Class: EMDatasetCell

erDiagram EMDatasetCell { } Organizational { } Funder { string funder_name OrganizationTypeEnum type_org string country } Author { string orcid string country string role string name_org OrganizationTypeEnum type_org string family_name string given_name boolean job_title string email string telephone } Grant { string grant_name datetime start_date datetime end_date string project_id string country } SampleCell { } TomogramFeatures { string cellular_features stringList organelles string main_target string details_tomo } Thinning { string method_thin string instrument_thin string ion_source boolean lift_out } Freezing { string cryogen_sample_env FreezingMethodEnum method boolean blotting string atmosphere string details } SpecimenEnv { stringList organism string tissue string source_env string location date collection_date string handling } GrowthCondition { string media string growth_location string cell_cycle string treatment string atmosphere_growth } Instrument { string illumination string imaging string electron_source string operating_mode } QuantitySI { float valueSI string unitSI string unit float value } Microscope { string model string manufacturer } AcquisitionCelTomo { string technique float tilt_axis_angle integer nominal_magnification integer calibrated_magnification string holder string holder_cryogen string microscope_software datetime date_time string cryogen integer frames_per_movie integer grids_imaged integer images_generated integer beamtiltgroups string gainref_flip_rotate } BoundingBox2D { } SpecialistOptics { } ImageSize { integer height integer width } EnergyFilter { boolean used string model } Detector { string name string mode } Range { } TiltAngle { } EMDatasetCell ||--|| AcquisitionCelTomo : "acquisition" EMDatasetCell ||--|| Instrument : "instrument" EMDatasetCell ||--|| SampleCell : "sample" EMDatasetCell ||--|| Organizational : "organizational" Organizational ||--}o Grant : "grants" Organizational ||--}| Author : "authors" Organizational ||--}o Funder : "funder" Grant ||--|o QuantityValue : "budget" SampleCell ||--|o GrowthCondition : "growth_condition" SampleCell ||--|| SpecimenEnv : "specimen_env" SampleCell ||--|o Freezing : "freezing" SampleCell ||--|o Thinning : "thinning" SampleCell ||--|o TomogramFeatures : "tomogram_features" Thinning ||--|o QuantitySI : "target_thickness" Freezing ||--|o QuantitySI : "humidity_env" Freezing ||--|o QuantitySI : "temperature_env" GrowthCondition ||--|o QuantitySI : "temperature_growth" Instrument ||--|| Microscope : "microscope" Instrument ||--|| QuantitySI : "acceleration_voltage" Instrument ||--|o QuantitySI : "c2_aperture" Instrument ||--|o QuantitySI : "cs" Instrument ||--|o QuantitySI : "beam_convergence" AcquisitionCelTomo ||--|| TiltAngle : "tilt_angle" AcquisitionCelTomo ||--|o QuantitySI : "screen_current" AcquisitionCelTomo ||--|o Range : "nominal_defocus" AcquisitionCelTomo ||--|o Range : "calibrated_defocus" AcquisitionCelTomo ||--|o Range : "temperature_range" AcquisitionCelTomo ||--}| Detector : "detectors" AcquisitionCelTomo ||--|o QuantitySI : "dose_per_movie" AcquisitionCelTomo ||--|o EnergyFilter : "energy_filter" AcquisitionCelTomo ||--|o ImageSize : "image_size" AcquisitionCelTomo ||--|o QuantitySI : "exposure_time" AcquisitionCelTomo ||--|| ImageSize : "binning_camera" AcquisitionCelTomo ||--|| QuantitySI : "pixel_size" AcquisitionCelTomo ||--|o SpecialistOptics : "specialist_optics" AcquisitionCelTomo ||--|o BoundingBox2D : "beamshift" AcquisitionCelTomo ||--|o BoundingBox2D : "beamtilt" AcquisitionCelTomo ||--|o BoundingBox2D : "imageshift" BoundingBox2D ||--|o QuantitySI : "x_min" BoundingBox2D ||--|o QuantitySI : "x_max" BoundingBox2D ||--|o QuantitySI : "y_min" BoundingBox2D ||--|o QuantitySI : "y_max" SpecialistOptics ||--|o Phaseplate : "phaseplate" SpecialistOptics ||--|o SphericalAberrationCorrector : "spherical_aberration_corrector" SpecialistOptics ||--|o ChromaticAberrationCorrector : "chromatic_aberration_corrector" EnergyFilter ||--|| QuantitySI : "width_energy_filter" Detector ||--|o QuantitySI : "dispersion" Detector ||--|o Range : "collection_angle" Range ||--|o QuantitySI : "minimal" Range ||--|o QuantitySI : "maximal" TiltAngle ||--|| QuantitySI : "increment" TiltAngle ||--|| QuantitySI : "minimal" TiltAngle ||--|| QuantitySI : "maximal"

name: EMDatasetCell
description: cryo electron tomography dataset of a cellular sample, lab grown
from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionCelTomo
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    range: SampleCell
    required: true
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: true
tree_root: true

name: EMDatasetCell
description: cryo electron tomography dataset of a cellular sample, lab grown
from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionCelTomo
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    range: SampleCell
    required: true
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: true
attributes:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
    rank: 1000
    alias: acquisition
    owner: EMDatasetCell
    domain_of:
    - EMDatasetBase
    range: AcquisitionCelTomo
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
    rank: 1000
    alias: instrument
    owner: EMDatasetCell
    domain_of:
    - EMDatasetBase
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
    rank: 1000
    alias: sample
    owner: EMDatasetCell
    domain_of:
    - EMDatasetBase
    range: SampleCell
    required: true
  organizational:
    name: organizational
    description: Information on authors and grants
    from_schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
    rank: 1000
    alias: organizational
    owner: EMDatasetCell
    domain_of:
    - EMDatasetBase
    range: Organizational
    required: true
tree_root: true