi-bot]

Overall these are useful terms and helpful definitions. We should therefore get them in quickly; maybe some minor rewordings.

Two concerns: - electron microscope' is defined misleadingly (wiki def is misleading as well. Compare the talk page). It would currently include a camera with electronic zoom as a electron microscope. Would change to =def: A microscope that creates an image of a specimen by targeting it with an electron beam.

Original comment by: bpeters42

[obi-bot]

Forgot the 2nd: PCR machine should distinguish Real Time PCR machines which have a measurement function from regular PCR machines which provide a temperature controlled environment (and what else?)

Original comment by: bpeters42

[obi-bot]

• assigned_to: parkinso --> bjoernpeters
• status: open --> closed

Original comment by: bpeters42

[obi-bot]

Added these terms to the file. - I used 'device' in the textual definition of terms for which no OBI class exists (the '[ ]' terms) - Did not add MRI scanner, as I think it overlaps with NMR instrument (which is unfortunately poorly defined) - contacted Melanie, Melissa and Trish to clarify if thermal cycler and PCR instrument should be equivalent.

I am closing this ticket. Reopen if there are remaining general issues with what I did. If there are issues with individual terms, please open individual tracker items.

Original comment by: bpeters42

[obi-bot]

I found all terms submitted have been added into OBI except 'MRI scanner'.

PET scanner with label 'positron emission tomography scanner' and 'Light Microscope' renamed as 'optical microscope'

Original comment by: zhengj2007