imzml 0.0.2

data/data/imagingMS.obo

@@ -0,0 +1,560 @@
+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: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: 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