Class: EMDatasetSpa
Single particle cryo electron microscopy dataset
URI: https://w3id.org/osc-em/oscem-schemas-spa/:EMDatasetSpa
erDiagram
EMDatasetSpa {
}
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  
}
AcquisitionSpa {
    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  
}
BoundingBox2D {
}
SpecialistOptics {
}
ImageSize {
    integer height  
    integer width  
}
EnergyFilter {
    boolean used  
    string model  
}
Detector {
    string name  
    string mode  
}
Range {
}
Processing {
}
Volumes {
    string volume_type  
    integer vol_number_particles  
    integerList size  
}
Classes3D {
    integerList particles_per_3Dclass  
    string images_classes_3D  
}
Classes2D {
    integerList particles_per_2Dclass  
    string images_classes_2D  
}
Coordinates {
    integer number_particles  
    float particles_per_micrograph  
    integer num_source_micrographs  
    string particles_histogram  
    string micrograph_examples  
}
CTFs {
    float amplitude_contrast  
}
Micrographs {
    float number_micrographs  
}
Movies {
    string gain_image  
    string dark_image  
}
EMDatasetSpa ||--|o Processing : "processing"
EMDatasetSpa ||--|| AcquisitionSpa : "acquisition"
EMDatasetSpa ||--|| Instrument : "instrument"
EMDatasetSpa ||--|| SampleMolecular : "sample"
EMDatasetSpa ||--|| 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"
AcquisitionSpa ||--|o QuantitySI : "screen_current"
AcquisitionSpa ||--|o Range : "nominal_defocus"
AcquisitionSpa ||--|o Range : "calibrated_defocus"
AcquisitionSpa ||--|o Range : "temperature_range"
AcquisitionSpa ||--}| Detector : "detectors"
AcquisitionSpa ||--|o QuantitySI : "dose_per_movie"
AcquisitionSpa ||--|o EnergyFilter : "energy_filter"
AcquisitionSpa ||--|o ImageSize : "image_size"
AcquisitionSpa ||--|o QuantitySI : "exposure_time"
AcquisitionSpa ||--|| ImageSize : "binning_camera"
AcquisitionSpa ||--|| QuantitySI : "pixel_size"
AcquisitionSpa ||--|o SpecialistOptics : "specialist_optics"
AcquisitionSpa ||--|o BoundingBox2D : "beamshift"
AcquisitionSpa ||--|o BoundingBox2D : "beamtilt"
AcquisitionSpa ||--|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"
Processing ||--|o Movies : "movies"
Processing ||--|o Micrographs : "micrographs"
Processing ||--|o CTFs : "ctfs"
Processing ||--|o Coordinates : "coordinates"
Processing ||--|o Classes2D : "classes2D"
Processing ||--|o Classes3D : "classes3D"
Processing ||--}o Volumes : "volumes"
Volumes ||--|o OrthogonalSlices : "orthogonal_slices"
Volumes ||--|o IsosurfaceImages : "isosurface_images"
Volumes ||--|o QuantityValue : "vol_resolution"
Volumes ||--}o Descriptors : "descriptors"
Classes3D ||--}o Volume : "volume"
Classes3D ||--|o QuantityValue : "resolution_classes_3D"
Classes3D ||--}o Descriptors : "descriptors"
Classes2D ||--|o QuantityValue : "resolution_classes_2D"
Classes2D ||--}o Descriptors : "descriptors"
Coordinates ||--}o Descriptors : "descriptors"
CTFs ||--|o Defocus : "defocus"
CTFs ||--|o Resolution : "resolution"
CTFs ||--|o Astigmatism : "astigmatism"
CTFs ||--}o Descriptors : "descriptors"
Micrographs ||--}o Descriptors : "descriptors"
Movies ||--|o QuantityValue : "dose_per_image"
Movies ||--|o QuantityValue : "initial_dose"
Movies ||--}o Descriptors : "descriptors"
Inheritance
- EMDatasetBase- EMDatasetSpa
 
Slots
| Name | Cardinality and Range | Description | Inheritance | 
|---|---|---|---|
| processing | 0..1 Processing | Processing information on the dataset | direct | 
| acquisition | 1 AcquisitionSpa | 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-spa
Mappings
| Mapping Type | Mapped Value | 
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-spa/:EMDatasetSpa | 
| native | https://w3id.org/osc-em/oscem-schemas-spa/:EMDatasetSpa | 
LinkML Source
Direct
name: EMDatasetSpa
description: Single particle cryo electron microscopy dataset
from_schema: https://w3id.org/osc-em/oscem-schemas-spa
is_a: EMDatasetBase
slots:
- processing
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionSpa
    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: EMDatasetSpa
description: Single particle cryo electron microscopy dataset
from_schema: https://w3id.org/osc-em/oscem-schemas-spa
is_a: EMDatasetBase
slot_usage:
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    range: AcquisitionSpa
    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:
  processing:
    name: processing
    description: Processing information on the dataset
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: processing
    owner: EMDatasetSpa
    domain_of:
    - EMDatasetSpa
    range: Processing
    required: false
  acquisition:
    name: acquisition
    description: Describe the data acquisition parameters
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: acquisition
    owner: EMDatasetSpa
    domain_of:
    - EMDatasetBase
    range: AcquisitionSpa
    required: true
  instrument:
    name: instrument
    description: Describe the instrument used to acquire the data
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: instrument
    owner: EMDatasetSpa
    domain_of:
    - EMDatasetBase
    range: Instrument
    required: true
  sample:
    name: sample
    description: Sample information
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: sample
    owner: EMDatasetSpa
    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-spa
    rank: 1000
    alias: organizational
    owner: EMDatasetSpa
    domain_of:
    - EMDatasetBase
    range: Organizational
    required: true
tree_root: true