Class: EMDatasetTomo

erDiagram AcquisitionSubTomo { 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 } EMDatasetTomo { } EnergyFilter { boolean used string model } Funder { string funder_name OrganizationTypeEnum type_org string country } Grant { string grant_name datetime start_date datetime end_date string project_id string country } Grid { string manufacturer string material float mesh boolean film_support string film_material string film_topology string film_thickness string pretreatment_type string pretreatment_atmosphere } ImageSize { integer height integer width } Instrument { string illumination string imaging string electron_source string operating_mode } Ligand { boolean present string smiles string reference } Microscope { string model string manufacturer } Molecule { string name_mol string molecular_type string molecular_class string sequence string natural_source string taxonomy_id_source string expression_system string taxonomy_id_expression string gene_name } Organizational { } OverallMolecule { MoleculeClassEnum molecular_overall_type string name_sample string source AssemblyEnum assembly } QuantitySI { float valueSI string unitSI string unit float value } Range { } SampleMolecular { string name string description } SpecialistOptics { } Specimen { string buffer float ph boolean vitrification string vitrification_cryogen boolean staining boolean embedding boolean shadowing } TiltAngle { } AcquisitionSubTomo ||--|o BoundingBox2D : "beamshift" AcquisitionSubTomo ||--|o BoundingBox2D : "beamtilt" AcquisitionSubTomo ||--|o BoundingBox2D : "imageshift" AcquisitionSubTomo ||--|o EnergyFilter : "energy_filter" AcquisitionSubTomo ||--|o ImageSize : "image_size" AcquisitionSubTomo ||--|o QuantitySI : "dose_per_movie" AcquisitionSubTomo ||--|o QuantitySI : "exposure_time" AcquisitionSubTomo ||--|o QuantitySI : "screen_current" AcquisitionSubTomo ||--|o Range : "calibrated_defocus" AcquisitionSubTomo ||--|o Range : "nominal_defocus" AcquisitionSubTomo ||--|o Range : "temperature_range" AcquisitionSubTomo ||--|o SpecialistOptics : "specialist_optics" AcquisitionSubTomo ||--|| ImageSize : "binning_camera" AcquisitionSubTomo ||--|| QuantitySI : "pixel_size" AcquisitionSubTomo ||--|| TiltAngle : "tilt_angle" AcquisitionSubTomo ||--}| 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" EMDatasetTomo ||--|o Organizational : "organizational" EMDatasetTomo ||--|o SampleMolecular : "sample" EMDatasetTomo ||--|| AcquisitionSubTomo : "acquisition" EMDatasetTomo ||--|| Instrument : "instrument" EnergyFilter ||--|| QuantitySI : "width_energy_filter" Grant ||--|o QuantityValue : "budget" Grid ||--|o QuantitySI : "pretreatment_pressure" Grid ||--|o QuantitySI : "pretreatment_time" 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" OverallMolecule ||--|o QuantitySI : "molecular_weight" Range ||--|o QuantitySI : "maximal" Range ||--|o QuantitySI : "minimal" SampleMolecular ||--|o Grid : "grid" SampleMolecular ||--|o Specimen : "specimen" SampleMolecular ||--|| OverallMolecule : "overall_molecule" SampleMolecular ||--}o Ligand : "ligands" SampleMolecular ||--}o Molecule : "molecule" SpecialistOptics ||--|o ChromaticAberrationCorrector : "chromatic_aberration_corrector" SpecialistOptics ||--|o Phaseplate : "phaseplate" SpecialistOptics ||--|o SphericalAberrationCorrector : "spherical_aberration_corrector" Specimen ||--|o QuantitySI : "concentration" Specimen ||--|o QuantitySI : "humidity" Specimen ||--|o QuantitySI : "temperature" TiltAngle ||--|| QuantitySI : "increment" TiltAngle ||--|| QuantitySI : "maximal" TiltAngle ||--|| QuantitySI : "minimal"

name: EMDatasetTomo
description: cryo electron tomography dataset, with a focus on a single protein (complex)
  & subtomogram averaging
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionSubTomo
    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: SampleMolecular
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: false
tree_root: true

name: EMDatasetTomo
description: cryo electron tomography dataset, with a focus on a single protein (complex)
  & subtomogram averaging
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionSubTomo
    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: SampleMolecular
    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-subtomo
    rank: 1000
    alias: acquisition
    owner: EMDatasetTomo
    domain_of:
    - EMDatasetBase
    range: AcquisitionSubTomo
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: instrument
    owner: EMDatasetTomo
    domain_of:
    - EMDatasetBase
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: sample
    owner: EMDatasetTomo
    domain_of:
    - EMDatasetBase
    range: SampleMolecular
    required: false
  organizational:
    name: organizational
    description: Information on authors and grants
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: organizational
    owner: EMDatasetTomo
    domain_of:
    - EMDatasetBase
    range: Organizational
    required: false
tree_root: true