Class: EMDatasetEnv

erDiagram AcquisitionEnvTomo { float tilt_axis_angle string technique 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 } 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 } BoundingBox2D { } Detector { string name string mode } EMDatasetEnv { } EnergyFilter { boolean used string model } Freezing { string cryogen_sample_env FreezingMethodEnum method boolean blotting string atmosphere string details } Funder { string funder_name OrganizationTypeEnum type_org string country } Grant { string grant_name datetime start_date datetime end_date string project_id string country } ImageSize { integer height integer width } Instrument { string illumination string imaging string electron_source string operating_mode } Microscope { string model string manufacturer } Organizational { } QuantitySI { float valueSI string unitSI string unit float value } Range { } SampleEnv { } SpecialistOptics { } SpecimenEnv { stringList organism string tissue string source_env string location date collection_date string handling } Thinning { string method_thin string instrument_thin string ion_source boolean lift_out } TiltAngle { } TomogramFeatures { string cellular_features stringList organelles string main_target string details_tomo } AcquisitionEnvTomo ||--|o BoundingBox2D : "beamshift" AcquisitionEnvTomo ||--|o BoundingBox2D : "beamtilt" AcquisitionEnvTomo ||--|o BoundingBox2D : "imageshift" AcquisitionEnvTomo ||--|o EnergyFilter : "energy_filter" AcquisitionEnvTomo ||--|o ImageSize : "image_size" AcquisitionEnvTomo ||--|o QuantitySI : "dose_per_movie" AcquisitionEnvTomo ||--|o QuantitySI : "exposure_time" AcquisitionEnvTomo ||--|o QuantitySI : "screen_current" AcquisitionEnvTomo ||--|o Range : "calibrated_defocus" AcquisitionEnvTomo ||--|o Range : "nominal_defocus" AcquisitionEnvTomo ||--|o Range : "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" BoundingBox2D ||--|o QuantitySI : "x_min" BoundingBox2D ||--|o QuantitySI : "y_max" BoundingBox2D ||--|o QuantitySI : "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" Freezing ||--|o QuantitySI : "temperature_env" Grant ||--|o QuantityValue : "budget" Instrument ||--|o QuantitySI : "beam_convergence" Instrument ||--|o QuantitySI : "c2_aperture" Instrument ||--|o QuantitySI : "cs" Instrument ||--|| Microscope : "microscope" Instrument ||--|| QuantitySI : "acceleration_voltage" Organizational ||--}o Funder : "funder" Organizational ||--}o Grant : "grants" Organizational ||--}| Author : "authors" Range ||--|o QuantitySI : "maximal" Range ||--|o QuantitySI : "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" TiltAngle ||--|| QuantitySI : "maximal" TiltAngle ||--|| QuantitySI : "minimal"

name: EMDatasetEnv
description: cryo electron tomography dataset of an environmental sample
from_schema: https://w3id.org/osc-em/oscem-schemas-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/osc-em/oscem-schemas-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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: acquisition
    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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: instrument
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: sample
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: SampleEnv
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: organizational
    owner: EMDatasetEnv
    domain_of:
    - EMDatasetBase
    range: Organizational
    required: false
tree_root: true