Person
type: NodeShape
closed: true
description: personal information
ignored properties: type org
ignored properties: country
ignored properties: role
ignored properties: type
ignored properties: orcid
ignored properties: name org
property:
  datatype: string
  description: first name
  max count: 1
  node kind: Literal
  order: 1
  path: givenName
property:
  datatype: string
  description: email
  max count: 1
  node kind: Literal
  order: 3
  path: email
  pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
property:
  datatype: boolean
  description: job title
  max count: 1
  node kind: Literal
  order: 2
  path: jobTitle
property:
  datatype: string
  description: last name
  max count: 1
  node kind: Literal
  order: 0
  path: familyName
property:
  datatype: string
  description: work phone
  max count: 1
  node kind: Literal
  order: 4
  path: telephone

OSCEM schemasEMDatasetBase
type: NodeShape
closed: false
description: OSC-EM Metadata for a dataset
ignored properties: type
property:
  class: Any
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: OSCEM schemassample
property:
  class: Any
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: OSCEM schemasinstrument
property:
  class: Any
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: OSCEM schemasacquisition
property:
  class: Any
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: OSCEM schemasorganizational

acquisitionAcquisition
type: NodeShape
closed: true
description: General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
ignored properties: type
ignored properties: tilt axis angle
ignored properties: tilt angle
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitionholder cryogen
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitionenergy filter
property:
  datatype: string
  description: Specifies which Acquisition subschema/class is in use.
  max count: 1
  node kind: Literal
  order: 0
  path: acquisitiontechnique
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 8
  path: acquisitiontemperature range
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionspecialist optics
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionholder
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionnominal defocus
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 11
  path: acquisitiondose per movie
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 14
  path: acquisitiondate time
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionimageshift
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 17
  path: acquisitionframes per movie
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionscreen current
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 26
  path: acquisitionbeamtiltgroups
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 4
  path: acquisitionnominal magnification
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionbeamtilt
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 27
  path: acquisitiongainref flip rotate
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionexposure time
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 20
  path: acquisitionbinning camera
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncalibrated defocus
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitionimage size
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 5
  path: acquisitioncalibrated magnification
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 21
  path: acquisitionpixel size
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 16
  path: acquisitioncryogen
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitiongrids imaged
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionmicroscope software
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionbeamshift
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiondetectors
property:
  datatype: integer
  description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionimages generated

acquisitionAcquisitionSpa
type: NodeShape
closed: true
ignored properties: type
property:
  datatype: integer
  description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionimages generated
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionexposure time
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionbeamtilt
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 26
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 16
  path: acquisitioncryogen
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionmicroscope software
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 14
  path: acquisitiondate time
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionholder
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionbeamshift
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitionimage size
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 21
  path: acquisitionpixel size
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 5
  path: acquisitioncalibrated magnification
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 8
  path: acquisitiontemperature range
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitionenergy filter
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitionholder cryogen
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 17
  path: acquisitionframes per movie
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionscreen current
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 20
  path: acquisitionbinning camera
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitiongrids imaged
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 27
  path: acquisitiongainref flip rotate
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionimageshift
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 11
  path: acquisitiondose per movie
property:
  datatype: string
  description: Single particle acquisition
  in: spa
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitiontechnique
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiondetectors
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionnominal defocus
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncalibrated defocus
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionspecialist optics
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 4
  path: acquisitionnominal magnification

custom typesDescriptor
type: NodeShape
closed: false
description: List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
ignored properties: type
property:
  class: Any
  description: Description of the descriptor
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesdescriptor thing
property:
  datatype: string
  description: Name defining the descriptor
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: custom typesdescriptor name

custom typesDescriptors
type: NodeShape
closed: true
ignored properties: type
property:
  class: Any
  description: Description of the descriptor
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesdescriptor thing
property:
  datatype: string
  description: Name defining the descriptor
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: custom typesdescriptor name

custom typesSeries
type: NodeShape
closed: true
description: A series of numbers constructed from min, max, and increment
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesmaximal
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesminimal
property:
  class: custom typesQuantitySI
  description: Increment between elements of a series
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesincrement

environmental sampleSampleEnv
type: NodeShape
closed: true
description: Unifying class to describe the full sample.
ignored properties: type
ignored properties: cellular tomogrowth condition
property:
  class: environmental sampleSpecimenEnv
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: environmental samplespecimen env
property:
  class: environmental sampleFreezing
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: environmental samplefreezing
property:
  class: environmental sampleTomogramFeatures
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: environmental sampletomogram features
property:
  class: environmental sampleThinning
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: environmental samplethinning

EMDatasetCell
type: NodeShape
closed: true
description: cryo electron tomography dataset of a cellular sample, lab grown
ignored properties: type
property:
  class: Organizational
  description: Information on authors and grants
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: OSCEM schemasorganizational
property:
  class: instrumentInstrument
  description: Describe the instrument used to acquire the data
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: OSCEM schemasinstrument
property:
  class: cellular tomoSampleCell
  description: Sample information
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: OSCEM schemassample
property:
  class: AcquisitionCelTomo
  description: Describe the data acquisition parameters
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: OSCEM schemasacquisition

AcquisitionEnvTomo
type: NodeShape
closed: true
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  datatype: string
  description: Environmental tomography
  in: env_tomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  datatype: integer
  description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus

AcquisitionSubTomo
type: NodeShape
closed: true
ignored properties: type
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
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  path: acquisitionexposure time
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
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  path: acquisitionmicroscope software
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Subtomogram averaging
  in: subtomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionholder cryogen

AcquisitionTomo
type: NodeShape
closed: true
ignored properties: type
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  datatype: string
  description: Specifies which Acquisition subschema/class is in use.
  max count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  datatype: integer
  description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionholder cryogen
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle

quantityValue
type: NodeShape
closed: true
description: if a value has a unit, it should be given as a unit value pair.
ignored properties: custom typesvalueSI
ignored properties: type
ignored properties: custom typesunitSI
property:
  datatype: float
  description: the value of a field with a unit
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: hasQuantityKind
property:
  datatype: string
  description: the unit of a given value
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: hasUnit

Grant
type: NodeShape
closed: true
description: Grant
ignored properties: type
property:
  datatype: string
  description: Country of the institution
  max count: 1
  node kind: Literal
  order: 5
  path: country
property:
  datatype: string
  description: name of the grant
  max count: 1
  node kind: Literal
  order: 0
  path: grant name
property:
  class: quantityValue
  description: budget
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: budget
property:
  datatype: dateTime
  description: start date
  max count: 1
  node kind: Literal
  order: 1
  path: start date
property:
  datatype: string
  description: project id
  max count: 1
  node kind: Literal
  order: 4
  path: identifier
property:
  datatype: dateTime
  description: end date
  max count: 1
  node kind: Literal
  order: 2
  path: end date

Microscope
type: NodeShape
closed: true
description: Microscope information
ignored properties: type
property:
  datatype: string
  description: The name of the manufacturer
  max count: 1
  node kind: Literal
  order: 1
  path: custom typesmanufacturer
property:
  datatype: string
  description: The model of the item
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: custom typesmodel

acquisitionChromaticAberrationCorrector
type: NodeShape
closed: true
description: Special device used to correct instrument inherent chromatic aberration.
ignored properties: type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: Details of a given specialist instrument
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type

acquisitionPhaseplate
type: NodeShape
closed: true
description: Used to modulate the phase of the electron wave.
ignored properties: type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: Type of phaseplate
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type

acquisitionSphericalAberrationCorrector
type: NodeShape
closed: true
description: Special device used to correct instrument inherent spherical aberration.
ignored properties: type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: Details of a given specialist instrument
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type

cellular tomoGrowthCondition
type: NodeShape
closed: true
description: how the cells were grown
ignored properties: type
property:
  datatype: string
  description: What growth media was used
  max count: 1
  node kind: Literal
  order: 0
  path: cellular tomomedia
property:
  class: custom typesQuantitySI
  description: temperature of the sample; in K.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: cellular tomotemperature growth
property:
  datatype: string
  description: were there any special treatment conditions; such as addition of certain chemicals etc
  max count: 1
  node kind: Literal
  order: 3
  path: cellular tomotreatment
property:
  datatype: string
  description: What was the targeted cell cycle state, if any
  max count: 1
  node kind: Literal
  order: 2
  path: cellular tomocell cycle
property:
  datatype: string
  description: What was the atmosphere the sample was in, elaborate on any special gases present etc.
  max count: 1
  node kind: Literal
  order: 4
  path: cellular tomoatmosphere growth
property:
  datatype: string
  description: In/on what kind of surface/container the cells were grown; i.e. directly on a grid
  max count: 1
  node kind: Literal
  order: 1
  path: cellular tomogrowth location

cellular tomoSampleCell
type: NodeShape
closed: true
description: Unifying class to describe the full sample with growth conditions
ignored properties: type
property:
  class: environmental sampleFreezing
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: environmental samplefreezing
property:
  class: environmental sampleTomogramFeatures
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: environmental sampletomogram features
property:
  class: environmental sampleSpecimenEnv
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: environmental samplespecimen env
property:
  class: cellular tomoGrowthCondition
  description: how the specimen was grown
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: cellular tomogrowth condition
property:
  class: environmental sampleThinning
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: environmental samplethinning

instrumentInstrument
type: NodeShape
closed: true
description: Instrument values, mostly constant across a data collection.
ignored properties: type
property:
  datatype: string
  description: Mode of imaging used during data collection
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: instrumentimaging
property:
  datatype: string
  description: Mode of illumination used during data collection
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: instrumentillumination
property:
  datatype: string
  description: Operating mode of the microscope, i.e. "TEM", "STEM"
  max count: 1
  node kind: Literal
  order: 7
  path: instrumentoperating mode
property:
  class: Microscope
  description: Microscope information
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: instrumentmicroscope
property:
  datatype: string
  description: Type of electron source used in the microscope, such as FEG
  max count: 1
  min count: 1
  node kind: Literal
  order: 3
  path: instrumentelectron source
property:
  class: custom typesQuantitySI
  description: Refers to how tightly or widely the electron beam is focused onto the sample, in mrad. Typically low convergence for TEM and high for STEM.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 8
  path: instrumentbeam convergence
property:
  class: custom typesQuantitySI
  description: Spherical aberration of the instrument, in mm
  max count: 1
  node kind: BlankNodeOrIRI
  order: 6
  path: instrumentcs
property:
  class: custom typesQuantitySI
  description: Voltage used for the electron acceleration, in kV
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: instrumentacceleration voltage
property:
  class: custom typesQuantitySI
  description: C2 aperture size used in data acquisition, in µm
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: instrumentc2 aperture

Author
type: NodeShape
closed: true
description: Details on the person performing the experiment.
ignored properties: type
property:
  datatype: string
  description: Country of the institution
  max count: 1
  node kind: Literal
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  path: country
property:
  datatype: string
  description: email
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  node kind: Literal
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  path: email
  pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
property:
  datatype: string
  description: Name of the organization
  max count: 1
  node kind: Literal
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  path: name org
property:
  datatype: string
  description: ORCID of the author, a type of unique identifier
  max count: 1
  node kind: Literal
  order: 0
  path: orcid
property:
  datatype: string
  description: first name
  max count: 1
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  node kind: Literal
  order: 6
  path: givenName
property:
  datatype: string
  description: last name
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  node kind: Literal
  order: 5
  path: familyName
property:
  datatype: string
  description: Role of the author, for example principal investigator
  max count: 1
  node kind: Literal
  order: 2
  path: role
property:
  description: Type of organization, academic, commercial, governmental, etc.
  in: Academic
  in: Commercial
  in: Government
  in: Other
  max count: 1
  min count: 1
  order: 4
  path: type org
property:
  datatype: boolean
  description: job title
  max count: 1
  node kind: Literal
  order: 7
  path: jobTitle
property:
  datatype: string
  description: work phone
  max count: 1
  node kind: Literal
  order: 9
  path: telephone

Funder
type: NodeShape
closed: true
description: Description of the project funding
ignored properties: type
property:
  description: Type of organization, academic, commercial, governmental, etc.
  in: Academic
  in: Commercial
  in: Government
  in: Other
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  path: type org
property:
  datatype: string
  description: Country of the institution
  max count: 1
  node kind: Literal
  order: 2
  path: country
property:
  datatype: string
  description: funding organization/person.
  max count: 1
  node kind: Literal
  order: 0
  path: funder name

Organizational
type: NodeShape
closed: true
description: Overarching category for authors and grants
ignored properties: type
property:
  class: Funder
  description: funding organization/person.
  node kind: BlankNodeOrIRI
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  path: funder
property:
  class: Grant
  description: List of grants associated with the project
  node kind: BlankNodeOrIRI
  order: 0
  path: grants
property:
  class: Author
  description: List of authors associated with the project
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: authors

AcquisitionCelTomo
type: NodeShape
closed: true
ignored properties: type
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  datatype: string
  description: Cellular tomography
  in: cellular_tomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  datatype: integer
  description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: integer
  description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  class: custom typesBoundingBox2D
  description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionholder cryogen
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification

environmental sampleFreezing
type: NodeShape
closed: true
description: how the sample was frozen.
ignored properties: type
property:
  description: freezing method - such as plunge freezing, high pressure freezing etc.
  in: plunge_freezing
  in: high_pressure_freezing
  max count: 1
  order: 1
  path: environmental samplemethod
property:
  datatype: string
  description: Any further comments on the freezing process go here.
  max count: 1
  node kind: Literal
  order: 6
  path: environmental sampledetails
property:
  datatype: string
  description: the cryogen used to freeze the sample, i.e. ethane
  max count: 1
  node kind: Literal
  order: 0
  path: environmental samplecryogen sample env
property:
  class: custom typesQuantitySI
  description: temperature of the sample right before freezing; in K.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: environmental sampletemperature env
property:
  datatype: boolean
  description: whether blotting was performed.
  max count: 1
  node kind: Literal
  order: 2
  path: environmental sampleblotting
property:
  datatype: string
  description: What was the atmosphere the sample was in right before freezing, elaborate on any special gases present etc.
  max count: 1
  node kind: Literal
  order: 5
  path: environmental sampleatmosphere
property:
  class: custom typesQuantitySI
  description: humidity of the atmosphere right before/ during freezing; in %.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: environmental samplehumidity env

environmental sampleSpecimenEnv
type: NodeShape
closed: true
description: base information on the acquisition and treatment of the sample itself.
ignored properties: type
property:
  datatype: string
  description: if the sample is a tissue sample please indicate what type of tissue.
  max count: 1
  node kind: Literal
  order: 1
  path: environmental sampletissue
property:
  datatype: string
  description: the organism(s) present in your sample, if not perfectly defined try to asses as close as possible.
  min count: 1
  node kind: Literal
  order: 0
  path: environmental sampleorganism
property:
  datatype: string
  description: the geographical location of your source, optimally in a geographic coordinate system.
  max count: 1
  node kind: Literal
  order: 3
  path: environmental samplelocation
property:
  datatype: string
  description: where is this sample from? i.e. Hospital
  max count: 1
  node kind: Literal
  order: 2
  path: environmental samplesource env
property:
  datatype: date
  description: When the sample was collected
  max count: 1
  node kind: Literal
  order: 4
  path: environmental samplecollection date
property:
  datatype: string
  description: What was done to the sample, please give an overview of relevant treatments.
  max count: 1
  node kind: Literal
  order: 5
  path: environmental samplehandling

environmental sampleThinning
type: NodeShape
closed: true
description: how the frozen sample was thinned by i.e. FiB-milling
ignored properties: type
property:
  datatype: boolean
  description: whether a lift out was performed
  max count: 1
  node kind: Literal
  order: 4
  path: environmental samplelift out
property:
  datatype: string
  description: The thinning method used, such as FIB milling.
  max count: 1
  node kind: Literal
  order: 0
  path: environmental samplemethod thin
property:
  datatype: string
  description: what ion source was used?
  max count: 1
  node kind: Literal
  order: 2
  path: environmental sampleion source
property:
  datatype: string
  description: Instrument used for thinning the sample
  max count: 1
  node kind: Literal
  order: 1
  path: environmental sampleinstrument thin
property:
  class: custom typesQuantitySI
  description: What was the target thickness of the lamella; in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: environmental sampletarget thickness

environmental sampleTomogramFeatures
type: NodeShape
closed: true
description: what was the target of the tomograms, and what area of a cell do they cover.
ignored properties: type
property:
  datatype: string
  description: What was the main biological target of your research for this tomogram?
  max count: 1
  node kind: Literal
  order: 2
  path: environmental samplemain target
property:
  datatype: string
  description: What type of cellular features are present in your tomograms?
  max count: 1
  node kind: Literal
  order: 0
  path: environmental samplecellular features
property:
  datatype: string
  description: What organelles; if any; are present?
  node kind: Literal
  order: 1
  path: environmental sampleorganelles
property:
  datatype: string
  description: If you have any further comments on your tomograms please leave them here
  max count: 1
  node kind: Literal
  order: 3
  path: environmental sampledetails tomo

TiltAngle
type: NodeShape
closed: true
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Increment between elements of a series
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesincrement
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesminimal
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesmaximal

Any
type: NodeShape
closed: true
description: Any type, used as the base for type-narrowing.
ignored properties: type

acquisitionDetector
type: NodeShape
closed: true
description: Class representing a detector
ignored properties: type
property:
  datatype: string
  description: Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
  max count: 1
  node kind: Literal
  order: 1
  path: acquisitionmode
property:
  class: custom typesRange
  description: Collection angle set, min and max values in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncollection angle
property:
  class: custom typesQuantitySI
  description: Dispersion of an analytical detector, in eV
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitiondispersion
property:
  datatype: string
  description: The name of the item
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesname

acquisitionEnergyFilter
type: NodeShape
closed: true
description: A device used to filter for electrons with specific energy.
ignored properties: type
property:
  datatype: string
  description: The model of the item
  max count: 1
  node kind: Literal
  order: 1
  path: custom typesmodel
property:
  class: custom typesQuantitySI
  description: Width of the energy filter used.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionwidth energy filter
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused

acquisitionSpecialistOptics
type: NodeShape
closed: true
description: Optional optics used to correct for instrument limitations.
ignored properties: type
property:
  class: acquisitionChromaticAberrationCorrector
  description: Specialist device to correct for chromatic aberration of the microscope lenses
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionchromatic aberration corrector
property:
  class: acquisitionSphericalAberrationCorrector
  description: Specialist device to correct for spherical aberration of the microscope lenses
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionspherical aberration corrector
property:
  class: acquisitionPhaseplate
  description: Phaseplate is a special optics device that can be used to enhance contrast
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: acquisitionphaseplate

custom typesImageSize
type: NodeShape
closed: true
description: size of a 2D image (in integer units)
ignored properties: type
property:
  datatype: integer
  description: The height of a given item - unit depends on item
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesheight
property:
  datatype: integer
  description: The width of a given item - unit depends on item
  max count: 1
  node kind: Literal
  order: 1
  path: custom typeswidth

custom typesBoundingBox2D
type: NodeShape
closed: true
description: an axis-aligned 2D bounding box (float units)
ignored properties: type
property:
  class: custom typesQuantitySI
  description: minimum x
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesx min
property:
  class: custom typesQuantitySI
  description: maximum x
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesx max
property:
  class: custom typesQuantitySI
  description: minimum y
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesy min
property:
  class: custom typesQuantitySI
  description: maximum y
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: custom typesy max

custom typesRange
type: NodeShape
closed: true
description: A range constructed from min and max
ignored properties: type
ignored properties: custom typesincrement
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesmaximal
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesminimal

custom typesQuantitySI
type: NodeShape
closed: true
description: unit value extended to have two additional fields si_value and si_unit
ignored properties: type
property:
  datatype: float
  description: the value of a field with a unit
  max count: 1
  min count: 1
  node kind: Literal
  order: 3
  path: hasQuantityKind
property:
  datatype: float
  description: value of a given field in respect to its SI unit
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesvalueSI
property:
  datatype: string
  description: the unit of a given value
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: hasUnit
property:
  datatype: string
  description: the SI unit attached to a si value
  max count: 1
  node kind: Literal
  order: 1
  path: custom typesunitSI

datatype: string
description: Type of cryogen used in the holder - if the holder is cooled seperately
max count: 1
node kind: Literal
order: 9
path: acquisitionholder cryogen

class: custom typesQuantitySI
description: Pixel size, in Angstrom
max count: 1
min count: 1
node kind: BlankNodeOrIRI
order: 23
path: acquisitionpixel size

datatype: integer
description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
max count: 1
node kind: Literal
order: 21
path: acquisitionimages generated

class: TiltAngle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
max count: 1
min count: 1
node kind: BlankNodeOrIRI
order: 1
path: tilt angle

class: custom typesQuantitySI
description: Pixel size, in Angstrom
max count: 1
min count: 1
node kind: BlankNodeOrIRI
order: 23
path: acquisitionpixel size

datatype: dateTime
description: Time and date of the data acquisition
max count: 1
min count: 1
node kind: Literal
order: 16
path: acquisitiondate time

class: custom typesRange
description: Temperature during data collection, in K with min and max values.
max count: 1
node kind: BlankNodeOrIRI
order: 10
path: acquisitiontemperature range

datatype: float
description: The tilt axis angle of a tomography series
max count: 1
min count: 1
node kind: Literal
order: 0
path: tilt axis angle