AcquisitionSpa
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: :technique
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: spa
  on property: :technique
subclass of: Restriction
  min cardinality: 1
  on property: :technique
subclass of: Acquisition
in scheme: acquisition

descriptors
type: ObjectProperty
type: SlotDefinition
range: Descriptors
definition: List of custom descriptors for user-defined key-value pairs describing how movies were obtained or any related information
in scheme: custom types

person
type: ObjectProperty
type: SlotDefinition
range: Person
definition: person
in scheme: organizational

EMDatasetTomo
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Organizational
  on property: :organizational
subclass of: Restriction
  max cardinality: 1
  on property: :acquisition
subclass of: Restriction
  min cardinality: 0
  on property: :sample
subclass of: Restriction
  min cardinality: 0
  on property: :organizational
subclass of: Restriction
  all values from: Instrument
  on property: :instrument
subclass of: Restriction
  all values from: AcquisitionSubTomo
  on property: :acquisition
subclass of: Restriction
  max cardinality: 1
  on property: :organizational
subclass of: Restriction
  min cardinality: 1
  on property: :acquisition
subclass of: Restriction
  max cardinality: 1
  on property: :instrument
subclass of: Restriction
  all values from: SampleMolecular
  on property: :sample
subclass of: Restriction
  max cardinality: 1
  on property: :sample
subclass of: Restriction
  min cardinality: 1
  on property: :instrument
subclass of: EMDatasetBase
definition: cryo electron tomography dataset, with a focus on a single protein (complex) & subtomogram averaging
in scheme: oscem-schemas-tomo

AcquisitionCelTomo
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: :technique
subclass of: Restriction
  min cardinality: 1
  on property: :technique
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: cellular_tomo
  on property: :technique
subclass of: AcquisitionTomo
in scheme: tomography

AcquisitionEnvTomo
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: env_tomo
  on property: :technique
subclass of: Restriction
  max cardinality: 1
  on property: :technique
subclass of: Restriction
  min cardinality: 1
  on property: :technique
subclass of: AcquisitionTomo
in scheme: tomography

EMDatasetBase
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Any
  on property: organizational
subclass of: Restriction
  max cardinality: 1
  on property: sample
subclass of: Restriction
  min cardinality: 0
  on property: instrument
subclass of: Restriction
  min cardinality: 0
  on property: sample
subclass of: Restriction
  min cardinality: 0
  on property: organizational
subclass of: Restriction
  all values from: Any
  on property: acquisition
subclass of: Restriction
  max cardinality: 1
  on property: acquisition
subclass of: Restriction
  all values from: Any
  on property: instrument
subclass of: Restriction
  all values from: Any
  on property: sample
subclass of: Restriction
  min cardinality: 0
  on property: acquisition
subclass of: Restriction
  max cardinality: 1
  on property: instrument
subclass of: Restriction
  max cardinality: 1
  on property: organizational
definition: OSC-EM Metadata for a dataset
in scheme: oscem-emdataset

Descriptor
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: descriptor_name
subclass of: Restriction
  max cardinality: 1
  on property: descriptor_name
subclass of: Restriction
  min cardinality: 1
  on property: descriptor_name
subclass of: Restriction
  all values from: Any
  on property: descriptor_thing
subclass of: Restriction
  min cardinality: 0
  on property: descriptor_thing
subclass of: Restriction
  max cardinality: 1
  on property: descriptor_thing
definition: List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
in scheme: custom types

Descriptors
type: Class
type: ClassDefinition
subclass of: Descriptor
in scheme: custom types

Series
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: increment
subclass of: Restriction
  max cardinality: 1
  on property: increment
subclass of: Restriction
  all values from: QuantitySI
  on property: increment
subclass of: Range
definition: A series of numbers constructed from min, max, and increment
in scheme: custom types

Instrument
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 1
  on property: acceleration_voltage
subclass of: Restriction
  all values from: QuantitySI
  on property: acceleration_voltage
subclass of: Restriction
  max cardinality: 1
  on property: electron_source
subclass of: Restriction
  all values from: QuantitySI
  on property: beam_convergence
subclass of: Restriction
  max cardinality: 1
  on property: acceleration_voltage
subclass of: Restriction
  min cardinality: 0
  on property: cs
subclass of: Restriction
  max cardinality: 1
  on property: imaging
subclass of: Restriction
  max cardinality: 1
  on property: cs
subclass of: Restriction
  all values from: QuantitySI
  on property: c2_aperture
subclass of: Restriction
  min cardinality: 0
  on property: c2_aperture
subclass of: Restriction
  all values from: Microscope
  on property: microscope
subclass of: Restriction
  min cardinality: 1
  on property: electron_source
subclass of: Restriction
  min cardinality: 1
  on property: imaging
subclass of: Restriction
  all values from: String
  on property: imaging
subclass of: Restriction
  min cardinality: 0
  on property: operating_mode
subclass of: Restriction
  all values from: String
  on property: illumination
subclass of: Restriction
  max cardinality: 1
  on property: illumination
subclass of: Restriction
  max cardinality: 1
  on property: operating_mode
subclass of: Restriction
  min cardinality: 1
  on property: illumination
subclass of: Restriction
  max cardinality: 1
  on property: beam_convergence
subclass of: Restriction
  all values from: String
  on property: operating_mode
subclass of: Restriction
  min cardinality: 0
  on property: beam_convergence
subclass of: Restriction
  min cardinality: 1
  on property: microscope
subclass of: Restriction
  all values from: String
  on property: electron_source
subclass of: Restriction
  max cardinality: 1
  on property: c2_aperture
subclass of: Restriction
  max cardinality: 1
  on property: microscope
subclass of: Restriction
  all values from: QuantitySI
  on property: cs
definition: Instrument values, mostly constant across a data collection.
in scheme: instrument

Organizational
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Grant
  on property: grants
subclass of: Restriction
  min cardinality: 0
  on property: funder
subclass of: Restriction
  min cardinality: 1
  on property: authors
subclass of: Restriction
  all values from: Author
  on property: authors
subclass of: Restriction
  min cardinality: 0
  on property: grants
subclass of: Restriction
  all values from: Funder
  on property: funder
definition: Overarching category for authors and grants
in scheme: organizational

oscem-schemas-tomo
type: Ontology
license: CC-BY
definition: Schema for the Open Standards Community for Electron Microscopy (OSC-EM)

Sample
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  all values from: Grid
  on property: grid
subclass of: Restriction
  min cardinality: 0
  on property: grid
subclass of: Restriction
  max cardinality: 1
  on property: grid
subclass of: Restriction
  max cardinality: 1
  on property: overall_molecule
subclass of: Restriction
  all values from: String
  on property: description
subclass of: Restriction
  all values from: String
  on property: name
subclass of: Restriction
  all values from: OverallMolecule
  on property: overall_molecule
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: molecule
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: specimen
subclass of: Restriction
  min cardinality: 0
  on property: overall_molecule
subclass of: Restriction
  all values from: Specimen
  on property: specimen
subclass of: Restriction
  all values from: Ligand
  on property: ligands
subclass of: Restriction
  min cardinality: 1
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: ligands
subclass of: Restriction
  min cardinality: 0
  on property: specimen
subclass of: Restriction
  all values from: Molecule
  on property: molecule
definition: Unifying class to describe the full sample.
in scheme: sample

SampleMolecular
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: :overall molecule
subclass of: Restriction
  min cardinality: 0
  on property: :name
subclass of: Restriction
  all values from: Thing
  on property: :overall molecule
subclass of: Restriction
  max cardinality: 1
  on property: :name
subclass of: Restriction
  min cardinality: 1
  on property: :overall molecule
subclass of: Restriction
  all values from: Thing
  on property: :description
subclass of: Restriction
  min cardinality: 0
  on property: :description
subclass of: Restriction
  max cardinality: 1
  on property: :description
subclass of: Restriction
  all values from: Thing
  on property: :name
subclass of: Sample
in scheme: sample

AcquisitionSubTomo
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: subtomo
  on property: :technique
subclass of: Restriction
  min cardinality: 1
  on property: :technique
subclass of: Restriction
  max cardinality: 1
  on property: :technique
subclass of: AcquisitionTomo
in scheme: tomography

Acquisition
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: QuantitySI
  on property: exposure_time
subclass of: Restriction
  min cardinality: 0
  on property: holder_cryogen
subclass of: Restriction
  max cardinality: 1
  on property: grids_imaged
subclass of: Restriction
  all values from: QuantitySI
  on property: dose_per_movie
subclass of: Restriction
  min cardinality: 0
  on property: grids_imaged
subclass of: Restriction
  min cardinality: 0
  on property: frames_per_movie
subclass of: Restriction
  min cardinality: 1
  on property: pixel_size
subclass of: Restriction
  max cardinality: 1
  on property: holder_cryogen
subclass of: Restriction
  min cardinality: 0
  on property: beamshift
subclass of: Restriction
  min cardinality: 1
  on property: date_time
subclass of: Restriction
  all values from: EnergyFilter
  on property: energy_filter
subclass of: Restriction
  min cardinality: 0
  on property: nominal_magnification
subclass of: Restriction
  min cardinality: 0
  on property: gainref_flip_rotate
subclass of: Restriction
  min cardinality: 0
  on property: microscope_software
subclass of: Restriction
  all values from: QuantitySI
  on property: screen_current
subclass of: Restriction
  all values from: String
  on property: holder
subclass of: Restriction
  max cardinality: 1
  on property: screen_current
subclass of: Restriction
  all values from: String
  on property: holder_cryogen
subclass of: Restriction
  all values from: Range
  on property: calibrated_defocus
subclass of: Restriction
  all values from: Range
  on property: temperature_range
subclass of: Restriction
  min cardinality: 0
  on property: images_generated
subclass of: Restriction
  max cardinality: 1
  on property: energy_filter
subclass of: Restriction
  all values from: Integer
  on property: images_generated
subclass of: Restriction
  max cardinality: 1
  on property: beamshift
subclass of: Restriction
  max cardinality: 1
  on property: nominal_magnification
subclass of: Restriction
  min cardinality: 0
  on property: calibrated_magnification
subclass of: Restriction
  min cardinality: 0
  on property: beamtilt
subclass of: Restriction
  min cardinality: 0
  on property: specialist_optics
subclass of: Restriction
  all values from: Range
  on property: nominal_defocus
subclass of: Restriction
  max cardinality: 1
  on property: specialist_optics
subclass of: Restriction
  min cardinality: 0
  on property: dose_per_movie
subclass of: Restriction
  all values from: Integer
  on property: beamtiltgroups
subclass of: Restriction
  all values from: String
  on property: technique
subclass of: Restriction
  all values from: String
  on property: cryogen
subclass of: Restriction
  max cardinality: 1
  on property: binning_camera
subclass of: Restriction
  min cardinality: 0
  on property: exposure_time
subclass of: Restriction
  min cardinality: 0
  on property: calibrated_defocus
subclass of: Restriction
  max cardinality: 1
  on property: imageshift
subclass of: Restriction
  max cardinality: 1
  on property: beamtiltgroups
subclass of: Restriction
  max cardinality: 1
  on property: exposure_time
subclass of: Restriction
  all values from: String
  on property: microscope_software
subclass of: Restriction
  all values from: Datetime
  on property: date_time
subclass of: Restriction
  max cardinality: 1
  on property: dose_per_movie
subclass of: Restriction
  max cardinality: 1
  on property: microscope_software
subclass of: Restriction
  all values from: Integer
  on property: grids_imaged
subclass of: Restriction
  min cardinality: 0
  on property: screen_current
subclass of: Restriction
  min cardinality: 0
  on property: holder
subclass of: Restriction
  all values from: BoundingBox2D
  on property: imageshift
subclass of: Restriction
  max cardinality: 1
  on property: frames_per_movie
subclass of: Restriction
  min cardinality: 0
  on property: beamtiltgroups
subclass of: Restriction
  all values from: Integer
  on property: nominal_magnification
subclass of: Restriction
  min cardinality: 0
  on property: temperature_range
subclass of: Restriction
  all values from: BoundingBox2D
  on property: beamtilt
subclass of: Restriction
  min cardinality: 0
  on property: technique
subclass of: Restriction
  all values from: SpecialistOptics
  on property: specialist_optics
subclass of: Restriction
  max cardinality: 1
  on property: pixel_size
subclass of: Restriction
  max cardinality: 1
  on property: technique
subclass of: Restriction
  min cardinality: 0
  on property: nominal_defocus
subclass of: Restriction
  max cardinality: 1
  on property: holder
subclass of: Restriction
  max cardinality: 1
  on property: gainref_flip_rotate
subclass of: Restriction
  all values from: ImageSize
  on property: image_size
subclass of: Restriction
  min cardinality: 0
  on property: image_size
subclass of: Restriction
  max cardinality: 1
  on property: calibrated_magnification
subclass of: Restriction
  all values from: Detector
  on property: detectors
subclass of: Restriction
  max cardinality: 1
  on property: images_generated
subclass of: Restriction
  all values from: Integer
  on property: frames_per_movie
definition: General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
in scheme: acquisition

ChromaticAberrationCorrector
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: instrument_type
subclass of: Restriction
  min cardinality: 1
  on property: used
subclass of: Restriction
  max cardinality: 1
  on property: used
subclass of: Restriction
  min cardinality: 1
  on property: instrument_type
subclass of: Restriction
  all values from: Boolean
  on property: used
subclass of: Restriction
  max cardinality: 1
  on property: instrument_type
definition: Special device used to correct instrument inherent chromatic aberration.
in scheme: acquisition

Detector
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: QuantitySI
  on property: dispersion
subclass of: Restriction
  all values from: Range
  on property: collection_angle
subclass of: Restriction
  max cardinality: 1
  on property: collection_angle
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: dispersion
subclass of: Restriction
  min cardinality: 0
  on property: collection_angle
subclass of: Restriction
  all values from: String
  on property: mode
subclass of: Restriction
  max cardinality: 1
  on property: mode
subclass of: Restriction
  min cardinality: 0
  on property: dispersion
subclass of: Restriction
  all values from: String
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: mode
definition: Class representing a detector
in scheme: acquisition

EnergyFilter
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Boolean
  on property: used
subclass of: Restriction
  min cardinality: 0
  on property: model
subclass of: Restriction
  min cardinality: 1
  on property: width_energy_filter
subclass of: Restriction
  all values from: QuantitySI
  on property: width_energy_filter
subclass of: Restriction
  max cardinality: 1
  on property: width_energy_filter
subclass of: Restriction
  all values from: String
  on property: model
subclass of: Restriction
  max cardinality: 1
  on property: model
subclass of: Restriction
  max cardinality: 1
  on property: used
subclass of: Restriction
  min cardinality: 1
  on property: used
definition: A device used to filter for electrons with specific energy.
in scheme: acquisition

Phaseplate
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 1
  on property: instrument_type
subclass of: Restriction
  min cardinality: 1
  on property: used
subclass of: Restriction
  all values from: String
  on property: instrument_type
subclass of: Restriction
  all values from: Boolean
  on property: used
subclass of: Restriction
  max cardinality: 1
  on property: instrument_type
subclass of: Restriction
  max cardinality: 1
  on property: used
definition: Used to modulate the phase of the electron wave.
in scheme: acquisition

SpecialistOptics
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: phaseplate
subclass of: Restriction
  max cardinality: 1
  on property: phaseplate
subclass of: Restriction
  all values from: ChromaticAberrationCorrector
  on property: chromatic_aberration_corrector
subclass of: Restriction
  min cardinality: 0
  on property: spherical_aberration_corrector
subclass of: Restriction
  all values from: Phaseplate
  on property: phaseplate
subclass of: Restriction
  max cardinality: 1
  on property: spherical_aberration_corrector
subclass of: Restriction
  all values from: SphericalAberrationCorrector
  on property: spherical_aberration_corrector
subclass of: Restriction
  max cardinality: 1
  on property: chromatic_aberration_corrector
subclass of: Restriction
  min cardinality: 0
  on property: chromatic_aberration_corrector
definition: Optional optics used to correct for instrument limitations.
in scheme: acquisition

SphericalAberrationCorrector
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: instrument_type
subclass of: Restriction
  max cardinality: 1
  on property: used
subclass of: Restriction
  all values from: Boolean
  on property: used
subclass of: Restriction
  min cardinality: 1
  on property: instrument_type
subclass of: Restriction
  max cardinality: 1
  on property: instrument_type
subclass of: Restriction
  min cardinality: 1
  on property: used
definition: Special device used to correct instrument inherent spherical aberration.
in scheme: acquisition

detectors
type: ObjectProperty
type: SlotDefinition
range: Detector
in scheme: acquisition

Microscope
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: manufacturer
subclass of: Restriction
  min cardinality: 1
  on property: model
subclass of: Restriction
  max cardinality: 1
  on property: model
subclass of: Restriction
  min cardinality: 0
  on property: manufacturer
subclass of: Restriction
  all values from: String
  on property: manufacturer
subclass of: Restriction
  all values from: String
  on property: model
definition: Microscope information
in scheme: instrument

Author
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: country
subclass of: Restriction
  all values from: Thing
  on property: :family name
subclass of: Restriction
  min cardinality: 1
  on property: :family name
subclass of: Restriction
  min cardinality: 0
  on property: country
subclass of: Restriction
  min cardinality: 1
  on property: :email
subclass of: Restriction
  all values from: String
  on property: name_org
subclass of: Restriction
  max cardinality: 1
  on property: role
subclass of: Restriction
  all values from: :OrganizationTypeEnum
  on property: type_org
subclass of: Restriction
  min cardinality: 0
  on property: name_org
subclass of: Restriction
  all values from: String
  on property: orcid
subclass of: Restriction
  min cardinality: 0
  on property: role
subclass of: Restriction
  max cardinality: 1
  on property: orcid
subclass of: Restriction
  max cardinality: 1
  on property: :family name
subclass of: Restriction
  all values from: String
  on property: role
subclass of: Restriction
  max cardinality: 1
  on property: type_org
subclass of: Restriction
  all values from: Thing
  on property: :email
subclass of: Restriction
  max cardinality: 1
  on property: name_org
subclass of: Restriction
  all values from: String
  on property: country
subclass of: Restriction
  max cardinality: 1
  on property: :email
subclass of: Restriction
  min cardinality: 1
  on property: :given name
subclass of: Restriction
  all values from: Thing
  on property: :given name
subclass of: Restriction
  min cardinality: 0
  on property: orcid
subclass of: Restriction
  max cardinality: 1
  on property: :given name
subclass of: Restriction
  min cardinality: 1
  on property: type_org
subclass of: Person
definition: Details on the person performing the experiment.
in scheme: organizational

Funder
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: type_org
subclass of: Restriction
  max cardinality: 1
  on property: type_org
subclass of: Restriction
  min cardinality: 0
  on property: country
subclass of: Restriction
  max cardinality: 1
  on property: funder_name
subclass of: Restriction
  all values from: String
  on property: country
subclass of: Restriction
  max cardinality: 1
  on property: country
subclass of: Restriction
  all values from: :OrganizationTypeEnum
  on property: type_org
subclass of: Restriction
  all values from: String
  on property: funder_name
subclass of: Restriction
  min cardinality: 0
  on property: funder_name
definition: Description of the project funding
in scheme: organizational

Grant
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: start_date
subclass of: Restriction
  min cardinality: 0
  on property: country
subclass of: Restriction
  max cardinality: 1
  on property: budget
subclass of: Restriction
  max cardinality: 1
  on property: country
subclass of: Restriction
  min cardinality: 0
  on property: grant_name
subclass of: Restriction
  all values from: Datetime
  on property: start_date
subclass of: Restriction
  max cardinality: 1
  on property: grant_name
subclass of: Restriction
  max cardinality: 1
  on property: start_date
subclass of: Restriction
  all values from: String
  on property: project_id
subclass of: Restriction
  max cardinality: 1
  on property: project_id
subclass of: Restriction
  min cardinality: 0
  on property: project_id
subclass of: Restriction
  min cardinality: 0
  on property: budget
subclass of: Restriction
  max cardinality: 1
  on property: end_date
subclass of: Restriction
  all values from: QuantityValue
  on property: budget
subclass of: Restriction
  all values from: Datetime
  on property: end_date
subclass of: Restriction
  all values from: String
  on property: country
subclass of: Restriction
  min cardinality: 0
  on property: end_date
subclass of: Restriction
  all values from: String
  on property: grant_name
definition: Grant
in scheme: organizational

Person
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: job_title
subclass of: Restriction
  min cardinality: 0
  on property: family_name
subclass of: Restriction
  all values from: String
  on property: given_name
subclass of: Restriction
  max cardinality: 1
  on property: telephone
subclass of: Restriction
  min cardinality: 0
  on property: given_name
subclass of: Restriction
  max cardinality: 1
  on property: family_name
subclass of: Restriction
  max cardinality: 1
  on property: given_name
subclass of: Restriction
  max cardinality: 1
  on property: email
subclass of: Restriction
  min cardinality: 0
  on property: email
subclass of: Restriction
  all values from: Datatype
    intersection of: String
    intersection of: Datatype
      on datatype: string
      with restrictions:
        pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
  on property: email
subclass of: Restriction
  min cardinality: 0
  on property: telephone
subclass of: Restriction
  all values from: Boolean
  on property: job_title
subclass of: Restriction
  all values from: String
  on property: family_name
subclass of: Restriction
  all values from: String
  on property: telephone
subclass of: Restriction
  max cardinality: 1
  on property: job_title
definition: personal information
in scheme: organizational

authors
type: ObjectProperty
type: SlotDefinition
range: Author
definition: List of authors associated with the project
in scheme: organizational

funder
type: ObjectProperty
type: SlotDefinition
range: Funder
definition: funding organization/person.
in scheme: organizational

grants
type: ObjectProperty
type: SlotDefinition
range: Grant
definition: List of grants associated with the project
in scheme: organizational

cellular_tomo
type: Class
type: :AcquisitionTechnique
subclass of: :AcquisitionTechnique

env_tomo
type: Class
type: :AcquisitionTechnique
subclass of: :AcquisitionTechnique

spa
type: Class
type: :AcquisitionTechnique
subclass of: :AcquisitionTechnique

subtomo
type: Class
type: :AcquisitionTechnique
subclass of: :AcquisitionTechnique

FILAMENT
type: Class
type: :AssemblyEnum
subclass of: :AssemblyEnum

HELICAL ARRAY
type: Class
type: :AssemblyEnum
subclass of: :AssemblyEnum

PARTICLE
type: Class
type: :AssemblyEnum
subclass of: :AssemblyEnum

CELL
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

COMPLEX
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

ORGANELLE OR CELLULAR COMPONENT
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

RIBOSOME
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

TISSUE
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

VIRUS
type: Class
type: :MoleculeClassEnum
subclass of: :MoleculeClassEnum

Academic
type: Class
type: :OrganizationTypeEnum
subclass of: :OrganizationTypeEnum

Commercial
type: Class
type: :OrganizationTypeEnum
subclass of: :OrganizationTypeEnum

Government
type: Class
type: :OrganizationTypeEnum
subclass of: :OrganizationTypeEnum

Other
type: Class
type: :OrganizationTypeEnum
subclass of: :OrganizationTypeEnum

Grid
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: pretreatment_type
subclass of: Restriction
  min cardinality: 0
  on property: film_topology
subclass of: Restriction
  all values from: QuantitySI
  on property: pretreatment_pressure
subclass of: Restriction
  all values from: String
  on property: material
subclass of: Restriction
  max cardinality: 1
  on property: manufacturer
subclass of: Restriction
  min cardinality: 0
  on property: material
subclass of: Restriction
  max cardinality: 1
  on property: pretreatment_type
subclass of: Restriction
  all values from: Float
  on property: mesh
subclass of: Restriction
  max cardinality: 1
  on property: material
subclass of: Restriction
  all values from: String
  on property: film_thickness
subclass of: Restriction
  all values from: String
  on property: pretreatment_atmosphere
subclass of: Restriction
  max cardinality: 1
  on property: pretreatment_pressure
subclass of: Restriction
  max cardinality: 1
  on property: pretreatment_atmosphere
subclass of: Restriction
  min cardinality: 0
  on property: pretreatment_type
subclass of: Restriction
  max cardinality: 1
  on property: film_thickness
subclass of: Restriction
  all values from: String
  on property: film_topology
subclass of: Restriction
  max cardinality: 1
  on property: mesh
subclass of: Restriction
  min cardinality: 0
  on property: film_thickness
subclass of: Restriction
  max cardinality: 1
  on property: film_topology
subclass of: Restriction
  min cardinality: 0
  on property: manufacturer
subclass of: Restriction
  all values from: String
  on property: manufacturer
subclass of: Restriction
  min cardinality: 0
  on property: pretreatment_time
subclass of: Restriction
  all values from: String
  on property: film_material
subclass of: Restriction
  min cardinality: 0
  on property: pretreatment_atmosphere
subclass of: Restriction
  max cardinality: 1
  on property: film_support
subclass of: Restriction
  max cardinality: 1
  on property: film_material
subclass of: Restriction
  all values from: QuantitySI
  on property: pretreatment_time
subclass of: Restriction
  min cardinality: 0
  on property: film_support
subclass of: Restriction
  min cardinality: 0
  on property: mesh
subclass of: Restriction
  min cardinality: 0
  on property: film_material
subclass of: Restriction
  all values from: Boolean
  on property: film_support
subclass of: Restriction
  max cardinality: 1
  on property: pretreatment_time
subclass of: Restriction
  min cardinality: 0
  on property: pretreatment_pressure
definition: Details on the grid used in the experiment.
in scheme: sample

Ligand
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: smiles
subclass of: Restriction
  min cardinality: 0
  on property: reference
subclass of: Restriction
  all values from: String
  on property: smiles
subclass of: Restriction
  max cardinality: 1
  on property: smiles
subclass of: Restriction
  min cardinality: 0
  on property: present
subclass of: Restriction
  max cardinality: 1
  on property: reference
subclass of: Restriction
  max cardinality: 1
  on property: present
subclass of: Restriction
  all values from: Boolean
  on property: present
subclass of: Restriction
  all values from: String
  on property: reference
definition: Information on ligands if present.
in scheme: sample

Molecule
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: molecular_type
subclass of: Restriction
  min cardinality: 0
  on property: expression_system
subclass of: Restriction
  all values from: String
  on property: gene_name
subclass of: Restriction
  min cardinality: 0
  on property: gene_name
subclass of: Restriction
  min cardinality: 0
  on property: molecular_class
subclass of: Restriction
  max cardinality: 1
  on property: molecular_type
subclass of: Restriction
  max cardinality: 1
  on property: sequence
subclass of: Restriction
  min cardinality: 0
  on property: taxonomy_id_source
subclass of: Restriction
  max cardinality: 1
  on property: expression_system
subclass of: Restriction
  all values from: String
  on property: natural_source
subclass of: Restriction
  max cardinality: 1
  on property: natural_source
subclass of: Restriction
  all values from: String
  on property: taxonomy_id_expression
subclass of: Restriction
  all values from: String
  on property: molecular_class
subclass of: Restriction
  max cardinality: 1
  on property: taxonomy_id_source
subclass of: Restriction
  all values from: String
  on property: sequence
subclass of: Restriction
  min cardinality: 0
  on property: taxonomy_id_expression
subclass of: Restriction
  max cardinality: 1
  on property: gene_name
subclass of: Restriction
  max cardinality: 1
  on property: taxonomy_id_expression
subclass of: Restriction
  min cardinality: 1
  on property: sequence
subclass of: Restriction
  max cardinality: 1
  on property: molecular_class
subclass of: Restriction
  min cardinality: 1
  on property: name_mol
subclass of: Restriction
  all values from: String
  on property: name_mol
subclass of: Restriction
  all values from: String
  on property: expression_system
subclass of: Restriction
  all values from: String
  on property: taxonomy_id_source
subclass of: Restriction
  max cardinality: 1
  on property: name_mol
subclass of: Restriction
  min cardinality: 1
  on property: natural_source
subclass of: Restriction
  min cardinality: 0
  on property: molecular_type
definition: More detailed information about individual molecules.
in scheme: sample

OverallMolecule
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: name_sample
subclass of: Restriction
  all values from: :AssemblyEnum
  on property: assembly
subclass of: Restriction
  min cardinality: 0
  on property: assembly
subclass of: Restriction
  max cardinality: 1
  on property: assembly
subclass of: Restriction
  min cardinality: 1
  on property: name_sample
subclass of: Restriction
  max cardinality: 1
  on property: molecular_overall_type
subclass of: Restriction
  all values from: :MoleculeClassEnum
  on property: molecular_overall_type
subclass of: Restriction
  all values from: QuantitySI
  on property: molecular_weight
subclass of: Restriction
  min cardinality: 1
  on property: source
subclass of: Restriction
  min cardinality: 0
  on property: molecular_weight
subclass of: Restriction
  max cardinality: 1
  on property: molecular_weight
subclass of: Restriction
  min cardinality: 0
  on property: molecular_overall_type
subclass of: Restriction
  max cardinality: 1
  on property: source
subclass of: Restriction
  all values from: String
  on property: source
subclass of: Restriction
  max cardinality: 1
  on property: name_sample
definition: Description of the overall molecule
in scheme: sample

Specimen
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Boolean
  on property: vitrification
subclass of: Restriction
  max cardinality: 1
  on property: concentration
subclass of: Restriction
  max cardinality: 1
  on property: vitrification
subclass of: Restriction
  max cardinality: 1
  on property: temperature
subclass of: Restriction
  min cardinality: 0
  on property: temperature
subclass of: Restriction
  min cardinality: 0
  on property: shadowing
subclass of: Restriction
  min cardinality: 0
  on property: staining
subclass of: Restriction
  all values from: String
  on property: buffer
subclass of: Restriction
  all values from: Float
  on property: ph
subclass of: Restriction
  min cardinality: 0
  on property: vitrification
subclass of: Restriction
  all values from: QuantitySI
  on property: temperature
subclass of: Restriction
  max cardinality: 1
  on property: buffer
subclass of: Restriction
  max cardinality: 1
  on property: humidity
subclass of: Restriction
  min cardinality: 0
  on property: embedding
subclass of: Restriction
  min cardinality: 0
  on property: buffer
subclass of: Restriction
  all values from: Boolean
  on property: shadowing
subclass of: Restriction
  all values from: Boolean
  on property: embedding
subclass of: Restriction
  max cardinality: 1
  on property: shadowing
subclass of: Restriction
  min cardinality: 0
  on property: concentration
subclass of: Restriction
  all values from: String
  on property: vitrification_cryogen
subclass of: Restriction
  min cardinality: 0
  on property: humidity
subclass of: Restriction
  max cardinality: 1
  on property: embedding
subclass of: Restriction
  min cardinality: 0
  on property: ph
subclass of: Restriction
  all values from: QuantitySI
  on property: concentration
subclass of: Restriction
  all values from: Boolean
  on property: staining
subclass of: Restriction
  max cardinality: 1
  on property: ph
subclass of: Restriction
  max cardinality: 1
  on property: staining
subclass of: Restriction
  all values from: QuantitySI
  on property: humidity
subclass of: Restriction
  max cardinality: 1
  on property: vitrification_cryogen
subclass of: Restriction
  min cardinality: 0
  on property: vitrification_cryogen
definition: Description of specimen handling.
in scheme: sample

ligands
type: ObjectProperty
type: SlotDefinition
range: Ligand
definition: List of ligands associated with the sample
in scheme: sample

molecule
type: ObjectProperty
type: SlotDefinition
range: Molecule
definition: List of molecule associated with the sample
in scheme: sample

TiltAngle
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: :maximal
subclass of: Restriction
  max cardinality: 1
  on property: :increment
subclass of: Restriction
  min cardinality: 1
  on property: :maximal
subclass of: Restriction
  max cardinality: 1
  on property: :minimal
subclass of: Restriction
  all values from: Thing
  on property: :increment
subclass of: Restriction
  all values from: Thing
  on property: :maximal
subclass of: Restriction
  min cardinality: 1
  on property: :minimal
subclass of: Restriction
  all values from: Thing
  on property: :minimal
subclass of: Restriction
  min cardinality: 1
  on property: :increment
subclass of: Series
definition: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
in scheme: tomography

acquisition
type: ObjectProperty
type: SlotDefinition
range: Any
in scheme: oscem-emdataset

instrument
type: ObjectProperty
type: SlotDefinition
range: Any
in scheme: oscem-emdataset

organizational
type: ObjectProperty
type: SlotDefinition
range: Any
in scheme: oscem-emdataset

sample
type: ObjectProperty
type: SlotDefinition
range: Any
in scheme: oscem-emdataset

beamshift
type: ObjectProperty
type: SlotDefinition
range: BoundingBox2D
definition: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
in scheme: acquisition

beamtilt
type: ObjectProperty
type: SlotDefinition
range: BoundingBox2D
definition: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
in scheme: acquisition

beamtiltgroups
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: 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.
in scheme: acquisition

binning_camera
type: ObjectProperty
type: SlotDefinition
range: ImageSize
definition: Level of binning on the images applied during data collection
in scheme: acquisition

calibrated_defocus
type: ObjectProperty
type: SlotDefinition
range: Range
definition: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
in scheme: acquisition

calibrated_magnification
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: Calculated magnification, no unit
in scheme: acquisition

chromatic_aberration_corrector
type: ObjectProperty
type: SlotDefinition
range: ChromaticAberrationCorrector
definition: Specialist device to correct for chromatic aberration of the microscope lenses
in scheme: acquisition

collection_angle
type: ObjectProperty
type: SlotDefinition
range: Range
definition: Collection angle set, min and max values in mrad.
in scheme: acquisition

cryogen
type: ObjectProperty
type: SlotDefinition
range: String
definition: Cryogen used in cooling the instrument and sample, usually nitrogen
in scheme: acquisition

date_time
type: ObjectProperty
type: SlotDefinition
range: Datetime
definition: Time and date of the data acquisition
in scheme: acquisition

dispersion
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Dispersion of an analytical detector, in eV
in scheme: acquisition

dose_per_movie
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Average dose per image/movie/tilt - given in electrons per square Angstrom
in scheme: acquisition

energy_filter
type: ObjectProperty
type: SlotDefinition
range: EnergyFilter
definition: Whether an energy filter was used and its specifics.
in scheme: acquisition

exposure_time
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Time of data acquisition per movie/tilt - in s
in scheme: acquisition

frames_per_movie
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
in scheme: acquisition

gainref_flip_rotate
type: ObjectProperty
type: SlotDefinition
range: String
definition: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
in scheme: acquisition

grids_imaged
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: Number of grids imaged for this project - here with qualifier during this data acquisition
in scheme: acquisition

holder
type: ObjectProperty
type: SlotDefinition
range: String
definition: Speciman holder model
in scheme: acquisition

holder_cryogen
type: ObjectProperty
type: SlotDefinition
range: String
definition: Type of cryogen used in the holder - if the holder is cooled seperately
in scheme: acquisition

image_size
type: ObjectProperty
type: SlotDefinition
range: ImageSize
definition: The size of the image in pixels, height and width given.
in scheme: acquisition

images_generated
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: 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
in scheme: acquisition

imageshift
type: ObjectProperty
type: SlotDefinition
range: BoundingBox2D
definition: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
in scheme: acquisition

microscope_software
type: ObjectProperty
type: SlotDefinition
range: String
definition: Software used for instrument control,
in scheme: acquisition

mode
type: ObjectProperty
type: SlotDefinition
range: String
definition: Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
in scheme: acquisition

nominal_defocus
type: ObjectProperty
type: SlotDefinition
range: Range
definition: Target defocus set, min and max values in nm.
in scheme: acquisition

nominal_magnification
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: Magnification level as indicated by the instrument, no unit
in scheme: acquisition

phaseplate
type: ObjectProperty
type: SlotDefinition
range: Phaseplate
definition: Phaseplate is a special optics device that can be used to enhance contrast
in scheme: acquisition

pixel_size
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Pixel size, in Angstrom
in scheme: acquisition

screen_current
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: The total electron beam current hitting the viewing screen, in nA.
in scheme: acquisition

specialist_optics
type: ObjectProperty
type: SlotDefinition
range: SpecialistOptics
definition: Any type of special optics, such as a phaseplate
in scheme: acquisition

spherical_aberration_corrector
type: ObjectProperty
type: SlotDefinition
range: SphericalAberrationCorrector
definition: Specialist device to correct for spherical aberration of the microscope lenses
in scheme: acquisition

technique
type: ObjectProperty
type: SlotDefinition
range: String
definition: Specifies which Acquisition subschema/class is in use.
in scheme: acquisition

temperature_range
type: ObjectProperty
type: SlotDefinition
range: Range
definition: Temperature during data collection, in K with min and max values.
in scheme: acquisition
preferred label: temperature

width_energy_filter
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Width of the energy filter used.
in scheme: acquisition

QuantityValue
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: String
  on property: unit
subclass of: Restriction
  min cardinality: 1
  on property: unit
subclass of: Restriction
  all values from: Float
  on property: value
subclass of: Restriction
  min cardinality: 1
  on property: value
subclass of: Restriction
  max cardinality: 1
  on property: unit
subclass of: Restriction
  max cardinality: 1
  on property: value
definition: if a value has a unit, it should be given as a unit value pair.
in scheme: custom types

description
type: ObjectProperty
type: SlotDefinition
range: String
definition: The description of the item
in scheme: custom types

descriptor_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name defining the descriptor
in scheme: custom types

descriptor_thing
type: ObjectProperty
type: SlotDefinition
range: Any
definition: Description of the descriptor
in scheme: custom types

height
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: The height of a given item - unit depends on item
in scheme: custom types

increment
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Increment between elements of a series
in scheme: custom types

maximal
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Maximal value of a given dataset property
in scheme: custom types

minimal
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Minimal value of a given dataset property
in scheme: custom types

unit
type: ObjectProperty
type: SlotDefinition
range: String
definition: the unit of a given value
in scheme: custom types

unitSI
type: ObjectProperty
type: SlotDefinition
range: String
definition: the SI unit attached to a si value
in scheme: custom types

value
type: ObjectProperty
type: SlotDefinition
range: Float
definition: the value of a field with a unit
in scheme: custom types

valueSI
type: ObjectProperty
type: SlotDefinition
range: Float
definition: value of a given field in respect to its SI unit
in scheme: custom types

width
type: ObjectProperty
type: SlotDefinition
range: Integer
definition: The width of a given item - unit depends on item
in scheme: custom types

x_max
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: maximum x
in scheme: custom types

x_min
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: minimum x
in scheme: custom types

y_max
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: maximum y
in scheme: custom types

y_min
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: minimum y
in scheme: custom types

acceleration_voltage
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Voltage used for the electron acceleration, in kV
in scheme: instrument

beam_convergence
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: 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.
in scheme: instrument

c2_aperture
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: C2 aperture size used in data acquisition, in µm
in scheme: instrument

cs
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Spherical aberration of the instrument, in mm
in scheme: instrument

electron_source
type: ObjectProperty
type: SlotDefinition
range: String
definition: Type of electron source used in the microscope, such as FEG
in scheme: instrument

illumination
type: ObjectProperty
type: SlotDefinition
range: String
definition: Mode of illumination used during data collection
in scheme: instrument

imaging
type: ObjectProperty
type: SlotDefinition
range: String
definition: Mode of imaging used during data collection
in scheme: instrument

microscope
type: ObjectProperty
type: SlotDefinition
range: Microscope
definition: Microscope information
in scheme: instrument

operating_mode
type: ObjectProperty
type: SlotDefinition
range: String
definition: Operating mode of the microscope, i.e. "TEM", "STEM"
in scheme: instrument

budget
type: ObjectProperty
type: SlotDefinition
range: QuantityValue
definition: budget
in scheme: organizational

email
type: ObjectProperty
type: SlotDefinition
range: Datatype
  intersection of: String
  intersection of: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
definition: email
in scheme: organizational

end_date
type: ObjectProperty
type: SlotDefinition
range: Datetime
definition: end date
in scheme: organizational

family_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: last name
in scheme: organizational

funder_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: funding organization/person.
in scheme: organizational

given_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: first name
in scheme: organizational

grant_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: name of the grant
in scheme: organizational

job_title
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: job title
in scheme: organizational

name_org
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name of the organization
in scheme: organizational

orcid
type: ObjectProperty
type: SlotDefinition
range: String
definition: ORCID of the author, a type of unique identifier
in scheme: organizational

project_id
type: ObjectProperty
type: SlotDefinition
range: String
definition: project id
in scheme: organizational

role
type: ObjectProperty
type: SlotDefinition
range: String
definition: Role of the author, for example principal investigator
in scheme: organizational

start_date
type: ObjectProperty
type: SlotDefinition
range: Datetime
definition: start date
in scheme: organizational

telephone
type: ObjectProperty
type: SlotDefinition
range: String
definition: work phone
in scheme: organizational

assembly
type: ObjectProperty
type: SlotDefinition
range: :AssemblyEnum
definition: What type of higher order structure your sample forms - if any.
in scheme: sample

buffer
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name/composition of the (chemical) sample buffer during grid preparation
in scheme: sample

concentration
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Concentration of the (supra)molecule in the sample, in mg/ml
in scheme: sample

embedding
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether the sample was embedded
in scheme: sample

expression_system
type: ObjectProperty
type: SlotDefinition
range: String
definition: Scientific name of the organism used to produce the molecule of interest
in scheme: sample

film_material
type: ObjectProperty
type: SlotDefinition
range: String
definition: Type of material the support film is made of
in scheme: sample

film_support
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether a support film was used
in scheme: sample

film_thickness
type: ObjectProperty
type: SlotDefinition
range: String
definition: Thickness of the support film
in scheme: sample

film_topology
type: ObjectProperty
type: SlotDefinition
range: String
definition: Topology of the support film
in scheme: sample

gene_name
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name of the gene of interest
in scheme: sample

grid
type: ObjectProperty
type: SlotDefinition
range: Grid
definition: Description of the grid used
in scheme: sample

humidity
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Environmental humidity just before vitrification, in %
in scheme: sample

material
type: ObjectProperty
type: SlotDefinition
range: String
definition: Material out of which the grid is made
in scheme: sample

mesh
type: ObjectProperty
type: SlotDefinition
range: Float
definition: Grid mesh in lines per inch
in scheme: sample

molecular_class
type: ObjectProperty
type: SlotDefinition
range: String
definition: Class of the molecule
in scheme: sample

molecular_overall_type
type: ObjectProperty
type: SlotDefinition
range: :MoleculeClassEnum
definition: Description of the overall molecular type, i.e., a complex
in scheme: sample

molecular_type
type: ObjectProperty
type: SlotDefinition
range: String
definition: Description of the overall molecular type, i.e., a complex
in scheme: sample

molecular_weight
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Molecular weight in Da
in scheme: sample

name_mol
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name of an individual molecule (often protein) in the sample
in scheme: sample

name_sample
type: ObjectProperty
type: SlotDefinition
range: String
definition: Name of the full sample
in scheme: sample

natural_source
type: ObjectProperty
type: SlotDefinition
range: String
definition: Scientific name of the natural host organism
in scheme: sample

overall_molecule
type: ObjectProperty
type: SlotDefinition
range: OverallMolecule
definition: Description of the overall molecule
in scheme: sample

ph
type: ObjectProperty
type: SlotDefinition
range: Float
definition: pH of the sample buffer
in scheme: sample

present
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether the model contains any ligands
in scheme: sample

pretreatment_atmosphere
type: ObjectProperty
type: SlotDefinition
range: String
definition: Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.
in scheme: sample

pretreatment_pressure
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Pressure of the chamber during pretreatment, in Pa
in scheme: sample

pretreatment_time
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Length of time of the pretreatment in s
in scheme: sample

pretreatment_type
type: ObjectProperty
type: SlotDefinition
range: String
definition: Type of pretreatment of the grid, i.e., glow discharge
in scheme: sample

reference
type: ObjectProperty
type: SlotDefinition
range: String
definition: Link to a reference of your ligand, i.e., CCD, PubChem, etc.
in scheme: sample

sequence
type: ObjectProperty
type: SlotDefinition
range: String
definition: Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here
in scheme: sample

shadowing
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether the sample was shadowed
in scheme: sample

smiles
type: ObjectProperty
type: SlotDefinition
range: String
definition: Provide a valid SMILES string of your ligand
in scheme: sample

source
type: ObjectProperty
type: SlotDefinition
range: String
definition: Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.
in scheme: sample

specimen
type: ObjectProperty
type: SlotDefinition
range: Specimen
definition: Description of the specimen
in scheme: sample

staining
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether the sample was stained
in scheme: sample

taxonomy_id_expression
type: ObjectProperty
type: SlotDefinition
range: String
definition: Taxonomy ID of the expression system organism
in scheme: sample

taxonomy_id_source
type: ObjectProperty
type: SlotDefinition
range: String
definition: Taxonomy ID of the natural source organism
in scheme: sample

temperature
type: ObjectProperty
type: SlotDefinition
range: QuantitySI
definition: Environmental temperature just before vitrification, in K
in scheme: sample

vitrification
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: Whether the sample was vitrified
in scheme: sample

vitrification_cryogen
type: ObjectProperty
type: SlotDefinition
range: String
definition: Which cryogen was used for vitrification
in scheme: sample

AcquisitionTomo
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: TiltAngle
  on property: tilt_angle
subclass of: Restriction
  min cardinality: 1
  on property: tilt_axis_angle
subclass of: Restriction
  max cardinality: 1
  on property: tilt_angle
subclass of: Restriction
  min cardinality: 1
  on property: tilt_angle
subclass of: Restriction
  all values from: Float
  on property: tilt_axis_angle
subclass of: Restriction
  max cardinality: 1
  on property: tilt_axis_angle
subclass of: Acquisition
in scheme: tomography

tilt_angle
type: ObjectProperty
type: SlotDefinition
range: TiltAngle
definition: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
in scheme: tomography

tilt_axis_angle
type: ObjectProperty
type: SlotDefinition
range: Float
definition: The tilt axis angle of a tomography series
in scheme: tomography

ImageSize
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: Integer
  on property: width
subclass of: Restriction
  min cardinality: 0
  on property: height
subclass of: Restriction
  max cardinality: 1
  on property: height
subclass of: Restriction
  all values from: Integer
  on property: height
subclass of: Restriction
  max cardinality: 1
  on property: width
subclass of: Restriction
  min cardinality: 0
  on property: width
definition: size of a 2D image (in integer units)
in scheme: custom types

BoundingBox2D
type: Class
type: ClassDefinition
subclass of: Restriction
  max cardinality: 1
  on property: y_max
subclass of: Restriction
  min cardinality: 0
  on property: y_max
subclass of: Restriction
  all values from: QuantitySI
  on property: y_min
subclass of: Restriction
  max cardinality: 1
  on property: x_max
subclass of: Restriction
  all values from: QuantitySI
  on property: x_min
subclass of: Restriction
  max cardinality: 1
  on property: x_min
subclass of: Restriction
  max cardinality: 1
  on property: y_min
subclass of: Restriction
  min cardinality: 0
  on property: x_min
subclass of: Restriction
  all values from: QuantitySI
  on property: x_max
subclass of: Restriction
  min cardinality: 0
  on property: y_min
subclass of: Restriction
  min cardinality: 0
  on property: x_max
subclass of: Restriction
  all values from: QuantitySI
  on property: y_max
definition: an axis-aligned 2D bounding box (float units)
in scheme: custom types

manufacturer
type: ObjectProperty
type: SlotDefinition
range: String
definition: The name of the manufacturer
in scheme: custom types

model
type: ObjectProperty
type: SlotDefinition
range: String
definition: The model of the item
in scheme: custom types

name
type: ObjectProperty
type: SlotDefinition
range: String
definition: The name of the item
in scheme: custom types

type_org
type: ObjectProperty
type: SlotDefinition
range: :OrganizationTypeEnum
definition: Type of organization, academic, commercial, governmental, etc.
in scheme: organizational

instrument_type
type: ObjectProperty
type: SlotDefinition
range: String
definition: Details of a given specialist instrument
in scheme: acquisition

Range
type: Class
type: ClassDefinition
subclass of: Restriction
  all values from: QuantitySI
  on property: minimal
subclass of: Restriction
  min cardinality: 0
  on property: maximal
subclass of: Restriction
  all values from: QuantitySI
  on property: maximal
subclass of: Restriction
  max cardinality: 1
  on property: minimal
subclass of: Restriction
  min cardinality: 0
  on property: minimal
subclass of: Restriction
  max cardinality: 1
  on property: maximal
definition: A range constructed from min and max
in scheme: custom types

country
type: ObjectProperty
type: SlotDefinition
range: String
definition: Country of the institution
in scheme: organizational

Any
type: Class
type: ClassDefinition
definition: Any type, used as the base for type-narrowing.
in scheme: custom types

used
type: ObjectProperty
type: SlotDefinition
range: Boolean
definition: whether a specific instrument was used during data acquisition
in scheme: acquisition

QuantitySI
type: Class
type: ClassDefinition
subclass of: Restriction
  min cardinality: 0
  on property: valueSI
subclass of: Restriction
  all values from: Float
  on property: valueSI
subclass of: Restriction
  all values from: String
  on property: unitSI
subclass of: Restriction
  max cardinality: 1
  on property: unitSI
subclass of: Restriction
  min cardinality: 0
  on property: unitSI
subclass of: Restriction
  max cardinality: 1
  on property: valueSI
subclass of: QuantityValue
definition: unit value extended to have two additional fields si_value and si_unit
in scheme: custom types

Restriction
max cardinality: 1
on property: temperature_range

Restriction
max cardinality: 1
on property: nominal_defocus

Restriction
max cardinality: 1
on property: date_time

Restriction
max cardinality: 1
on property: calibrated_defocus

Restriction
min cardinality: 1
on property: detectors

Restriction
max cardinality: 1
on property: cryogen

Restriction
max cardinality: 1
on property: beamtilt

Restriction
min cardinality: 0
on property: energy_filter

Restriction
min cardinality: 1
on property: binning_camera

Restriction
max cardinality: 1
on property: image_size

Restriction
min cardinality: 0
on property: imageshift

Restriction
min cardinality: 0
on property: cryogen