Class: EMDatasetCell
cryo electron tomography dataset of a cellular sample, lab grown
URI: https://w3id.org/osc-em/oscem-schemas-cellular-tomo/: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"
Inheritance
- EMDatasetBase- EMDatasetCell
 
Slots
| Name | Cardinality and Range | Description | Inheritance | 
|---|---|---|---|
| acquisition | 1 AcquisitionCelTomo | Describe the data acquisition parameters | EMDatasetBase | 
| instrument | 1 Instrument | Describe the instrument used to acquire the data | EMDatasetBase | 
| sample | 1 SampleCell | Sample information | EMDatasetBase | 
| organizational | 1 Organizational | Information on authors and grants | EMDatasetBase | 
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/osc-em/oscem-schemas-cellular-tomo
Mappings
| Mapping Type | Mapped Value | 
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-cellular-tomo/:EMDatasetCell | 
| native | https://w3id.org/osc-em/oscem-schemas-cellular-tomo/:EMDatasetCell | 
LinkML Source
Direct
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
Induced
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