Class: EMDatasetSpa
Single particle cryo electron microscopy dataset
URI: https://w3id.org/oscem-schemas/latest/spa/EMDatasetSpa
erDiagram
AcquisitionSpa {
string technique
integer beamtiltgroups
integer calibrated_magnification
string cryogen
datetime date_time
integer frames_per_movie
string gainref_flip_rotate
integer grids_imaged
string holder
string holder_cryogen
integer images_generated
string microscope_software
integer nominal_magnification
}
Author {
string country
string email
string family_name
string given_name
string name_org
string orcid
string role
OrganizationTypeEnum type_org
boolean job_title
string telephone
}
BoundingBox2D {
}
CTFs {
float amplitude_contrast
}
Classes2D {
string images_classes_2D
integerList particles_per_2Dclass
}
Classes3D {
string images_classes_3D
integerList particles_per_3Dclass
}
Coordinates {
string micrograph_examples
integer num_source_micrographs
integer number_particles
string particles_histogram
float particles_per_micrograph
}
Detector {
string name
string mode
}
EMDatasetSpa {
}
EnergyFilter {
string model
boolean used
}
Funder {
string country
string funder_name
OrganizationTypeEnum type_org
}
Grant {
string country
datetime end_date
string grant_name
string project_id
datetime start_date
}
Grid {
string film_material
boolean film_support
string film_thickness
string film_topology
string manufacturer
string material
float mesh
string pretreatment_atmosphere
string pretreatment_type
}
ImageSize {
integer height
integer width
}
Instrument {
string electron_source
string illumination
string imaging
string operating_mode
}
Ligand {
boolean present
string reference
string smiles
}
Micrographs {
float number_micrographs
}
Microscope {
string manufacturer
string model
}
Molecule {
string expression_system
string gene_name
string molecular_class
string molecular_type
string name_mol
string natural_source
string sequence
string taxonomy_id_expression
string taxonomy_id_source
}
Movies {
string dark_image
string gain_image
}
Organizational {
}
OverallMolecule {
AssemblyEnum assembly
MoleculeClassEnum molecular_overall_type
string name_sample
string source
}
Processing {
}
QuantitySI {
string unitSI
float valueSI
string unit
float value
}
Range {
}
SampleMolecular {
string name
string description
}
SpecialistOptics {
}
Specimen {
string buffer
boolean embedding
float ph
boolean shadowing
boolean staining
boolean vitrification
string vitrification_cryogen
}
Volumes {
integerList size
integer vol_number_particles
string volume_type
}
AcquisitionSpa ||--|o BoundingBox2D : "beamshift, beamtilt, imageshift"
AcquisitionSpa ||--|o EnergyFilter : "energy_filter"
AcquisitionSpa ||--|o ImageSize : "image_size"
AcquisitionSpa ||--|o QuantitySI : "dose_per_movie, exposure_time, screen_current"
AcquisitionSpa ||--|o Range : "calibrated_defocus, nominal_defocus, temperature_range"
AcquisitionSpa ||--|o SpecialistOptics : "specialist_optics"
AcquisitionSpa ||--|| ImageSize : "binning_camera"
AcquisitionSpa ||--|| QuantitySI : "pixel_size"
AcquisitionSpa ||--}| Detector : "detectors"
BoundingBox2D ||--|o QuantitySI : "x_max, x_min, y_max, y_min"
CTFs ||--|o Astigmatism : "astigmatism"
CTFs ||--|o Defocus : "defocus"
CTFs ||--|o Resolution : "resolution"
CTFs ||--}o Descriptors : "descriptors"
Classes2D ||--|o QuantityValue : "resolution_classes_2D"
Classes2D ||--}o Descriptors : "descriptors"
Classes3D ||--|o QuantityValue : "resolution_classes_3D"
Classes3D ||--}o Descriptors : "descriptors"
Classes3D ||--}o Volume : "volume"
Coordinates ||--}o Descriptors : "descriptors"
Detector ||--|o QuantitySI : "dispersion"
Detector ||--|o Range : "collection_angle"
EMDatasetSpa ||--|o Organizational : "organizational"
EMDatasetSpa ||--|o Processing : "processing"
EMDatasetSpa ||--|o SampleMolecular : "sample"
EMDatasetSpa ||--|| AcquisitionSpa : "acquisition"
EMDatasetSpa ||--|| Instrument : "instrument"
EnergyFilter ||--|| QuantitySI : "width_energy_filter"
Grant ||--|o QuantityValue : "budget"
Grid ||--|o QuantitySI : "pretreatment_pressure, pretreatment_time"
Instrument ||--|o QuantitySI : "beam_convergence, c2_aperture, cs"
Instrument ||--|| Microscope : "microscope"
Instrument ||--|| QuantitySI : "acceleration_voltage"
Micrographs ||--}o Descriptors : "descriptors"
Movies ||--|o QuantityValue : "dose_per_image, initial_dose"
Movies ||--}o Descriptors : "descriptors"
Organizational ||--}o Funder : "funder"
Organizational ||--}o Grant : "grants"
Organizational ||--}| Author : "authors"
OverallMolecule ||--|o QuantitySI : "molecular_weight"
Processing ||--|o CTFs : "ctfs"
Processing ||--|o Classes2D : "classes2D"
Processing ||--|o Classes3D : "classes3D"
Processing ||--|o Coordinates : "coordinates"
Processing ||--|o Micrographs : "micrographs"
Processing ||--|o Movies : "movies"
Processing ||--}o Volumes : "volumes"
Range ||--|o QuantitySI : "maximal, minimal"
SampleMolecular ||--|o Grid : "grid"
SampleMolecular ||--|o Specimen : "specimen"
SampleMolecular ||--|| OverallMolecule : "overall_molecule"
SampleMolecular ||--}o Ligand : "ligands"
SampleMolecular ||--}o Molecule : "molecule"
SpecialistOptics ||--|o ChromaticAberrationCorrector : "chromatic_aberration_corrector"
SpecialistOptics ||--|o Phaseplate : "phaseplate"
SpecialistOptics ||--|o SphericalAberrationCorrector : "spherical_aberration_corrector"
Specimen ||--|o QuantitySI : "concentration, humidity, temperature"
Volumes ||--|o IsosurfaceImages : "isosurface_images"
Volumes ||--|o OrthogonalSlices : "orthogonal_slices"
Volumes ||--|o QuantityValue : "vol_resolution"
Volumes ||--}o Descriptors : "descriptors"
Inheritance
- EMDatasetBase
- EMDatasetSpa
Class Properties
| Property | Value |
|---|---|
| Tree Root | Yes |
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 | 0..1 SampleMolecular |
Sample information | EMDatasetBase |
| organizational | 0..1 Organizational |
Information on authors and grants | EMDatasetBase |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/oscem-schemas/latest/spa
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | https://w3id.org/oscem-schemas/latest/spa/EMDatasetSpa |
| native | https://w3id.org/oscem-schemas/latest/spa/EMDatasetSpa |
LinkML Source
Direct
name: EMDatasetSpa
description: Single particle cryo electron microscopy dataset
from_schema: https://w3id.org/oscem-schemas/latest/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: false
organizational:
name: organizational
description: Information on authors and grants
range: Organizational
required: false
tree_root: true
Induced
name: EMDatasetSpa
description: Single particle cryo electron microscopy dataset
from_schema: https://w3id.org/oscem-schemas/latest/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: false
organizational:
name: organizational
description: Information on authors and grants
range: Organizational
required: false
attributes:
processing:
name: processing
description: Processing information on the dataset
from_schema: https://w3id.org/oscem-schemas/latest/spa
rank: 1000
owner: EMDatasetSpa
domain_of:
- EMDatasetSpa
range: Processing
required: false
acquisition:
name: acquisition
description: Describe the data acquisition parameters
from_schema: https://w3id.org/oscem-schemas/latest/spa
rank: 1000
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/oscem-schemas/latest/spa
rank: 1000
owner: EMDatasetSpa
domain_of:
- EMDatasetBase
range: Instrument
required: true
sample:
name: sample
description: Sample information
from_schema: https://w3id.org/oscem-schemas/latest/spa
rank: 1000
owner: EMDatasetSpa
domain_of:
- EMDatasetBase
range: SampleMolecular
required: false
organizational:
name: organizational
description: Information on authors and grants
from_schema: https://w3id.org/oscem-schemas/latest/spa
rank: 1000
owner: EMDatasetSpa
domain_of:
- EMDatasetBase
range: Organizational
required: false
tree_root: true