Class: EMDatasetTomo
cryo electron tomography dataset, with a focus on a single protein (complex) & subtomogram averaging
URI: https://w3id.org/osc-em/oscem-schemas-subtomo/:EMDatasetTomo
erDiagram
EMDatasetTomo {
}
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  
}
SampleMolecular {
    string name  
    string description  
}
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  
}
Specimen {
    string buffer  
    float ph  
    boolean vitrification  
    string vitrification_cryogen  
    boolean staining  
    boolean embedding  
    boolean shadowing  
}
Ligand {
    boolean present  
    string smiles  
    string reference  
}
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  
}
OverallMolecule {
    MoleculeClassEnum molecular_overall_type  
    string name_sample  
    string source  
    AssemblyEnum assembly  
}
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  
}
AcquisitionSubTomo {
    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 {
}
EMDatasetTomo ||--|| AcquisitionSubTomo : "acquisition"
EMDatasetTomo ||--|| Instrument : "instrument"
EMDatasetTomo ||--|| SampleMolecular : "sample"
EMDatasetTomo ||--|| Organizational : "organizational"
Organizational ||--}o Grant : "grants"
Organizational ||--}| Author : "authors"
Organizational ||--}o Funder : "funder"
Grant ||--|o QuantityValue : "budget"
SampleMolecular ||--|| OverallMolecule : "overall_molecule"
SampleMolecular ||--}o Molecule : "molecule"
SampleMolecular ||--}o Ligand : "ligands"
SampleMolecular ||--|o Specimen : "specimen"
SampleMolecular ||--|o Grid : "grid"
Grid ||--|o QuantitySI : "pretreatment_time"
Grid ||--|o QuantitySI : "pretreatment_pressure"
Specimen ||--|o QuantitySI : "concentration"
Specimen ||--|o QuantitySI : "humidity"
Specimen ||--|o QuantitySI : "temperature"
OverallMolecule ||--|o QuantitySI : "molecular_weight"
Instrument ||--|| Microscope : "microscope"
Instrument ||--|| QuantitySI : "acceleration_voltage"
Instrument ||--|o QuantitySI : "c2_aperture"
Instrument ||--|o QuantitySI : "cs"
Instrument ||--|o QuantitySI : "beam_convergence"
AcquisitionSubTomo ||--|| TiltAngle : "tilt_angle"
AcquisitionSubTomo ||--|o QuantitySI : "screen_current"
AcquisitionSubTomo ||--|o Range : "nominal_defocus"
AcquisitionSubTomo ||--|o Range : "calibrated_defocus"
AcquisitionSubTomo ||--|o Range : "temperature_range"
AcquisitionSubTomo ||--}| Detector : "detectors"
AcquisitionSubTomo ||--|o QuantitySI : "dose_per_movie"
AcquisitionSubTomo ||--|o EnergyFilter : "energy_filter"
AcquisitionSubTomo ||--|o ImageSize : "image_size"
AcquisitionSubTomo ||--|o QuantitySI : "exposure_time"
AcquisitionSubTomo ||--|| ImageSize : "binning_camera"
AcquisitionSubTomo ||--|| QuantitySI : "pixel_size"
AcquisitionSubTomo ||--|o SpecialistOptics : "specialist_optics"
AcquisitionSubTomo ||--|o BoundingBox2D : "beamshift"
AcquisitionSubTomo ||--|o BoundingBox2D : "beamtilt"
AcquisitionSubTomo ||--|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- EMDatasetTomo
 
Slots
| Name | Cardinality and Range | Description | Inheritance | 
|---|---|---|---|
| acquisition | 1 AcquisitionSubTomo | Describe the data acquisition parameters | EMDatasetBase | 
| instrument | 1 Instrument | Describe the instrument used to acquire the data | EMDatasetBase | 
| sample | 1 SampleMolecular | 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-subtomo
Mappings
| Mapping Type | Mapped Value | 
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-subtomo/:EMDatasetTomo | 
| native | https://w3id.org/osc-em/oscem-schemas-subtomo/:EMDatasetTomo | 
LinkML Source
Direct
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: true
  organizational:
    name: organizational
    description: Information on authors and grants
    range: Organizational
    required: true
tree_root: true
Induced
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: 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-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: true
  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: true
tree_root: true