Class: EMDatasetEnv

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

name: EMDatasetEnv
description: Cryo electron tomography dataset of an environmental sample
from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionEnvTomo
    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: SampleEnv
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: false
tree_root: true

name: EMDatasetEnv
description: Cryo electron tomography dataset of an environmental sample
from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionEnvTomo
    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: SampleEnv
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: false
attributes:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
    rank: 1000
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: AcquisitionEnvTomo
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
    rank: 1000
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
    rank: 1000
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: SampleEnv
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    from_schema: https://w3id.org/oscem-schemas/latest/env_tomo
    rank: 1000
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: Organizational
    required: false
tree_root: true