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