format-version: 1.2
data-version: 1.1.0
date: 04:01:2018 15:52
saved-by: Alan Race
default-namespace: imagingMS.ontology
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>
remark: creator: Alan Race <alan.race@uni-bayreuth.de>
import: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
ontology: ims

[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 parameter
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: probe scan mode 
def: "Describes the method how the probe was moved across the sample while acquiring data." [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: "OBSOLETE Terms to describe units" [COMPUTIS:IMS]
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology
comment: This is unneccessary as UO:0000000 (unit) exists, so was made obsolete.
is_obsolete: true

[Term]
id: IMS:1000014
name: ibd data type
def: "OBSOLETE Encoding type of binary data, e.g. 32-bit integer." [COMPUTIS:IMS]
is_a: MS:1000518 ! binary data type
relationship: part_of IMS:0000000 ! Imaging Mass Spectrometry Ontology
comment: Binary data type (MS:1000518) exists in PSI ontology so making this obsolete.
is_obsolete: true

[Term]
id: IMS:1000015
name: charge density
def: "A measure of electric charge, the amount of electric charge per unit area" [COMPUTIS:IMS]
is_a: UO:0000000 ! unit

[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]
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]
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."
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."
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."
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."
is_a: IMS:1000004 ! Image
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000046
name: pixel size (x)
def: "Describes the length of a pixel in the x dimension. If no pixel size y (IMS:1000047) is explicitly specified, then this also describes the length of a pixel in the y dimension." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1000004 ! Image
relationship: has_units UO:0000001 ! length unit

[Term]
id: IMS:1000047
name: pixel size y
def: "Describes the length of a pixel in the y dimension." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1000004 ! Image
relationship: has_units UO:0000001 ! length unit

[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."
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."
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."
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."
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."
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."
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."
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."
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."
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."
is_a: IMS:1000008 ! Ibd Indentification

[Term]
id: IMS:1000090
name: ibd MD5
def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) 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."
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. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1000009 ! Ibd Checksum

[Term]
id: IMS:1000092
name: ibd SHA-256
def: "SHA-256 (member of Secure Hash Algorithm-2 family) 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." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1000009 ! data file checksum type

[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."
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."
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."
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."
is_a: IMS:1000001 ! Ibd Offest Handle
relationship: has_units UO:0000233 ! Byte

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

[Term]
id: IMS:1000111
name: raster mode
def: "probe is moved while continuously acquiring data from the sample." [COMPUTIS:IMS]
is_a: IMS:1000011 ! probe mode

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

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

[Term]
id: IMS:1000121
name: DESI parameter
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]
is_a: IMS:1000015 ! charge density unit

[Term]
id: IMS:1000131
name: milliliters per minute
def: "A flow rate describes the throughput per time." [COMPUTIS:IMS]
is_a: UO:0000270 ! volumetric flow rate unit

[Term]
id: IMS:1000141
name: 32-bit integer
def: "OBSOLETE Signed 32 bit integer." [COMPUTIS:IMS]
is_a: IMS:1000014 ! ibd data type
comment: 32-bit integer (MS:1000519) exists in PSI obo so making obsolete.
is_obsolete: true

[Term]
id: IMS:1000142
name: 64-bit integer
def: "Signed 64 bit integer." [COMPUTIS:IMS]
is_a: IMS:1000014 ! ibd data type
comment: 64-bit integer (MS:1000520) exists in PSI obo so making obsolete.
is_obsolete: true

[Term]
id: IMS:1000199
name: sample stage attribute
def: "Properties related to and describing the sample stage." [COMPUTIS:IMS]
relationship: part_of IMS:1000002 ! Sample Stage

[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."
is_a: IMS:1000199 ! sample stage attribute
relationship: has_units UO:0000187 ! Percent

[Term]
id: IMS:1000201
name: step size
def: "Specify the distance between two different messuring points on the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1000199 ! sample stage attribute
relationship: has_units UO:0000017 ! Micrometer

[Term]
id: IMS:1000202
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: part_of IMS:1000002 ! Sample Stage

[Term]
id: IMS:1000203
name: stage scan speed
def: "Speed at which the stage moves." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1000199 ! sample stage attribute
relationship: has_units UO:0000094 ! meter per second

[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]
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]
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]
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]
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]
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]
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]
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]
is_a: IMS:1000041 ! Scan Pattern

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

[Term]
id: IMS:1000481
name: vertical line scan
def: "The scanning line is a vertical one." [COMPUTIS:IMS]
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]
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]
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]
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]
is_a: IMS:1000049 ! Line Scan Direction

[Term]
id: IMS:1000500
name: conversion to imzML
def: "Conversion of a file format to Mass Spectrometry Imaging imzML file format." [COMPUTIS:IMS]
is_a: MS:1000530 ! file format conversion

[Term]
id: IMS:1000501
name: imzMLParser
def: "imzMLParser library for reading and writing imzML." [COMPUTIS:IMS]
is_a: MS:1001457 ! data processing software

[Term]
id: IMS:1000502
name: imzMLConverter
def: "imzMLConverter software for conversion from proprietary formats to imzML." [COMPUTIS:IMS]
is_a: MS:1001457 ! data processing software

[Term]
id: IMS:1000503
name: imzMLValidator
def: "imzMLValidator software for validation of imzML." [COMPUTIS:IMS]
is_a: MS:1001457 ! data processing software

[Term]
id: IMS:1000504
name: SpectralAnalysis
def: "SpectralAnalysis software for visualisation, processing and multivariate analysis of spectral imaging data." [COMPUTIS:IMS]
is_a: MS:1001457 ! data processing software

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

[Term]
id: IMS:1100001
name: 16-bit integer
def: "Signed 16-bit integer." [COMPUTIS:IMS]
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]
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."
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."
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."
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."
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]
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."
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]
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."
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."
is_a: IMS:1000121 ! DESI
relationship: has_units UO:0000270 ! volumetric flow rate unit

[Term]
id: IMS:1001500
name: sample type
def: "Broad category describing the sample." [COMPUTIS:IMS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000457 ! sample

[Term]
id: IMS:1001510
name: inorganic sample
def: "A sample not consisting of or deriving from living matter." [COMPUTIS:IMS]
is_a: IMS:1001500 ! sample type

[Term]
id: IMS:1001520
name: organic sample
def: "A sample related to or derived from living matter." [COMPUTIS:IMS]
is_a: IMS:1001500 ! sample type

[Term]
id: IMS:1001521
name: biological sample
def: "A sample related to biology or living organisms." [COMPUTIS:IMS]
is_a: IMS:1001520 ! organic sample

[Term]
id: IMS:1001522
name: clinical sample
def: "A sample related to or deriving from actual patients." [COMPUTIS:IMS]
is_a: IMS:1001521 ! biological sample

[Term]
id: IMS:1001523
name: pathological sample
def: "A sample related to pathology." [COMPUTIS:IMS]
is_a: IMS:1001522 ! clinical sample

[Term]
id: IMS:1001524
name: food sample
def: "A sample related to or deriving from any nutritious substance." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1001520 ! biological sample

[Term]
id: IMS:1001525
name: bacteria sample
def: "A sample consisting of or related to bacteria." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1001520 ! biological sample

[Term]
id: IMS:1001600
name: sample origin attribute
def: "An attribute related to the origin of the sample." [COMPUTIS:IMS]
relationship: part_of MS:1000457 ! sample

[Term]
id: IMS:1001601
name: sample ethical approval
def: "Ethical approval required for experiments to be performed on the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1001600 ! sample origin attribute

[Term]
id: IMS:1001602
name: sample origin institution
def: "Institution at which the sample originated." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1001600 ! sample origin attribute

[Term]
id: IMS:1002000
name: analysed sample portion
def: "Description of how much of the sample was analysed." [COMPUTIS:IMS]
relationship: part_of MS:1000548 ! sample attribute

[Term]
id: IMS:1002001
name: sectioned sample
def: "Analysis performed on a section of the sample." [COMPUTIS:IMS]
is_a: IMS:1002000 ! analysed sample portion

[Term]
id: IMS:1002002
name: whole sample
def: "Analysis performed on entire sample." [COMPUTIS:IMS]
is_a: IMS:1002000 ! analysed sample portion

[Term]
id: IMS:1002003
name: blockface sample
def: "Analysis performed on the blockface of a cut sample." [COMPUTIS:IMS]
is_a: IMS:1002000 ! analysed sample portion

[Term]
id: IMS:1002005
name: sampling method
def: "Method used to extract the sample from a larger encompassing object." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1000457 ! sample

[Term]
id: IMS:1002010
name: sample storage condition
def: "Storage condition of the sample prior to analysis." [COMPUTIS:IMS]
relationship: part_of MS:1000548 ! sample attribute

[Term]
id: IMS:1002011
name: fixed
def: "Sample has undergone a fixation process." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002010 ! sample storage condition

[Term]
id: IMS:1002012
name: fresh frozen
def: "Sample has been frozen." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002010 ! sample storage condition

[Term]
id: IMS:1002013
name: embedded
def: "Sample has undergone an embedding procedure." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002010 ! sample storage condition

[Term]
id: IMS:1002014
name: sample storage attribute
def: "Attribute related to the storage of a sample." [COMPUTIS:IMS]
relationship: part_of IMS:1002010 ! sample storage condition

[Term]
id: IMS:1002015
name: sample storage time before sectioning
def: "Duration of time between the sample being acquired and sectioning being performed." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002014 ! sample storage attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
relationship: has_units UO:0000032 ! hour
relationship: has_units UO:0000033 ! day
relationship: has_units UO:0000034 ! week
relationship: has_units UO:0000035 ! month
relationship: has_units UO:0000036 ! year

[Term]
id: IMS:1002016
name: section storage time after sectioning and before analysis
def: "Duration of time between sectioning having been performed and performing MSI analysis." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002014 ! sample storage attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
relationship: has_units UO:0000032 ! hour
relationship: has_units UO:0000033 ! day
relationship: has_units UO:0000034 ! week
relationship: has_units UO:0000035 ! month
relationship: has_units UO:0000036 ! year

[Term]
id: IMS:1002017
name: sample storage temperature
def: "Temperature at which the sample was stored prior to analysis." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002014 ! sample storage attribute
relationship: has_units UO:0000027 ! degree Celsius
relationship: has_units UO:0000012 ! kelvin

[Term]
id: IMS:1002018
name: freezing method
def: "Method used for freezing the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of IMS:1002012 ! frozen

[Term]
id: IMS:1002019
name: flash frozen
def: "Flash frozen by slow immersion in liquid nitrogen cooled isopentane." [COMPUTIS:IMS]
is_a: IMS:1002016 ! freezing method

[Term]
id: IMS:1002020
name: sample storage time before analysis
def: "Duration of time between the sample being acquired and analysis being performed." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002014 ! sample storage attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
relationship: has_units UO:0000032 ! hour
relationship: has_units UO:0000033 ! day
relationship: has_units UO:0000034 ! week
relationship: has_units UO:0000035 ! month
relationship: has_units UO:0000036 ! year

[Term]
id: IMS:1002021
name: sample storage method
def: "Method used for storing the sample prior to analysis." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: IMS:1002050
name: stabilisation
def: "Application of a process to make the sample more stable, stopping degradation and changes from occurring." [COMPUTIS:IMS]
relationship: part_of MS:1000457 ! sample

[Term]
id: IMS:1002051
name: no stabilisation performed
def: "No stabilisation was performed." [COMPUTIS:IMS]
is_a: IMS:1002050 ! stabilisation

[Term]
id: IMS:1002052
name: stabilisation method
def: "Method used to perform stabilisation." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002050 ! stabilisation

[Term]
id: IMS:1002053
name: rapid heating stabilisation
def: "Stabilisation performed through rapid conductive heating." [COMPUTIS:IMS]
is_a: IMS:1002051 ! stabilisation method

[Term]
id: IMS:1002054
name: focused microwave irradiation stabilisation
def: "Stabilisation performed through focused microwave irradiation." [COMPUTIS:IMS]
is_a: IMS:1002051 ! stabilisation method

[Term]
id: IMS:1002100
name: sectioning method
def: "Description of the method used to section the sample." [COMPUTIS:IMS]
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002101
name: microtome sectioning
def: "Microtome used to perform sectioning." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of IMS:1002100 ! sectioning method

[Term]
id: IMS:1002102
name: microtome model
def: "Specific microtome model used to perform sectioning." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of IMS:1002101 ! microtome sectioning

[Term]
id: IMS:1002103
name: sectioning attribute
def: "Properties of the microtome sectioning process with an associated value." [COMPUTIS:IMS]
relationship: part_of IMS:1002101 ! microtome sectioning

[Term]
id: IMS:1002104
name: cutting temperature
def: "Temperature of the sample when the sectioning was performed." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002103 ! cryomicrotome sectioning attribute
relationship: has_units UO:0000027 ! degree Celsius
relationship: has_units UO:0000012 ! kelvin

[Term]
id: IMS:1002105
name: cutting thickness
def: "Thickness of the section as set on the microtome." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002103 ! sectioning attribute
relationship: has_units UO:0000017 ! micrometer

[Term]
id: IMS:1002106
name: blade sectioning
def: "Blade used to perform sectioning." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of IMS:1002100 ! sectioning method

[Term]
id: IMS:1002107
name: section thickness
def: "Measured thickness of the sample after sectioning." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1002103 ! sectioning attribute
relationship: has_units UO:0000017 ! micrometer

[Term]
id: IMS:1002200
name: mounting method
def: "Description of the method used to mount the sample onto the target." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002201
name: thaw mounting
def: "Mounting the sample onto the target by warming the reverse of the target." [COMPUTIS:IMS]
is_a: IMS:1002200 ! mounting method

[Term]
id: IMS:1002202
name: tape mounting
def: "Mounting the sample onto the target using tape." [COMPUTIS:IMS]
is_a: IMS:1002200 ! mounting method


[Term]
id: IMS:1002300
name: sample drying
def: "Application of a process to dry the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002301
name: drying method attribute
def: "Attribute related to the drying of a sample." [COMPUTIS:IMS]
relationship: part_of IMS:1002300 ! drying method

[Term]
id: IMS:1002302
name: drying time
def: "Duration of time that the drying procedure was applied." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a IMS:1002301 ! drying method attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: IMS:1002303
name: no drying performed
def: "No drying process performed." [COMPUTIS:IMS]
is_a: IMS:1002300 ! sample drying

[Term]
id: IMS:1002304
name: sample drying method
def: "Description of the method used to dry the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002300 ! sample drying

[Term]
id: IMS:1002400
name: sample washing
def: "Application of a process to wash the sample." [COMPUTIS:IMS]
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002401
name: no washing performed
def: "No washing method performed." [COMPUTIS:IMS]
is_a: IMS:1002400 ! sample washing

[Term]
id: IMS:1002402
name: sample washing method
def: "Method used to perform washing of the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002400 ! sample washing

[Term]
id: IMS:1002500
name: on-sample chemistry
def: "Additional treatment of the sample, such as enzymatic digestion or derivatisation." [COMPUTIS:IMS]
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002501
name: no on-sample chemistry performed
def: "No on-sample chemistry method performed." [COMPUTIS:IMS]
is_a: IMS:1002500 ! on-sample chemistry

[Term]
id: IMS:1002502
name: on-sample chemistry method
def: "Method used to perform on-sample chemistry." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002500 ! on-sample chemistry

[Term]
id: IMS:1002503
name: on-sample chemistry attribute
def: "Attribute related to the on-sample chemistry." [COMPUTIS:IMS]
relationship: part_of IMS:1002500 ! on-sample chemistry

[Term]
id: IMS:1002504
name: on-sample chemistry reagent
def: "Reagent used in the on-sample chemistry process." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002503 ! on-sample chemistry attribute

[Term]
id: IMS:1002600
name: in-experiment quantification
def: "Quantification integrated into the experiment." [COMPUTIS:IMS]
relationship: part_of MS:1000831 ! sample preparation

[Term]
id: IMS:1002601
name: no in-experiment quantification performed
def: "No in-experiment quantification method performed." [COMPUTIS:IMS]
is_a: IMS:1002600 ! in-experiment quantification

[Term]
id: IMS:1002602
name: in-experiment quantification method
def: "Method used to perform in-experiment quantification." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1002600 ! in-experiment quantification

[Term]
id: IMS:1002603
name: internal standard quantification
def: "Quantification performed through application of an internal standard." [COMPUTIS:IMS]
is_a: IMS:1002602 ! in-experiment quantification method

[Term]
id: IMS:1002604
name: adjacent dilution series quantification
def: "Quantification performed through a dilution series adjacent to the sample." [COMPUTIS:IMS]
is_a: IMS:1002602 ! in-experiment quantification method

[Term]
id: IMS:1002605
name: sprayed-on standard quantification
def: "Quantification performed through application of a standard via spraying." [COMPUTIS:IMS]
is_a: IMS:1002602 ! in-experiment quantification method

[Term]
id: IMS:1003000
name: spraying method
def: "Method used to perform spraying of a matrix." [COMPUTIS:IMS]
relationship: part_of MS:1000838 ! sprayed MALDI matrix preparation

[Term]
id: IMS:1003001
name: automated spraying of matrix
def: "Spraying performed using an automated method, such as a robotic system." [COMPUTIS:IMS]
is_a: IMS:1003000 ! spray method

[Term]
id: IMS:1003002
name: manual spraying of matrix
def: "Spraying performed manually by the user, such as with an artistic airbrush." [COMPUTIS:IMS]
is_a: IMS:1003000 ! spray method

[Term]
id: IMS:1003003
name: automated spraying device
def: "Robotic system for spraying a matrix." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of IMS:1003001 ! automated spraying of matrix

[Term]
id: IMS:1003004
name: automated sprayer attribute
def: "Attribute related to the automatic spraying device." [COMPUTIS:IMS]
relationship: part_of IMS:1003001 ! automated spraying of matrix

[Term]
id: IMS:1003005
name: automated sprayer nozzle movement speed
def: "Speed at which the spray head (including the nozzle) moves during spraying of the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1003004 ! automated spraying attribute

[Term]
id: IMS:1003006
name: automated sprayer flow-rate
def: "Flow-rate used to dispense the solvent to the sprayer." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1003004 ! automated spraying attribute

[Term]
id: IMS:1003007
name: automated sprayer nozzle temperature
def: "Temperature of the nozzle of the sprayer during spraying." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: IMS:1003004 ! automated spraying attribute

[Term]
id: IMS:1005001
name: xz compression
def: "XZ compression." [COMPUTIS:IMS]
is_a: MS:1000572 ! binary data compression type

[Term]
id: IMS:1005002
name: lz4 compression
def: "LZ4 compression." [COMPUTIS:IMS]
is_a: MS:1000572 ! binary data compression type

[Term]
id: IMS:1005003
name: zstd compression
def: "Zstandard compression." [COMPUTIS:IMS]
is_a: MS:1000572 ! binary data compression type

[Term]
id: IMS:1006000
name: repetition rate
def: "Describes the number of pulses per second when a laser is operating in pulsed mode." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000106 ! hertz

[Term]
id: IMS:1006001
name: laser shots per spectrum
def: "Describes the number of laser pulses interrogating the sample to generate a single spectrum." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute

[Term]
id: IMS:1006002
name: m/z at which resolution was measured
def: "m/z at which the mass resolution was measured." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: part_of MS:1000012 ! resolution measurement method
relationship: has_units MS:1000040 ! m/z

[Term]
id: IMS:1006003
name: postmortem time
def: "Time after sacrifice and before sampling occurs." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
relationship: has_units UO:0000032 ! hour
relationship: has_units UO:0000033 ! day
relationship: has_units UO:0000034 ! week
relationship: has_units UO:0000035 ! month
relationship: has_units UO:0000036 ! year

[Term]
id: IMS:1006004
name: age
def: "Age of the sample at time of analysis." [COMPUTIS:IMS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
relationship: has_units UO:0000032 ! hour
relationship: has_units UO:0000033 ! day
relationship: has_units UO:0000034 ! week
relationship: has_units UO:0000035 ! month
relationship: has_units UO:0000036 ! year

[Term]
id: IMS:1006005
name: sample species
def: "Species of the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: IMS:1006006
name: sample organ
def: "Analysed organ." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: IMS:1006007
name: sample condition
def: "Description of whether the sample is wildtype, diseased, control." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: IMS:1006008
name: optical image location
def: "Uniform resource identifier (URI) for the location of the optical image corresponding to the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: IMS:1006009
name: optical image attribute
def: "Attribute related to the optical image." [COMPUTIS:IMS]
part_of: MS:1006008 ! sample attribute

[Term]
id: IMS:1006010
name: optical image subject
def: "Subject of the optical image." [COMPUTIS:IMS]
is_a: IMS:1006009 ! optical image attribute

[Term]
id: IMS:1006011
name: optical image of analysed sample
def: "Subject of the optical image is the exact sample that was analysed." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1006010 ! optical image subject

[Term]
id: IMS:1006012
name: optical image of adjacent section of analysed sample
def: "Subject of the optical image is an adjacent section to the analysed section." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1006010 ! optical image subject

[Term]
id: IMS:1006013
name: sample morphological classification
def: "Morphological classification of the sample." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: IMS:1006014
name: sampling location
def: "OBSOLETE Location at which the sample was taken from the specimen." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
comment: This is unneccessary as IMS:1006013 (sample morphological classification) should cover this information.
is_obsolete: true

[Term]
id: IMS:1006015
name: staining method used for optical image 
def: "Method used for staining the sample prior to optical imaging." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1006010 ! optical image subject

[Term]
id: IMS:1006016
name: ion source model
def: "Model name and number of the ion source used." [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: IMS:1006017
name: method used to align optical image 
def: "method used to align optical image with MSI data" [COMPUTIS:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: IMS:1006009 ! optical image attribute
