format-version: 1.2
date: 08:09:2008 13:53
saved-by: Thorsten Schramm
auto-generated-by: OBO-Edit 1.101
default-namespace: imagingMS.ontology
remark: version: 0.9.1
remark: release date: 2008-12-09
remark: coverage: Imaging mass spectrometer output files
remark: 090506 Matrix and Laser Attributes removed -> put into PSI-MS.OBO
remark: 090506 "Attribute" in Term deleted and new entries: Scan Type, Line Scan Direction added
remark: 091123 Added attributes for imaging laser shot method. Attribute "one way" (IMS:1000411) obsoleted -> replaced by new attribute "fly back"
remark: 091207 Added attributes for SIMS experiments
remark: "subimage positions" parameters added for images which are composed of several subimages!
remark: creator: Thorsten Schramm <thorsten.schramm@anorg.chemie.uni-giessen.de>
import: Unit.obo
import: psi-ms.obo

[Term]
id: IMS:0000000
name: Imaging Mass Spectrometry Ontology
namespace: imagingMS.ontology
def: "Imaging Mass Spectrometry Ontology." [COMPUTIS:IMS]

[Term]
id: IMS:1000001
name: ibd offset handle
def: "Information for the access and checking of the binary data arrays." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000002
name: sample stage
def: "Device that positions the imaging target." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000003
name: ibd binary type
def: "Describes type of the binary (ibd) file ." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000004
name: image
def: "Sample properties only concerning imaging samples." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000005
name: spectrum position
def: "Attributes to describe the position of a spectrum in the image." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000007
name: ibd file
def: "Attributes to describe the ibd file." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000008
name: ibd identification
def: "Attributes to doubtlessly identify the ibd file." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000009
name: ibd checksum 
def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data of the ibd file." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000010
name: scan 
def: "Describes the attributes of the generation of the image." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000011
name: laser shot mode 
def: "Describes the method how the laser was moved across the sample while firing." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000012
name: imaging ion source 
def: "Parameters describing the imaging source, which is used to create the ions measured by the MS." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000013
name: unit
def: "Terms to describe units" [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000014
name: ibd data type
def: "Encoding type of binary data, e.g. 32-bit integer." [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology

[Term]
id: IMS:1000030
name: continuous
def: "Way of saving spectra in a imzML binary data file (ibd). The m/z values for all spectra are saved at the beginning of the ibd file. Then the spectral values follow." [COMPUTIS:IMS]
relationship: is_a IMS:1000003 ! IDB Binary Type

[Term]
id: IMS:1000031
name: processed
def: "Way of saving spectra in a imzML binary data file (ibd). Every spectrum is saved with it's own m/z and intensity values." [COMPUTIS:IMS]
relationship: is_a IMS:1000003 ! IDB Binary Type

[Term]
id: IMS:1000040
name: linescan sequence
def: "Description of the direction of the succession of the assembling of the linescans." [COMPUTIS:IMS]
relationship: part_of IMS:1000010 ! Scan

[Term]
id: IMS:1000041
name: scan pattern
def: "Description of the pattern how the image was scanned." [COMPUTIS:IMS]
relationship: part_of IMS:1000010 ! Scan

[Term]
id: IMS:1000042
name: max count of pixels x
def: "Maximum number of pixels of the x-axis of the image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000043
name: max count of pixels y
def: "Maximum number of pixels of the y-axis of the image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000044
name: max dimension x
def: "Maximum length of the image in x-axis." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000045
name: max dimension y
def: "Maximum length of the image in y-axis." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000046
name: pixel size
def: "Describes the area of the sample presented by one pixel." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000047 ! Area Unit

[Term]
id: IMS:1000047
name: image shape
def: "Describes the shape of the image." [COMPUTIS:IMS]
relationship: is_a IMS:1000004 ! Image

[Term]
id: IMS:1000048
name: scan type
def: "Shows the direction in which the lines were scanned." [COMPUTIS:IMS]
relationship: part_of IMS:1000010 ! Scan

[Term]
id: IMS:1000049
name: line scan direction
def: "Description in wich direction the lines of the sample were scanned." [COMPUTIS:IMS]
relationship: part_of IMS:1000010 ! Scan

[Term]
id: IMS:1000050
name: position x
def: "Attribute to describe the position of a spectrum in the direction of the x-axis in the image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000051
name: position y
def: "Attribute to describe the position of a spectrum in the direction of the y-axis in the image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000052
name: position z
def: "Attribute to describe the position of a spectrum in the direction of the z-axis in the image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000053
name: absolute position offset x
def: "Describes the position at the x-axis of the upper left point of the image on the target." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeFloat "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000054
name: absolute position offset y
def: "Describes the position at the y-axis of the upper left point of the image on the target." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeFloat "The allowed value-type for this CV term."
relationship: is_a IMS:1000004 ! Image
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000055
name: subimage position x
def: "Describes the position of a subimage in the direction of the x-axis of the complete image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000056
name: subimage position y
def: "Describes the position of a subimage in the direction of the y-axis of the complete image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000057
name: subimage position z
def: "Describes the position of a subimage in the direction of the z-axis of the complete image." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000005 ! Spectrum Position
relationship: has_units UO:0000189 ! Count Unit

[Term]
id: IMS:1000070
name: external binary uri
def: "Location as an URI where to find the ibd file." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a IMS:1000007 ! Ibd File

[Term]
id: IMS:1000080
name: universally unique identifier
def: "universally unique identifier is unique throughout the world and allows to doubtlessly identify the ibd file." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a IMS:1000008 ! Ibd Indentification

[Term]
id: IMS:1000090
name: ibd MD5
def: "MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a IMS:1000009 ! Ibd Checksum

[Term]
id: IMS:1000091
name: ibd SHA-1
def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a IMS:1000009 ! Ibd Checksum

[Term]
id: IMS:1000101
name: external data
def: "Shows that there is no data in the <binary> section of the file." [COMPUTIS:IMS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
relationship: is_a IMS:1000001 ! Ibd Offest Handle


[Term]
id: IMS:1000102
name: external offset
def: "The position where the data of an array of a mass spectrum begins." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000001 ! Ibd Offest Handle
relationship: has_units UO:0000233 ! Byte

[Term]
id: IMS:1000103
name: external array length
def: "Describes how many fields an array contains." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000001 ! Ibd Offest Handle
relationship: has_units UO:0000189 ! Count

[Term]
id: IMS:1000104
name: external encoded length
def: "Describes the length of the written data." [COMPUTIS:IMS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: is_a IMS:1000001 ! Ibd Offest Handle
relationship: has_units UO:0000233 ! Byte

[Term]
id: IMS:1000110
name: pixel mode
def: "laser keeps the position while firing at the same same spot one or several times." [COMPUTIS:IMS]
relationship: is_a IMS:1000011 ! laser shot mode

[Term]
id: IMS:1000111
name: raster mode
def: "laser is moved while continuously firing at the sample." [COMPUTIS:IMS]
relationship: is_a IMS:1000011 ! laser shot mode

[Term]
id: IMS:1000112
name: stigmatic mode
def: "laser is moved around one point firing until moved to the next position (pixel)." [COMPUTIS:IMS]
relationship: is_a IMS:1000011 ! laser shot mode

[Term]
id: IMS:1000120
name: SIMS
def: "Parameters describing SIMS sources." [COMPUTIS:IMS]
relationship: part_of IMS:1000012 ! Imaging Ion Source

[Term]
id: IMS:1000121
name: DESI
def: "Parameters describing DESI sources." [COMPUTIS:IMS]
relationship: part_of IMS:1000012 ! Imaging Ion Source

[Term]
id: IMS:1000130
name: ions per square centimeter
def: "An area density unit which is equal to the count of ions divided by the area in centimeters squared." [COMPUTIS:IMS]
relationship: is_a IMS:1000013 ! unit

[Term]
id: IMS:1000131
name: milliliter per minute
def: "A flow rate describes the throughput per time." [COMPUTIS:IMS]
relationship: is_a IMS:1000013 ! unit

[Term]
id: IMS:1000141
name: 32-bit integer
def: "Signed 32 bit integer." [COMPUTIS:IMS]
relationship: is_a IMS:1000014 ! ibd data type

[Term]
id: IMS:1000142
name: 64-bit integer
def: "Signed 64 bit integer." [COMPUTIS:IMS]
relationship: is_a IMS:1000014 ! ibd data type

[Term]
id: IMS:1000200
name: position accuracy
def: "Accuracy is the degree of conformity of a measured position to its actual value." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000002 ! Sample Stage
relationship: has_units UO:0000187 ! Percent

[Term]
id: IMS:1000201
name: step size
def: "Specify the range between two different messuring points on the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000002 ! Sample Stage
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:10000202
name: target material
def: "Describes the material the target is made of." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a IMS:1000002 ! Sample Stage

[Term]
id: IMS:1000400
name: bottom up
def: "The starting point is at the bottom of the sample and the scanning happens in up direction (parallel to the y-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000040 ! Scan Direction

[Term]
id: IMS:1000401
name: top down
def: "The starting point is at the top of the sample and the scanning happens in bottom direction (parallel to the y-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000040 ! Scan Direction

[Term]
id: IMS:1000402
name: left right
def: "The starting point is at the left of the sample and the scanning happens in right direction (parallel to the x-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000040 ! Scan Direction

[Term]
id: IMS:1000403
name: right left
def: "The starting point is at the right of the sample and the scanning happens in left direction. (parallel to the x-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000040 ! Scan Direction

[Term]
id: IMS:1000404
name: no direction
def: "The scanning points are randomly distributed on the sample." [COMPUTIS:IMS]
relationship: is_a IMS:1000040 ! Scan Direction

[Term]
id: IMS:1000410
name: meandering
def: "The scanning happens in nonstop way. As soon as the end of the sample is reached, the scanning direction will be switched and the scanning is continued. There is no new positioning neccessary." [COMPUTIS:IMS]
relationship: is_a IMS:1000041 ! Scan Pattern

[Term]
id: IMS:1000411
name: one way
def: "OBSOLETE The scanning always happens in the same direction. As soon as the end of the sample is reached, the stage is positioned at the starting edge to begin the next run." [COMPUTIS:IMS]
comment: Was made obsolete because the generally used term is "flyback" (IMS:1000413).
is_obsolete: true

[Term]
id: IMS:1000412
name: random access
def: "The scanning points are randomly chosen and do not follow a pattern." [COMPUTIS:IMS]
relationship: is_a IMS:1000041 ! Scan Pattern

[Term]
id: IMS:1000413
name: flyback
def: "The scanning always happens in the same direction. As soon as the end of the sample is reached, the stage is positioned at the starting edge to begin the next run." [COMPUTIS:IMS]
relationship: is_a IMS:1000041 ! Scan Pattern

[Term]
id: IMS:1000480
name: horizontal line scan
def: "The scanning line is a horizontal one." [COMPUTIS:IMS]
relationship: is_a IMS:1000048 ! Scan Type

[Term]
id: IMS:1000481
name: vertical line scan
def: "The scanning line is a vertical one." [COMPUTIS:IMS]
relationship: is_a IMS:1000048 ! Scan Type

[Term]
id: IMS:1000490
name: linescan right left
def: "The starting point is at the right of the sample and the scanning happens in left direction. (parallel to the x-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000049 ! Line Scan Direction

[Term]
id: IMS:1000491
name: linescan left right
def: "The starting point is at the left of the sample and the scanning happens in right direction (parallel to the x-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000049 ! Line Scan Direction

[Term]
id: IMS:1000492
name: linescan bottom up
def: "The starting point is at the bottom of the sample and the scanning happens in up direction (parallel to the y-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000049 ! Line Scan Direction

[Term]
id: IMS:1000493
name: linescan top down
def: "The starting point is at the top of the sample and the scanning happens in bottom direction (parallel to the y-axis)." [COMPUTIS:IMS]
relationship: is_a IMS:1000049 ! Line Scan Direction

[Term]
id: IMS:1100000
name: 8-bit integer
def: "Signed 8-bit integer." [COMPUTIS:IMS]
relationship: is_a MS:1000518 ! binary data type

[Term]
id: IMS:1100001
name: 16-bit integer
def: "Signed 16-bit integer." [COMPUTIS:IMS]
relationship: is_a MS:1000518 ! binary data type

[Term]
id: IMS:1001201
name: primary ion gun species
def: "Describes the species of ions used for ionizing the sample." [COMPUTIS:IMS]
relationship: is_a IMS:1000120 ! SIMS

[Term]
id: IMS:1001202
name: beam energy
def: "Energy of the shot of the primary ion gun species in electronvolt." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000120 ! SIMS
relationship: has_units UO:0000226 ! electronvolt

[Term]
id: IMS:1001203
name: beam current
def: "Number of charges per second shot at the surface of the analyte." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000120 ! SIMS
relationship: has_units UO:0000038 ! microampere

[Term]
id: IMS:1001204
name: cycle time
def: "Inversion of the number of ions shot at the surface in one second. The maximum depends on the maximum time of flight in the mass spectrometer." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000120 ! SIMS
relationship: has_units UO:0000029 ! microsecond

[Term]
id: IMS:1001205
name: time resolution
def: "Size of the bin of the time recorded by the time to digital converter measured in pico seconds" [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000120 ! SIMS
relationship: has_units UO:0000030 ! picosecond

[Term]
id: IMS:1001206
name: polarity
def: "Polarity of the measured secondary ions (?)" [COMPUTIS:IMS]
relationship: is_a IMS:1000120 ! SIMS

[Term]
id: IMS:1001207
name: primary ion dose density
def: "Density of the primary ions." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000120 ! SIMS
relationship: has_units UO:0000030 ! ions per square centimeter

[Term]
id: IMS:1001211
name: solvent
def: "The solvent which was used to pick up the analyte from the surface of the imaging object." [COMPUTIS:IMS]
relationship: is_a IMS:1000121 ! DESI

[Term]
id: IMS:1001212
name: spray voltage
def: "Voltage applied to the DESI source to get ions moving into the direction of the inlet of the mass spectrometer." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000121 ! DESI
relationship: has_units UO:0000248 ! kilovolt

[Term]
id: IMS:1001213
name: solvent flowrate
def: "Rate with which the solvent is flowing on the surface of the imaging object" [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a IMS:1000121 ! DESI
relationship: has_units IMS:1000131 ! milliliter per minute