Class: EMDatasetEnv
cryo electron tomography dataset of an environmental sample
URI: https://w3id.org/osc-em/oscem-schemas-env-tomo/:EMDatasetEnv
erDiagram
EMDatasetEnv {
}
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
}
SampleEnv {
}
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
}
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
}
AcquisitionEnvTomo {
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 {
}
EMDatasetEnv ||--|| AcquisitionEnvTomo : "acquisition"
EMDatasetEnv ||--|| Instrument : "instrument"
EMDatasetEnv ||--|| SampleEnv : "sample"
EMDatasetEnv ||--|| Organizational : "organizational"
Organizational ||--}o Grant : "grants"
Organizational ||--}| Author : "authors"
Organizational ||--}o Funder : "funder"
Grant ||--|o QuantityValue : "budget"
SampleEnv ||--|| SpecimenEnv : "specimen_env"
SampleEnv ||--|o Freezing : "freezing"
SampleEnv ||--|o Thinning : "thinning"
SampleEnv ||--|o TomogramFeatures : "tomogram_features"
Thinning ||--|o QuantitySI : "target_thickness"
Freezing ||--|o QuantitySI : "humidity_env"
Freezing ||--|o QuantitySI : "temperature_env"
Instrument ||--|| Microscope : "microscope"
Instrument ||--|| QuantitySI : "acceleration_voltage"
Instrument ||--|o QuantitySI : "c2_aperture"
Instrument ||--|o QuantitySI : "cs"
Instrument ||--|o QuantitySI : "beam_convergence"
AcquisitionEnvTomo ||--|| TiltAngle : "tilt_angle"
AcquisitionEnvTomo ||--|o QuantitySI : "screen_current"
AcquisitionEnvTomo ||--|o Range : "nominal_defocus"
AcquisitionEnvTomo ||--|o Range : "calibrated_defocus"
AcquisitionEnvTomo ||--|o Range : "temperature_range"
AcquisitionEnvTomo ||--}| Detector : "detectors"
AcquisitionEnvTomo ||--|o QuantitySI : "dose_per_movie"
AcquisitionEnvTomo ||--|o EnergyFilter : "energy_filter"
AcquisitionEnvTomo ||--|o ImageSize : "image_size"
AcquisitionEnvTomo ||--|o QuantitySI : "exposure_time"
AcquisitionEnvTomo ||--|| ImageSize : "binning_camera"
AcquisitionEnvTomo ||--|| QuantitySI : "pixel_size"
AcquisitionEnvTomo ||--|o SpecialistOptics : "specialist_optics"
AcquisitionEnvTomo ||--|o BoundingBox2D : "beamshift"
AcquisitionEnvTomo ||--|o BoundingBox2D : "beamtilt"
AcquisitionEnvTomo ||--|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
- EMDatasetEnv
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| acquisition | 1 AcquisitionEnvTomo |
Describe the data acquisition parameters | EMDatasetBase |
| instrument | 1 Instrument |
Describe the instrument used to acquire the data | EMDatasetBase |
| sample | 1 SampleEnv |
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-env-tomo
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-env-tomo/:EMDatasetEnv |
| native | https://w3id.org/osc-em/oscem-schemas-env-tomo/:EMDatasetEnv |
LinkML Source
Direct
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: true
organizational:
name: organizational
description: Information on authors and grants
range: Organizational
required: true
tree_root: true
Induced
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: 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-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: true
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: true
tree_root: true