oscem-schemas-tomo
type: SchemaDefinition
name: oscem-schemas-tomo
description: Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
see also: https://osc-em.github.io/oscem-schemas
id: https://w3id.org/osc-em/oscem-schemas-subtomo
imports: linkml:types
imports: ./acquisition
imports: ./instrument
imports: ./sample
imports: ./tomography
imports: ./organizational
imports: ./emdataset
imports: ./custom_types
imports: acquisition
license: CC-BY
prefixes:
  prefix prefix: linkml
  prefix reference: https://w3id.org/linkml/
default prefix: https://w3id.org/osc-em/oscem-schemas-subtomo/
default range: string
types: TypeDefinition
  name: string
  definition uri: https://w3id.org/linkml/String
  description: A character string
  notes: In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Text
  base: str
  uri: http://www.w3.org/2001/XMLSchema#string
types: TypeDefinition
  name: integer
  definition uri: https://w3id.org/linkml/Integer
  description: An integer
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Integer
  base: int
  uri: http://www.w3.org/2001/XMLSchema#integer
types: TypeDefinition
  name: boolean
  definition uri: https://w3id.org/linkml/Boolean
  description: A binary (true or false) value
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Boolean
  base: Bool
  uri: http://www.w3.org/2001/XMLSchema#boolean
  repr: bool
types: TypeDefinition
  name: float
  definition uri: https://w3id.org/linkml/Float
  description: A real number that conforms to the xsd:float specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Float
  base: float
  uri: http://www.w3.org/2001/XMLSchema#float
types: TypeDefinition
  name: double
  definition uri: https://w3id.org/linkml/Double
  description: A real number that conforms to the xsd:double specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  close mappings: schema:Float
  base: float
  uri: http://www.w3.org/2001/XMLSchema#double
types: TypeDefinition
  name: decimal
  definition uri: https://w3id.org/linkml/Decimal
  description: A real number with arbitrary precision that conforms to the xsd:decimal specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  broad mappings: schema:Number
  base: Decimal
  uri: http://www.w3.org/2001/XMLSchema#decimal
types: TypeDefinition
  name: time
  definition uri: https://w3id.org/linkml/Time
  description: A time object represents a (local) time of day, independent of any particular day
  notes: URI is dateTime because OWL reasoners do not work with straight date or time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Time
  base: XSDTime
  uri: http://www.w3.org/2001/XMLSchema#time
  repr: str
types: TypeDefinition
  name: date
  definition uri: https://w3id.org/linkml/Date
  description: a date (year, month and day) in an idealized calendar
  notes: URI is dateTime because OWL reasoners don't work with straight date or time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Date
  base: XSDDate
  uri: http://www.w3.org/2001/XMLSchema#date
  repr: str
types: TypeDefinition
  name: datetime
  definition uri: https://w3id.org/linkml/Datetime
  description: The combination of a date and time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:DateTime
  base: XSDDateTime
  uri: http://www.w3.org/2001/XMLSchema#dateTime
  repr: str
types: TypeDefinition
  name: date_or_datetime
  definition uri: https://w3id.org/linkml/DateOrDatetime
  description: Either a date or a datetime
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: str
  uri: https://w3id.org/linkml/DateOrDatetime
  repr: str
types: TypeDefinition
  name: uriorcurie
  definition uri: https://w3id.org/linkml/Uriorcurie
  description: a URI or a CURIE
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: URIorCURIE
  uri: http://www.w3.org/2001/XMLSchema#anyURI
  repr: str
types: TypeDefinition
  name: curie
  definition uri: https://w3id.org/linkml/Curie
  conforms to: https://www.w3.org/TR/curie/
  description: a compact URI
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie".
  comments: in RDF serializations this MUST be expanded to a URI
  comments: in non-RDF serializations MAY be serialized as the compact representation
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: Curie
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
types: TypeDefinition
  name: uri
  definition uri: https://w3id.org/linkml/Uri
  conforms to: https://www.ietf.org/rfc/rfc3987.txt
  description: a complete URI
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri".
  comments: in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  close mappings: schema:URL
  base: URI
  uri: http://www.w3.org/2001/XMLSchema#anyURI
  repr: str
types: TypeDefinition
  name: ncname
  definition uri: https://w3id.org/linkml/Ncname
  description: Prefix part of CURIE
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: NCName
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
types: TypeDefinition
  name: objectidentifier
  definition uri: https://w3id.org/linkml/Objectidentifier
  description: A URI or CURIE that represents an object in the model.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier".
  comments: Used for inheritance and type checking
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: ElementIdentifier
  uri: http://www.w3.org/ns/shex#iri
  repr: str
types: TypeDefinition
  name: nodeidentifier
  definition uri: https://w3id.org/linkml/Nodeidentifier
  description: A URI, CURIE or BNODE that represents a node in a model.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: NodeIdentifier
  uri: http://www.w3.org/ns/shex#nonLiteral
  repr: str
types: TypeDefinition
  name: jsonpointer
  definition uri: https://w3id.org/linkml/Jsonpointer
  conforms to: https://datatracker.ietf.org/doc/html/rfc6901
  description: A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: str
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
slots: SlotDefinition
classes: ClassDefinition
metamodel version: 1.7.0
source file: oscem_schemas_subtomo.yaml
source file date: 2025-11-25T16:26:34
source file size: 1212
generation date: 2025-11-25T16:28:19

TypeDefinition
name: jsonpath
definition uri: https://w3id.org/linkml/Jsonpath
conforms to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html
description: A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath".
from schema: https://w3id.org/linkml/types
imported from: linkml:types
base: str
uri: http://www.w3.org/2001/XMLSchema#string
repr: str

TypeDefinition
name: sparqlpath
definition uri: https://w3id.org/linkml/Sparqlpath
conforms to: https://www.w3.org/TR/sparql11-query/#propertypaths
description: A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath".
from schema: https://w3id.org/linkml/types
imported from: linkml:types
base: str
uri: http://www.w3.org/2001/XMLSchema#string
repr: str

name: AcquisitionTechnique
definition uri: https://w3id.org/osc-em/acquisitionAcquisitionTechnique
from schema: https://w3id.org/osc-em/acquisition
permissible values:
  text: spa
permissible values:
  text: subtomo
permissible values:
  text: env_tomo
permissible values:
  text: cellular_tomo

name: MoleculeClassEnum
definition uri: https://w3id.org/osc-em/sampleMoleculeClassEnum
description: Allowed molecule class values - compatible with the EMDB.
from schema: https://w3id.org/osc-em/sample
permissible values:
  text: CELL
  description: Cell
permissible values:
  text: COMPLEX
  description: complex of different parts e.g. protein complex
permissible values:
  text: ORGANELLE OR CELLULAR COMPONENT
  description: Some form of cellular component
permissible values:
  text: RIBOSOME
  description: A ribosome
permissible values:
  text: TISSUE
  description: Tissue of any type.
permissible values:
  text: VIRUS
  description: A virus particle - or part thereof.

name: AssemblyEnum
definition uri: https://w3id.org/osc-em/sampleAssemblyEnum
description: Allowed molecular assembly values - compatible with the EMDB.
from schema: https://w3id.org/osc-em/sample
permissible values:
  text: FILAMENT
  description: If your protein (complex) of interest is forming filaments
permissible values:
  text: HELICAL ARRAY
  description: If your protein (complex) of interest is forming helical arrays (i.e. tubes)
permissible values:
  text: PARTICLE
  description: If your protein (complex) of interest forms individual particles on the grid with no orderd interactions

name: OrganizationTypeEnum
definition uri: https://w3id.org/osc-em/organizational/OrganizationTypeEnum
description: Allowed values for authors organizations.
from schema: https://w3id.org/osc-em/organizational
permissible values:
  text: Academic
  description: Academic institution
permissible values:
  text: Commercial
  description: Commercial entity
permissible values:
  text: Government
  description: Government organization
permissible values:
  text: Other
  description: Other types of organizations

SlotDefinition
name: technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Specifies which Acquisition subschema/class is in use.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiontechnique
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: screen_current
definition uri: https://w3id.org/osc-em/acquisitionscreen_current
description: The total electron beam current hitting the viewing screen, in nA.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionscreen_current
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true

SlotDefinition
name: nominal_defocus
definition uri: https://w3id.org/osc-em/acquisitionnominal_defocus
description: Target defocus set, min and max values in nm.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionnominal_defocus
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true

SlotDefinition
name: calibrated_defocus
definition uri: https://w3id.org/osc-em/acquisitioncalibrated_defocus
description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitioncalibrated_defocus
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true

SlotDefinition
name: nominal_magnification
definition uri: https://w3id.org/osc-em/acquisitionnominal_magnification
description: Magnification level as indicated by the instrument, no unit
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionnominal_magnification
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: calibrated_magnification
definition uri: https://w3id.org/osc-em/acquisitioncalibrated_magnification
description: Calculated magnification, no unit
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitioncalibrated_magnification
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: holder
definition uri: https://w3id.org/osc-em/acquisitionholder
description: Speciman holder model
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionholder
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: holder_cryogen
definition uri: https://w3id.org/osc-em/acquisitionholder_cryogen
description: Type of cryogen used in the holder - if the holder is cooled seperately
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionholder_cryogen
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: temperature_range
definition uri: https://w3id.org/osc-em/acquisitiontemperature_range
description: Temperature during data collection, in K with min and max values.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiontemperature
alias: temperature
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true

SlotDefinition
name: microscope_software
definition uri: https://w3id.org/osc-em/acquisitionmicroscope_software
description: Software used for instrument control,
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionmicroscope_software
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: dose_per_movie
definition uri: https://w3id.org/osc-em/acquisitiondose_per_movie
description: Average dose per image/movie/tilt - given in electrons per square Angstrom
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiondose_per_movie
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true

SlotDefinition
name: energy_filter
definition uri: https://w3id.org/osc-em/acquisitionenergy_filter
description: Whether an energy filter was used and its specifics.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionenergy_filter
owner: Acquisition
domain of: Acquisition
range: EnergyFilter
inlined: true

SlotDefinition
name: detectors
definition uri: https://w3id.org/osc-em/acquisitiondetectors
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiondetectors
owner: Acquisition
domain of: Acquisition
range: Detector
multivalued: true
inlined: true

SlotDefinition
name: used
definition uri: https://w3id.org/osc-em/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionused
owner: ChromaticAberrationCorrector
domain of: EnergyFilter
domain of: Phaseplate
domain of: SphericalAberrationCorrector
domain of: ChromaticAberrationCorrector
range: boolean

SlotDefinition
name: image_size
definition uri: https://w3id.org/osc-em/acquisitionimage_size
description: The size of the image in pixels, height and width given.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionimage_size
owner: Acquisition
domain of: Acquisition
range: ImageSize
inlined: true

SlotDefinition
name: date_time
definition uri: https://w3id.org/osc-em/acquisitiondate_time
description: Time and date of the data acquisition
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiondate_time
owner: Acquisition
domain of: Acquisition
range: datetime

SlotDefinition
name: exposure_time
definition uri: https://w3id.org/osc-em/acquisitionexposure_time
description: Time of data acquisition per movie/tilt - in s
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionexposure_time
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true

SlotDefinition
name: cryogen
definition uri: https://w3id.org/osc-em/acquisitioncryogen
description: Cryogen used in cooling the instrument and sample, usually nitrogen
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitioncryogen
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: frames_per_movie
definition uri: https://w3id.org/osc-em/acquisitionframes_per_movie
description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionframes_per_movie
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: grids_imaged
definition uri: https://w3id.org/osc-em/acquisitiongrids_imaged
description: Number of grids imaged for this project - here with qualifier during this data acquisition
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiongrids_imaged
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: images_generated
definition uri: https://w3id.org/osc-em/acquisitionimages_generated
description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionimages_generated
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: binning_camera
definition uri: https://w3id.org/osc-em/acquisitionbinning_camera
description: Level of binning on the images applied during data collection
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionbinning_camera
owner: Acquisition
domain of: Acquisition
range: ImageSize
inlined: true

SlotDefinition
name: pixel_size
definition uri: https://w3id.org/osc-em/acquisitionpixel_size
description: Pixel size, in Angstrom
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionpixel_size
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true

SlotDefinition
name: specialist_optics
definition uri: https://w3id.org/osc-em/acquisitionspecialist_optics
description: Any type of special optics, such as a phaseplate
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionspecialist_optics
owner: Acquisition
domain of: Acquisition
range: SpecialistOptics
inlined: true

SlotDefinition
name: phaseplate
definition uri: https://w3id.org/osc-em/acquisitionphaseplate
description: Phaseplate is a special optics device that can be used to enhance contrast
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionphaseplate
owner: SpecialistOptics
domain of: SpecialistOptics
range: Phaseplate
inlined: true

SlotDefinition
name: instrument_type
definition uri: https://w3id.org/osc-em/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitioninstrument_type
owner: ChromaticAberrationCorrector
domain of: Phaseplate
domain of: SphericalAberrationCorrector
domain of: ChromaticAberrationCorrector
range: string

SlotDefinition
name: spherical_aberration_corrector
definition uri: https://w3id.org/osc-em/acquisitionspherical_aberration_corrector
description: Specialist device to correct for spherical aberration of the microscope lenses
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionspherical_aberration_corrector
owner: SpecialistOptics
domain of: SpecialistOptics
range: SphericalAberrationCorrector
inlined: true

SlotDefinition
name: chromatic_aberration_corrector
definition uri: https://w3id.org/osc-em/acquisitionchromatic_aberration_corrector
description: Specialist device to correct for chromatic aberration of the microscope lenses
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionchromatic_aberration_corrector
owner: SpecialistOptics
domain of: SpecialistOptics
range: ChromaticAberrationCorrector
inlined: true

SlotDefinition
name: beamshift
definition uri: https://w3id.org/osc-em/acquisitionbeamshift
description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionbeamshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true

SlotDefinition
name: beamtilt
definition uri: https://w3id.org/osc-em/acquisitionbeamtilt
description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionbeamtilt
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true

SlotDefinition
name: imageshift
definition uri: https://w3id.org/osc-em/acquisitionimageshift
description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionimageshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true

SlotDefinition
name: beamtiltgroups
definition uri: https://w3id.org/osc-em/acquisitionbeamtiltgroups
description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionbeamtiltgroups
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: gainref_flip_rotate
definition uri: https://w3id.org/osc-em/acquisitiongainref_flip_rotate
description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiongainref_flip_rotate
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: width_energy_filter
definition uri: https://w3id.org/osc-em/acquisitionwidth_energy_filter
description: Width of the energy filter used.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionwidth_energy_filter
owner: EnergyFilter
domain of: EnergyFilter
range: QuantitySI
inlined: true

SlotDefinition
name: mode
definition uri: https://w3id.org/osc-em/acquisitionmode
description: Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitionmode
owner: Detector
domain of: Detector
range: string

SlotDefinition
name: dispersion
definition uri: https://w3id.org/osc-em/acquisitiondispersion
description: Dispersion of an analytical detector, in eV
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitiondispersion
owner: Detector
domain of: Detector
range: QuantitySI
inlined: true

SlotDefinition
name: collection_angle
definition uri: https://w3id.org/osc-em/acquisitioncollection_angle
description: Collection angle set, min and max values in mrad.
from schema: https://w3id.org/osc-em/acquisition
slot uri: https://w3id.org/osc-em/acquisitioncollection_angle
owner: Detector
domain of: Detector
range: Range
inlined: true

SlotDefinition
name: microscope
definition uri: https://w3id.org/osc-em/instrumentmicroscope
description: Microscope information
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentmicroscope
owner: Instrument
domain of: Instrument
range: Microscope
inlined: true

SlotDefinition
name: illumination
definition uri: https://w3id.org/osc-em/instrumentillumination
description: Mode of illumination used during data collection
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentillumination
owner: Instrument
domain of: Instrument
range: string

SlotDefinition
name: imaging
definition uri: https://w3id.org/osc-em/instrumentimaging
description: Mode of imaging used during data collection
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentimaging
owner: Instrument
domain of: Instrument
range: string

SlotDefinition
name: electron_source
definition uri: https://w3id.org/osc-em/instrumentelectron_source
description: Type of electron source used in the microscope, such as FEG
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentelectron_source
owner: Instrument
domain of: Instrument
range: string

SlotDefinition
name: acceleration_voltage
definition uri: https://w3id.org/osc-em/instrumentacceleration_voltage
description: Voltage used for the electron acceleration, in kV
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentacceleration_voltage
owner: Instrument
domain of: Instrument
range: QuantitySI
inlined: true

SlotDefinition
name: c2_aperture
definition uri: https://w3id.org/osc-em/instrumentc2_aperture
description: C2 aperture size used in data acquisition, in µm
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentc2_aperture
owner: Instrument
domain of: Instrument
range: QuantitySI
inlined: true

SlotDefinition
name: cs
definition uri: https://w3id.org/osc-em/instrumentcs
description: Spherical aberration of the instrument, in mm
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentcs
owner: Instrument
domain of: Instrument
range: QuantitySI
inlined: true

SlotDefinition
name: operating_mode
definition uri: https://w3id.org/osc-em/instrumentoperating_mode
description: Operating mode of the microscope, i.e. "TEM", "STEM"
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentoperating_mode
owner: Instrument
domain of: Instrument
range: string

SlotDefinition
name: beam_convergence
definition uri: https://w3id.org/osc-em/instrumentbeam_convergence
description: Refers to how tightly or widely the electron beam is focused onto the sample, in mrad. Typically low convergence for TEM and high for STEM.
from schema: https://w3id.org/osc-em/instrument
slot uri: https://w3id.org/osc-em/instrumentbeam_convergence
owner: Instrument
domain of: Instrument
range: QuantitySI
inlined: true

SlotDefinition
name: molecular_type
definition uri: https://w3id.org/osc-em/samplemolecular_type
description: Description of the overall molecular type, i.e., a complex
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemolecular_type
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: name_sample
definition uri: https://w3id.org/osc-em/samplename_sample
description: Name of the full sample
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplename_sample
owner: OverallMolecule
domain of: OverallMolecule
range: string

SlotDefinition
name: source
definition uri: https://w3id.org/osc-em/samplesource
description: Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplesource
owner: OverallMolecule
domain of: OverallMolecule
range: string

SlotDefinition
name: molecular_weight
definition uri: https://w3id.org/osc-em/samplemolecular_weight
description: Molecular weight in Da
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemolecular_weight
owner: OverallMolecule
domain of: OverallMolecule
range: QuantitySI
inlined: true

SlotDefinition
name: molecular_overall_type
definition uri: https://w3id.org/osc-em/samplemolecular_overall_type
description: Description of the overall molecular type, i.e., a complex
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemolecular_overall_type
owner: OverallMolecule
domain of: OverallMolecule
range: MoleculeClassEnum

SlotDefinition
name: name_mol
definition uri: https://w3id.org/osc-em/samplename_mol
description: Name of an individual molecule (often protein) in the sample
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplename_mol
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: molecular_class
definition uri: https://w3id.org/osc-em/samplemolecular_class
description: Class of the molecule
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemolecular_class
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: sequence
definition uri: https://w3id.org/osc-em/samplesequence
description: Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplesequence
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: natural_source
definition uri: https://w3id.org/osc-em/samplenatural_source
description: Scientific name of the natural host organism
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplenatural_source
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: taxonomy_id_source
definition uri: https://w3id.org/osc-em/sampletaxonomy_id_source
description: Taxonomy ID of the natural source organism
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampletaxonomy_id_source
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: expression_system
definition uri: https://w3id.org/osc-em/sampleexpression_system
description: Scientific name of the organism used to produce the molecule of interest
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleexpression_system
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: taxonomy_id_expression
definition uri: https://w3id.org/osc-em/sampletaxonomy_id_expression
description: Taxonomy ID of the expression system organism
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampletaxonomy_id_expression
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: gene_name
definition uri: https://w3id.org/osc-em/samplegene_name
description: Name of the gene of interest
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplegene_name
owner: Molecule
domain of: Molecule
range: string

SlotDefinition
name: present
definition uri: https://w3id.org/osc-em/samplepresent
description: Whether the model contains any ligands
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplepresent
owner: Ligand
domain of: Ligand
range: boolean

SlotDefinition
name: smiles
definition uri: https://w3id.org/osc-em/samplesmiles
description: Provide a valid SMILES string of your ligand
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplesmiles
owner: Ligand
domain of: Ligand
range: string

SlotDefinition
name: reference
definition uri: https://w3id.org/osc-em/samplereference
description: Link to a reference of your ligand, i.e., CCD, PubChem, etc.
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplereference
owner: Ligand
domain of: Ligand
range: string

SlotDefinition
name: buffer
definition uri: https://w3id.org/osc-em/samplebuffer
description: Name/composition of the (chemical) sample buffer during grid preparation
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplebuffer
owner: Specimen
domain of: Specimen
range: string

SlotDefinition
name: concentration
definition uri: https://w3id.org/osc-em/sampleconcentration
description: Concentration of the (supra)molecule in the sample, in mg/ml
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleconcentration
owner: Specimen
domain of: Specimen
range: QuantitySI
inlined: true

SlotDefinition
name: ph
definition uri: https://w3id.org/osc-em/sampleph
description: pH of the sample buffer
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleph
owner: Specimen
domain of: Specimen
range: float

SlotDefinition
name: vitrification
definition uri: https://w3id.org/osc-em/samplevitrification
description: Whether the sample was vitrified
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplevitrification
owner: Specimen
domain of: Specimen
range: boolean

SlotDefinition
name: vitrification_cryogen
definition uri: https://w3id.org/osc-em/samplevitrification_cryogen
description: Which cryogen was used for vitrification
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplevitrification_cryogen
owner: Specimen
domain of: Specimen
range: string

SlotDefinition
name: humidity
definition uri: https://w3id.org/osc-em/samplehumidity
description: Environmental humidity just before vitrification, in %
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplehumidity
owner: Specimen
domain of: Specimen
range: QuantitySI
inlined: true

SlotDefinition
name: temperature
definition uri: https://w3id.org/osc-em/sampletemperature
description: Environmental temperature just before vitrification, in K
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampletemperature
owner: Specimen
domain of: Specimen
range: QuantitySI
inlined: true

SlotDefinition
name: staining
definition uri: https://w3id.org/osc-em/samplestaining
description: Whether the sample was stained
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplestaining
owner: Specimen
domain of: Specimen
range: boolean

SlotDefinition
name: embedding
definition uri: https://w3id.org/osc-em/sampleembedding
description: Whether the sample was embedded
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleembedding
owner: Specimen
domain of: Specimen
range: boolean

SlotDefinition
name: shadowing
definition uri: https://w3id.org/osc-em/sampleshadowing
description: Whether the sample was shadowed
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleshadowing
owner: Specimen
domain of: Specimen
range: boolean

SlotDefinition
name: material
definition uri: https://w3id.org/osc-em/samplematerial
description: Material out of which the grid is made
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplematerial
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: mesh
definition uri: https://w3id.org/osc-em/samplemesh
description: Grid mesh in lines per inch
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemesh
owner: Grid
domain of: Grid
range: float

SlotDefinition
name: film_support
definition uri: https://w3id.org/osc-em/samplefilm_support
description: Whether a support film was used
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplefilm_support
owner: Grid
domain of: Grid
range: boolean

SlotDefinition
name: film_material
definition uri: https://w3id.org/osc-em/samplefilm_material
description: Type of material the support film is made of
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplefilm_material
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: film_topology
definition uri: https://w3id.org/osc-em/samplefilm_topology
description: Topology of the support film
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplefilm_topology
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: film_thickness
definition uri: https://w3id.org/osc-em/samplefilm_thickness
description: Thickness of the support film
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplefilm_thickness
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: pretreatment_type
definition uri: https://w3id.org/osc-em/samplepretreatment_type
description: Type of pretreatment of the grid, i.e., glow discharge
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplepretreatment_type
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: pretreatment_time
definition uri: https://w3id.org/osc-em/samplepretreatment_time
description: Length of time of the pretreatment in s
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplepretreatment_time
owner: Grid
domain of: Grid
range: QuantitySI
inlined: true

SlotDefinition
name: pretreatment_pressure
definition uri: https://w3id.org/osc-em/samplepretreatment_pressure
description: Pressure of the chamber during pretreatment, in Pa
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplepretreatment_pressure
owner: Grid
domain of: Grid
range: QuantitySI
inlined: true

SlotDefinition
name: pretreatment_atmosphere
definition uri: https://w3id.org/osc-em/samplepretreatment_atmosphere
description: Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplepretreatment_atmosphere
owner: Grid
domain of: Grid
range: string

SlotDefinition
name: overall_molecule
definition uri: https://w3id.org/osc-em/sampleoverall_molecule
description: Description of the overall molecule
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleoverall_molecule
owner: Sample
domain of: Sample
range: OverallMolecule
inlined: true

SlotDefinition
name: molecule
definition uri: https://w3id.org/osc-em/samplemolecule
description: List of molecule associated with the sample
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplemolecule
owner: Sample
domain of: Sample
range: Molecule
multivalued: true
inlined: true

SlotDefinition
name: ligands
definition uri: https://w3id.org/osc-em/sampleligands
description: List of ligands associated with the sample
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleligands
owner: Sample
domain of: Sample
range: Ligand
multivalued: true
inlined: true

SlotDefinition
name: specimen
definition uri: https://w3id.org/osc-em/samplespecimen
description: Description of the specimen
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplespecimen
owner: Sample
domain of: Sample
range: Specimen
inlined: true

SlotDefinition
name: grid
definition uri: https://w3id.org/osc-em/samplegrid
description: Description of the grid used
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/samplegrid
owner: Sample
domain of: Sample
range: Grid
inlined: true

SlotDefinition
name: assembly
definition uri: https://w3id.org/osc-em/sampleassembly
description: What type of higher order structure your sample forms - if any.
from schema: https://w3id.org/osc-em/sample
slot uri: https://w3id.org/osc-em/sampleassembly
owner: OverallMolecule
domain of: OverallMolecule
range: AssemblyEnum

SlotDefinition
name: tilt_axis_angle
definition uri: https://w3id.org/osc-em/tomography/tilt_axis_angle
description: The tilt axis angle of a tomography series
from schema: https://w3id.org/osc-em/tomography
slot uri: https://w3id.org/osc-em/tomography/tilt_axis_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
range: float

SlotDefinition
name: tilt_angle
definition uri: https://w3id.org/osc-em/tomography/tilt_angle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/osc-em/tomography
slot uri: https://w3id.org/osc-em/tomography/tilt_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
range: TiltAngle
inlined: true

SlotDefinition
name: family_name
definition uri: https://w3id.org/osc-em/organizational/family_name
description: last name
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/familyName
slot uri: http://schema.org/familyName
owner: Person
domain of: Person
range: string

SlotDefinition
name: given_name
definition uri: https://w3id.org/osc-em/organizational/given_name
description: first name
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/givenName
slot uri: http://schema.org/givenName
owner: Person
domain of: Person
range: string

SlotDefinition
name: job_title
definition uri: https://w3id.org/osc-em/organizational/job_title
description: job title
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/jobTitle
slot uri: http://schema.org/jobTitle
owner: Person
domain of: Person
range: boolean

SlotDefinition
name: email
definition uri: https://w3id.org/osc-em/organizational/email
description: email
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/email
slot uri: http://schema.org/email
owner: Person
domain of: Person
range: string
pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$

SlotDefinition
name: telephone
definition uri: https://w3id.org/osc-em/organizational/telephone
description: work phone
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/telephone
slot uri: http://schema.org/telephone
owner: Person
domain of: Person
range: string

SlotDefinition
name: person
definition uri: https://w3id.org/osc-em/organizational/person
description: person
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/Person
slot uri: http://schema.org/Person
range: Person
inlined: true

SlotDefinition
name: name_org
definition uri: https://w3id.org/osc-em/organizational/name_org
description: Name of the organization
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/name_org
owner: Author
domain of: Author
range: string

SlotDefinition
name: type_org
definition uri: https://w3id.org/osc-em/organizational/type_org
description: Type of organization, academic, commercial, governmental, etc.
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/type_org
owner: Funder
domain of: Author
domain of: Funder
range: OrganizationTypeEnum

SlotDefinition
name: country
definition uri: https://w3id.org/osc-em/organizational/country
description: Country of the institution
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/country
owner: Funder
domain of: Author
domain of: Grant
domain of: Funder
range: string

SlotDefinition
name: role
definition uri: https://w3id.org/osc-em/organizational/role
description: Role of the author, for example principal investigator
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/role
owner: Author
domain of: Author
range: string

SlotDefinition
name: orcid
definition uri: https://w3id.org/osc-em/organizational/orcid
description: ORCID of the author, a type of unique identifier
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/orcid
owner: Author
domain of: Author
range: string

SlotDefinition
name: funder_name
definition uri: https://w3id.org/osc-em/organizational/funder_name
description: funding organization/person.
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/funder_name
owner: Funder
domain of: Funder
range: string

SlotDefinition
name: funder
definition uri: https://w3id.org/osc-em/organizational/funder
description: funding organization/person.
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/funder
owner: Organizational
domain of: Organizational
range: Funder
multivalued: true
inlined: true

SlotDefinition
name: start_date
definition uri: https://w3id.org/osc-em/organizational/start_date
description: start date
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/start_date
owner: Grant
domain of: Grant
range: datetime

SlotDefinition
name: end_date
definition uri: https://w3id.org/osc-em/organizational/end_date
description: end date
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/end_date
owner: Grant
domain of: Grant
range: datetime

SlotDefinition
name: budget
definition uri: https://w3id.org/osc-em/organizational/budget
description: budget
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/budget
owner: Grant
domain of: Grant
range: QuantityValue
inlined: true

SlotDefinition
name: project_id
definition uri: https://w3id.org/osc-em/organizational/project_id
description: project id
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/identifier
slot uri: http://schema.org/identifier
owner: Grant
domain of: Grant
range: string

SlotDefinition
name: grants
definition uri: https://w3id.org/osc-em/organizational/grants
description: List of grants associated with the project
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/grants
owner: Organizational
domain of: Organizational
range: Grant
multivalued: true
inlined: true

SlotDefinition
name: authors
definition uri: https://w3id.org/osc-em/organizational/authors
description: List of authors associated with the project
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/authors
owner: Organizational
domain of: Organizational
range: Author
multivalued: true
inlined: true

SlotDefinition
name: grant_name
definition uri: https://w3id.org/osc-em/organizational/grant_name
description: name of the grant
from schema: https://w3id.org/osc-em/organizational
slot uri: https://w3id.org/osc-em/organizational/grant_name
owner: Grant
domain of: Grant
range: string

SlotDefinition
name: acquisition
definition uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
from schema: https://w3id.org/osc-em/oscem-emdataset
slot uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true

SlotDefinition
name: instrument
definition uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
from schema: https://w3id.org/osc-em/oscem-emdataset
slot uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true

SlotDefinition
name: sample
definition uri: https://w3id.org/osc-em/OSCEM_schemassample
from schema: https://w3id.org/osc-em/oscem-emdataset
slot uri: https://w3id.org/osc-em/OSCEM_schemassample
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true

SlotDefinition
name: organizational
definition uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
from schema: https://w3id.org/osc-em/oscem-emdataset
slot uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true

SlotDefinition
name: name
definition uri: https://w3id.org/osc-em/custom_typesname
description: The name of the item
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesname
owner: Sample
domain of: Detector
domain of: Sample
range: string

SlotDefinition
name: description
definition uri: https://w3id.org/osc-em/custom_typesdescription
description: The description of the item
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesdescription
owner: Sample
domain of: Sample
range: string

SlotDefinition
name: manufacturer
definition uri: https://w3id.org/osc-em/custom_typesmanufacturer
description: The name of the manufacturer
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesmanufacturer
owner: Grid
domain of: Microscope
domain of: Grid
range: string

SlotDefinition
name: model
definition uri: https://w3id.org/osc-em/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesmodel
owner: Microscope
domain of: EnergyFilter
domain of: Microscope
range: string

SlotDefinition
name: minimal
definition uri: https://w3id.org/osc-em/custom_typesminimal
description: Minimal value of a given dataset property
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesminimal
owner: Range
domain of: Range
range: QuantitySI
inlined: true

SlotDefinition
name: maximal
definition uri: https://w3id.org/osc-em/custom_typesmaximal
description: Maximal value of a given dataset property
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesmaximal
owner: Range
domain of: Range
range: QuantitySI
inlined: true

SlotDefinition
name: increment
definition uri: https://w3id.org/osc-em/custom_typesincrement
description: Increment between elements of a series
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesincrement
owner: Series
domain of: Series
range: QuantitySI
inlined: true

SlotDefinition
name: width
definition uri: https://w3id.org/osc-em/custom_typeswidth
description: The width of a given item - unit depends on item
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typeswidth
owner: ImageSize
domain of: ImageSize
range: integer

SlotDefinition
name: height
definition uri: https://w3id.org/osc-em/custom_typesheight
description: The height of a given item - unit depends on item
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesheight
owner: ImageSize
domain of: ImageSize
range: integer

SlotDefinition
name: x_min
definition uri: https://w3id.org/osc-em/custom_typesx_min
description: minimum x
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesx_min
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true

SlotDefinition
name: x_max
definition uri: https://w3id.org/osc-em/custom_typesx_max
description: maximum x
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesx_max
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true

SlotDefinition
name: y_min
definition uri: https://w3id.org/osc-em/custom_typesy_min
description: minimum y
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesy_min
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true

SlotDefinition
name: y_max
definition uri: https://w3id.org/osc-em/custom_typesy_max
description: maximum y
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesy_max
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true

SlotDefinition
name: unit
definition uri: https://w3id.org/osc-em/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/osc-em/custom_types
mappings: http://qudt.org/schema/qudt/hasUnit
slot uri: http://qudt.org/schema/qudt/hasUnit
owner: QuantityValue
domain of: QuantityValue
range: string

SlotDefinition
name: value
definition uri: https://w3id.org/osc-em/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/osc-em/custom_types
mappings: http://qudt.org/schema/qudt/hasQuantityKind
slot uri: http://qudt.org/schema/qudt/hasQuantityKind
owner: QuantityValue
domain of: QuantityValue
range: float

SlotDefinition
name: descriptors
definition uri: https://w3id.org/osc-em/custom_typesdescriptors
description: List of custom descriptors for user-defined key-value pairs describing how movies were obtained or any related information
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesdescriptors
range: Descriptors
multivalued: true
inlined: true

SlotDefinition
name: descriptor_name
definition uri: https://w3id.org/osc-em/custom_typesdescriptor_name
description: Name defining the descriptor
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesdescriptor_name
owner: Descriptor
domain of: Descriptor
range: string

SlotDefinition
name: descriptor_thing
definition uri: https://w3id.org/osc-em/custom_typesdescriptor_thing
description: Description of the descriptor
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesdescriptor_thing
owner: Descriptor
domain of: Descriptor
range: Any
inlined: true

SlotDefinition
name: valueSI
definition uri: https://w3id.org/osc-em/custom_typesvalueSI
description: value of a given field in respect to its SI unit
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesvalueSI
owner: QuantitySI
domain of: QuantitySI
range: float

SlotDefinition
name: unitSI
definition uri: https://w3id.org/osc-em/custom_typesunitSI
description: the SI unit attached to a si value
from schema: https://w3id.org/osc-em/custom_types
slot uri: https://w3id.org/osc-em/custom_typesunitSI
owner: QuantitySI
domain of: QuantitySI
range: string

SlotDefinition
name: EMDatasetTomo_acquisition
definition uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
description: Describe the data acquisition parameters
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: acquisition
domain: EMDatasetTomo
slot uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
alias: acquisition
owner: EMDatasetTomo
domain of: EMDatasetTomo
is usage slot: true
usage slot name: acquisition
range: AcquisitionSubTomo
required: true
inlined: true

SlotDefinition
name: EMDatasetTomo_instrument
definition uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
description: Describe the instrument used to acquire the data
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: instrument
domain: EMDatasetTomo
slot uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
alias: instrument
owner: EMDatasetTomo
domain of: EMDatasetTomo
is usage slot: true
usage slot name: instrument
range: Instrument
required: true
inlined: true

SlotDefinition
name: EMDatasetTomo_sample
definition uri: https://w3id.org/osc-em/OSCEM_schemassample
description: Sample information
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: sample
domain: EMDatasetTomo
slot uri: https://w3id.org/osc-em/OSCEM_schemassample
alias: sample
owner: EMDatasetTomo
domain of: EMDatasetTomo
is usage slot: true
usage slot name: sample
range: SampleMolecular
inlined: true

SlotDefinition
name: EMDatasetTomo_organizational
definition uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
description: Information on authors and grants
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: organizational
domain: EMDatasetTomo
slot uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
alias: organizational
owner: EMDatasetTomo
domain of: EMDatasetTomo
is usage slot: true
usage slot name: organizational
range: Organizational
inlined: true

SlotDefinition
name: Acquisition_technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Specifies which Acquisition subschema/class is in use.
from schema: https://w3id.org/osc-em/acquisition
is a: technique
domain: Acquisition
slot uri: https://w3id.org/osc-em/acquisitiontechnique
alias: technique
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: technique
range: string

SlotDefinition
name: Acquisition_detectors
definition uri: https://w3id.org/osc-em/acquisitiondetectors
from schema: https://w3id.org/osc-em/acquisition
is a: detectors
domain: Acquisition
slot uri: https://w3id.org/osc-em/acquisitiondetectors
alias: detectors
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: detectors
range: Detector
required: true
multivalued: true
inlined: true

SlotDefinition
name: Acquisition_date_time
definition uri: https://w3id.org/osc-em/acquisitiondate_time
description: Time and date of the data acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: date_time
domain: Acquisition
slot uri: https://w3id.org/osc-em/acquisitiondate_time
alias: date_time
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: date_time
range: datetime
required: true

SlotDefinition
name: Acquisition_binning_camera
definition uri: https://w3id.org/osc-em/acquisitionbinning_camera
description: Level of binning on the images applied during data collection
from schema: https://w3id.org/osc-em/acquisition
is a: binning_camera
domain: Acquisition
slot uri: https://w3id.org/osc-em/acquisitionbinning_camera
alias: binning_camera
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: binning_camera
range: ImageSize
required: true
inlined: true

SlotDefinition
name: Acquisition_pixel_size
definition uri: https://w3id.org/osc-em/acquisitionpixel_size
description: Pixel size, in Angstrom
from schema: https://w3id.org/osc-em/acquisition
is a: pixel_size
domain: Acquisition
slot uri: https://w3id.org/osc-em/acquisitionpixel_size
alias: pixel_size
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: pixel_size
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: AcquisitionSpa_technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Single particle acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: Acquisition_technique
domain: AcquisitionSpa
slot uri: https://w3id.org/osc-em/acquisitiontechnique
alias: technique
owner: AcquisitionSpa
domain of: AcquisitionSpa
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: spa

SlotDefinition
name: EnergyFilter_used
definition uri: https://w3id.org/osc-em/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: used
domain: EnergyFilter
slot uri: https://w3id.org/osc-em/acquisitionused
alias: used
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: EnergyFilter_model
definition uri: https://w3id.org/osc-em/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/osc-em/custom_types
is a: model
domain: EnergyFilter
slot uri: https://w3id.org/osc-em/custom_typesmodel
alias: model
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: model
range: string

SlotDefinition
name: EnergyFilter_width_energy_filter
definition uri: https://w3id.org/osc-em/acquisitionwidth_energy_filter
description: Width of the energy filter used.
from schema: https://w3id.org/osc-em/acquisition
is a: width_energy_filter
domain: EnergyFilter
slot uri: https://w3id.org/osc-em/acquisitionwidth_energy_filter
alias: width_energy_filter
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: width_energy_filter
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: Phaseplate_used
definition uri: https://w3id.org/osc-em/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: used
domain: Phaseplate
slot uri: https://w3id.org/osc-em/acquisitionused
alias: used
owner: Phaseplate
domain of: Phaseplate
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: Phaseplate_instrument_type
definition uri: https://w3id.org/osc-em/acquisitioninstrument_type
description: Type of phaseplate
from schema: https://w3id.org/osc-em/acquisition
is a: instrument_type
domain: Phaseplate
slot uri: https://w3id.org/osc-em/acquisitioninstrument_type
alias: instrument_type
owner: Phaseplate
domain of: Phaseplate
is usage slot: true
usage slot name: instrument_type
range: string
required: true

SlotDefinition
name: SphericalAberrationCorrector_used
definition uri: https://w3id.org/osc-em/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: used
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/osc-em/acquisitionused
alias: used
owner: SphericalAberrationCorrector
domain of: SphericalAberrationCorrector
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: SphericalAberrationCorrector_instrument_type
definition uri: https://w3id.org/osc-em/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/osc-em/acquisition
is a: instrument_type
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/osc-em/acquisitioninstrument_type
alias: instrument_type
owner: SphericalAberrationCorrector
domain of: SphericalAberrationCorrector
is usage slot: true
usage slot name: instrument_type
range: string
required: true

SlotDefinition
name: ChromaticAberrationCorrector_used
definition uri: https://w3id.org/osc-em/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/osc-em/acquisition
is a: used
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/osc-em/acquisitionused
alias: used
owner: ChromaticAberrationCorrector
domain of: ChromaticAberrationCorrector
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: ChromaticAberrationCorrector_instrument_type
definition uri: https://w3id.org/osc-em/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/osc-em/acquisition
is a: instrument_type
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/osc-em/acquisitioninstrument_type
alias: instrument_type
owner: ChromaticAberrationCorrector
domain of: ChromaticAberrationCorrector
is usage slot: true
usage slot name: instrument_type
range: string
required: true

SlotDefinition
name: Instrument_microscope
definition uri: https://w3id.org/osc-em/instrumentmicroscope
description: Microscope information
from schema: https://w3id.org/osc-em/instrument
is a: microscope
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentmicroscope
alias: microscope
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: microscope
range: Microscope
required: true
inlined: true

SlotDefinition
name: Instrument_illumination
definition uri: https://w3id.org/osc-em/instrumentillumination
description: Mode of illumination used during data collection
from schema: https://w3id.org/osc-em/instrument
is a: illumination
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentillumination
alias: illumination
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: illumination
range: string
required: true

SlotDefinition
name: Instrument_imaging
definition uri: https://w3id.org/osc-em/instrumentimaging
description: Mode of imaging used during data collection
from schema: https://w3id.org/osc-em/instrument
is a: imaging
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentimaging
alias: imaging
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: imaging
range: string
required: true

SlotDefinition
name: Instrument_electron_source
definition uri: https://w3id.org/osc-em/instrumentelectron_source
description: Type of electron source used in the microscope, such as FEG
from schema: https://w3id.org/osc-em/instrument
is a: electron_source
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentelectron_source
alias: electron_source
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: electron_source
range: string
required: true

SlotDefinition
name: Instrument_acceleration_voltage
definition uri: https://w3id.org/osc-em/instrumentacceleration_voltage
description: Voltage used for the electron acceleration, in kV
from schema: https://w3id.org/osc-em/instrument
is a: acceleration_voltage
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentacceleration_voltage
alias: acceleration_voltage
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: acceleration_voltage
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: Instrument_c2_aperture
definition uri: https://w3id.org/osc-em/instrumentc2_aperture
description: C2 aperture size used in data acquisition, in µm
from schema: https://w3id.org/osc-em/instrument
is a: c2_aperture
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentc2_aperture
alias: c2_aperture
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: c2_aperture
range: QuantitySI
inlined: true

SlotDefinition
name: Instrument_cs
definition uri: https://w3id.org/osc-em/instrumentcs
description: Spherical aberration of the instrument, in mm
from schema: https://w3id.org/osc-em/instrument
is a: cs
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentcs
alias: cs
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: cs
range: QuantitySI
inlined: true

SlotDefinition
name: Instrument_operating_mode
definition uri: https://w3id.org/osc-em/instrumentoperating_mode
description: Operating mode of the microscope, i.e. "TEM", "STEM"
from schema: https://w3id.org/osc-em/instrument
is a: operating_mode
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentoperating_mode
alias: operating_mode
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: operating_mode
range: string

SlotDefinition
name: Instrument_beam_convergence
definition uri: https://w3id.org/osc-em/instrumentbeam_convergence
description: Refers to how tightly or widely the electron beam is focused onto the sample, in mrad. Typically low convergence for TEM and high for STEM.
from schema: https://w3id.org/osc-em/instrument
is a: beam_convergence
domain: Instrument
slot uri: https://w3id.org/osc-em/instrumentbeam_convergence
alias: beam_convergence
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: beam_convergence
range: QuantitySI
inlined: true

SlotDefinition
name: Microscope_model
definition uri: https://w3id.org/osc-em/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/osc-em/custom_types
is a: model
domain: Microscope
slot uri: https://w3id.org/osc-em/custom_typesmodel
alias: model
owner: Microscope
domain of: Microscope
is usage slot: true
usage slot name: model
range: string
required: true

SlotDefinition
name: Microscope_manufacturer
definition uri: https://w3id.org/osc-em/custom_typesmanufacturer
description: The name of the manufacturer
from schema: https://w3id.org/osc-em/custom_types
is a: manufacturer
domain: Microscope
slot uri: https://w3id.org/osc-em/custom_typesmanufacturer
alias: manufacturer
owner: Microscope
domain of: Microscope
is usage slot: true
usage slot name: manufacturer
range: string

SlotDefinition
name: Sample_name
definition uri: https://w3id.org/osc-em/custom_typesname
description: The name of the item
from schema: https://w3id.org/osc-em/custom_types
is a: name
domain: Sample
slot uri: https://w3id.org/osc-em/custom_typesname
alias: name
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: name
range: string
required: true

SlotDefinition
name: Sample_description
definition uri: https://w3id.org/osc-em/custom_typesdescription
description: The description of the item
from schema: https://w3id.org/osc-em/custom_types
is a: description
domain: Sample
slot uri: https://w3id.org/osc-em/custom_typesdescription
alias: description
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: description
range: string
required: true

SlotDefinition
name: Sample_overall_molecule
definition uri: https://w3id.org/osc-em/sampleoverall_molecule
description: Description of the overall molecule
from schema: https://w3id.org/osc-em/sample
is a: overall_molecule
domain: Sample
slot uri: https://w3id.org/osc-em/sampleoverall_molecule
alias: overall_molecule
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: overall_molecule
range: OverallMolecule
inlined: true

SlotDefinition
name: Sample_molecule
definition uri: https://w3id.org/osc-em/samplemolecule
description: List of molecule associated with the sample
from schema: https://w3id.org/osc-em/sample
is a: molecule
domain: Sample
slot uri: https://w3id.org/osc-em/samplemolecule
alias: molecule
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: molecule
range: Molecule
multivalued: true
inlined: true

SlotDefinition
name: Sample_ligands
definition uri: https://w3id.org/osc-em/sampleligands
description: List of ligands associated with the sample
from schema: https://w3id.org/osc-em/sample
is a: ligands
domain: Sample
slot uri: https://w3id.org/osc-em/sampleligands
alias: ligands
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: ligands
range: Ligand
multivalued: true
inlined: true

SlotDefinition
name: Sample_specimen
definition uri: https://w3id.org/osc-em/samplespecimen
description: Description of the specimen
from schema: https://w3id.org/osc-em/sample
is a: specimen
domain: Sample
slot uri: https://w3id.org/osc-em/samplespecimen
alias: specimen
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: specimen
range: Specimen
inlined: true

SlotDefinition
name: Sample_grid
definition uri: https://w3id.org/osc-em/samplegrid
description: Description of the grid used
from schema: https://w3id.org/osc-em/sample
is a: grid
domain: Sample
slot uri: https://w3id.org/osc-em/samplegrid
alias: grid
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: grid
range: Grid
inlined: true

SlotDefinition
name: OverallMolecule_molecular_overall_type
definition uri: https://w3id.org/osc-em/samplemolecular_overall_type
description: Description of the overall molecular type, i.e., a complex
from schema: https://w3id.org/osc-em/sample
is a: molecular_overall_type
domain: OverallMolecule
slot uri: https://w3id.org/osc-em/samplemolecular_overall_type
alias: molecular_overall_type
owner: OverallMolecule
domain of: OverallMolecule
is usage slot: true
usage slot name: molecular_overall_type
range: MoleculeClassEnum

SlotDefinition
name: OverallMolecule_name_sample
definition uri: https://w3id.org/osc-em/samplename_sample
description: Name of the full sample
from schema: https://w3id.org/osc-em/sample
is a: name_sample
domain: OverallMolecule
slot uri: https://w3id.org/osc-em/samplename_sample
alias: name_sample
owner: OverallMolecule
domain of: OverallMolecule
is usage slot: true
usage slot name: name_sample
range: string
required: true

SlotDefinition
name: OverallMolecule_source
definition uri: https://w3id.org/osc-em/samplesource
description: Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.
from schema: https://w3id.org/osc-em/sample
is a: source
domain: OverallMolecule
slot uri: https://w3id.org/osc-em/samplesource
alias: source
owner: OverallMolecule
domain of: OverallMolecule
is usage slot: true
usage slot name: source
range: string
required: true

SlotDefinition
name: OverallMolecule_molecular_weight
definition uri: https://w3id.org/osc-em/samplemolecular_weight
description: Molecular weight in Da
from schema: https://w3id.org/osc-em/sample
is a: molecular_weight
domain: OverallMolecule
slot uri: https://w3id.org/osc-em/samplemolecular_weight
alias: molecular_weight
owner: OverallMolecule
domain of: OverallMolecule
is usage slot: true
usage slot name: molecular_weight
range: QuantitySI
inlined: true

SlotDefinition
name: OverallMolecule_assembly
definition uri: https://w3id.org/osc-em/sampleassembly
description: What type of higher order structure your sample forms - if any.
from schema: https://w3id.org/osc-em/sample
is a: assembly
domain: OverallMolecule
slot uri: https://w3id.org/osc-em/sampleassembly
alias: assembly
owner: OverallMolecule
domain of: OverallMolecule
is usage slot: true
usage slot name: assembly
range: AssemblyEnum

SlotDefinition
name: Molecule_name_mol
definition uri: https://w3id.org/osc-em/samplename_mol
description: Name of an individual molecule (often protein) in the sample
from schema: https://w3id.org/osc-em/sample
is a: name_mol
domain: Molecule
slot uri: https://w3id.org/osc-em/samplename_mol
alias: name_mol
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: name_mol
range: string
required: true

SlotDefinition
name: Molecule_molecular_type
definition uri: https://w3id.org/osc-em/samplemolecular_type
description: Description of the overall molecular type, i.e., a complex
from schema: https://w3id.org/osc-em/sample
is a: molecular_type
domain: Molecule
slot uri: https://w3id.org/osc-em/samplemolecular_type
alias: molecular_type
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: molecular_type
range: string

SlotDefinition
name: Molecule_molecular_class
definition uri: https://w3id.org/osc-em/samplemolecular_class
description: Class of the molecule
from schema: https://w3id.org/osc-em/sample
is a: molecular_class
domain: Molecule
slot uri: https://w3id.org/osc-em/samplemolecular_class
alias: molecular_class
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: molecular_class
range: string

SlotDefinition
name: Molecule_sequence
definition uri: https://w3id.org/osc-em/samplesequence
description: Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here
from schema: https://w3id.org/osc-em/sample
is a: sequence
domain: Molecule
slot uri: https://w3id.org/osc-em/samplesequence
alias: sequence
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: sequence
range: string
required: true

SlotDefinition
name: Molecule_natural_source
definition uri: https://w3id.org/osc-em/samplenatural_source
description: Scientific name of the natural host organism
from schema: https://w3id.org/osc-em/sample
is a: natural_source
domain: Molecule
slot uri: https://w3id.org/osc-em/samplenatural_source
alias: natural_source
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: natural_source
range: string
required: true

SlotDefinition
name: Molecule_taxonomy_id_source
definition uri: https://w3id.org/osc-em/sampletaxonomy_id_source
description: Taxonomy ID of the natural source organism
from schema: https://w3id.org/osc-em/sample
is a: taxonomy_id_source
domain: Molecule
slot uri: https://w3id.org/osc-em/sampletaxonomy_id_source
alias: taxonomy_id_source
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: taxonomy_id_source
range: string

SlotDefinition
name: Molecule_expression_system
definition uri: https://w3id.org/osc-em/sampleexpression_system
description: Scientific name of the organism used to produce the molecule of interest
from schema: https://w3id.org/osc-em/sample
is a: expression_system
domain: Molecule
slot uri: https://w3id.org/osc-em/sampleexpression_system
alias: expression_system
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: expression_system
range: string

SlotDefinition
name: Molecule_taxonomy_id_expression
definition uri: https://w3id.org/osc-em/sampletaxonomy_id_expression
description: Taxonomy ID of the expression system organism
from schema: https://w3id.org/osc-em/sample
is a: taxonomy_id_expression
domain: Molecule
slot uri: https://w3id.org/osc-em/sampletaxonomy_id_expression
alias: taxonomy_id_expression
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: taxonomy_id_expression
range: string

SlotDefinition
name: Molecule_gene_name
definition uri: https://w3id.org/osc-em/samplegene_name
description: Name of the gene of interest
from schema: https://w3id.org/osc-em/sample
is a: gene_name
domain: Molecule
slot uri: https://w3id.org/osc-em/samplegene_name
alias: gene_name
owner: Molecule
domain of: Molecule
is usage slot: true
usage slot name: gene_name
range: string

SlotDefinition
name: Ligand_present
definition uri: https://w3id.org/osc-em/samplepresent
description: Whether the model contains any ligands
from schema: https://w3id.org/osc-em/sample
is a: present
domain: Ligand
slot uri: https://w3id.org/osc-em/samplepresent
alias: present
owner: Ligand
domain of: Ligand
is usage slot: true
usage slot name: present
range: boolean

SlotDefinition
name: Specimen_buffer
definition uri: https://w3id.org/osc-em/samplebuffer
description: Name/composition of the (chemical) sample buffer during grid preparation
from schema: https://w3id.org/osc-em/sample
is a: buffer
domain: Specimen
slot uri: https://w3id.org/osc-em/samplebuffer
alias: buffer
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: buffer
range: string

SlotDefinition
name: Specimen_concentration
definition uri: https://w3id.org/osc-em/sampleconcentration
description: Concentration of the (supra)molecule in the sample, in mg/ml
from schema: https://w3id.org/osc-em/sample
is a: concentration
domain: Specimen
slot uri: https://w3id.org/osc-em/sampleconcentration
alias: concentration
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: concentration
range: QuantitySI
inlined: true

SlotDefinition
name: Specimen_ph
definition uri: https://w3id.org/osc-em/sampleph
description: pH of the sample buffer
from schema: https://w3id.org/osc-em/sample
is a: ph
domain: Specimen
slot uri: https://w3id.org/osc-em/sampleph
alias: ph
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: ph
range: float

SlotDefinition
name: Specimen_vitrification
definition uri: https://w3id.org/osc-em/samplevitrification
description: Whether the sample was vitrified
from schema: https://w3id.org/osc-em/sample
is a: vitrification
domain: Specimen
slot uri: https://w3id.org/osc-em/samplevitrification
alias: vitrification
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: vitrification
range: boolean

SlotDefinition
name: Specimen_vitrification_cryogen
definition uri: https://w3id.org/osc-em/samplevitrification_cryogen
description: Which cryogen was used for vitrification
from schema: https://w3id.org/osc-em/sample
is a: vitrification_cryogen
domain: Specimen
slot uri: https://w3id.org/osc-em/samplevitrification_cryogen
alias: vitrification_cryogen
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: vitrification_cryogen
range: string

SlotDefinition
name: Specimen_humidity
definition uri: https://w3id.org/osc-em/samplehumidity
description: Environmental humidity just before vitrification, in %
from schema: https://w3id.org/osc-em/sample
is a: humidity
domain: Specimen
slot uri: https://w3id.org/osc-em/samplehumidity
alias: humidity
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: humidity
range: QuantitySI
inlined: true

SlotDefinition
name: Specimen_temperature
definition uri: https://w3id.org/osc-em/sampletemperature
description: Environmental temperature just before vitrification, in K
from schema: https://w3id.org/osc-em/sample
is a: temperature
domain: Specimen
slot uri: https://w3id.org/osc-em/sampletemperature
alias: temperature
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: temperature
range: QuantitySI
inlined: true

SlotDefinition
name: Specimen_staining
definition uri: https://w3id.org/osc-em/samplestaining
description: Whether the sample was stained
from schema: https://w3id.org/osc-em/sample
is a: staining
domain: Specimen
slot uri: https://w3id.org/osc-em/samplestaining
alias: staining
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: staining
range: boolean

SlotDefinition
name: Specimen_embedding
definition uri: https://w3id.org/osc-em/sampleembedding
description: Whether the sample was embedded
from schema: https://w3id.org/osc-em/sample
is a: embedding
domain: Specimen
slot uri: https://w3id.org/osc-em/sampleembedding
alias: embedding
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: embedding
range: boolean

SlotDefinition
name: Specimen_shadowing
definition uri: https://w3id.org/osc-em/sampleshadowing
description: Whether the sample was shadowed
from schema: https://w3id.org/osc-em/sample
is a: shadowing
domain: Specimen
slot uri: https://w3id.org/osc-em/sampleshadowing
alias: shadowing
owner: Specimen
domain of: Specimen
is usage slot: true
usage slot name: shadowing
range: boolean

SlotDefinition
name: Grid_manufacturer
definition uri: https://w3id.org/osc-em/custom_typesmanufacturer
description: The name of the manufacturer
from schema: https://w3id.org/osc-em/custom_types
is a: manufacturer
domain: Grid
slot uri: https://w3id.org/osc-em/custom_typesmanufacturer
alias: manufacturer
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: manufacturer
range: string

SlotDefinition
name: Grid_material
definition uri: https://w3id.org/osc-em/samplematerial
description: Material out of which the grid is made
from schema: https://w3id.org/osc-em/sample
is a: material
domain: Grid
slot uri: https://w3id.org/osc-em/samplematerial
alias: material
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: material
range: string

SlotDefinition
name: Grid_mesh
definition uri: https://w3id.org/osc-em/samplemesh
description: Grid mesh in lines per inch
from schema: https://w3id.org/osc-em/sample
is a: mesh
domain: Grid
slot uri: https://w3id.org/osc-em/samplemesh
alias: mesh
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: mesh
range: float

SlotDefinition
name: Grid_film_support
definition uri: https://w3id.org/osc-em/samplefilm_support
description: Whether a support film was used
from schema: https://w3id.org/osc-em/sample
is a: film_support
domain: Grid
slot uri: https://w3id.org/osc-em/samplefilm_support
alias: film_support
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: film_support
range: boolean

SlotDefinition
name: Grid_film_material
definition uri: https://w3id.org/osc-em/samplefilm_material
description: Type of material the support film is made of
from schema: https://w3id.org/osc-em/sample
is a: film_material
domain: Grid
slot uri: https://w3id.org/osc-em/samplefilm_material
alias: film_material
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: film_material
range: string

SlotDefinition
name: Grid_film_topology
definition uri: https://w3id.org/osc-em/samplefilm_topology
description: Topology of the support film
from schema: https://w3id.org/osc-em/sample
is a: film_topology
domain: Grid
slot uri: https://w3id.org/osc-em/samplefilm_topology
alias: film_topology
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: film_topology
range: string

SlotDefinition
name: Grid_film_thickness
definition uri: https://w3id.org/osc-em/samplefilm_thickness
description: Thickness of the support film
from schema: https://w3id.org/osc-em/sample
is a: film_thickness
domain: Grid
slot uri: https://w3id.org/osc-em/samplefilm_thickness
alias: film_thickness
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: film_thickness
range: string

SlotDefinition
name: Grid_pretreatment_type
definition uri: https://w3id.org/osc-em/samplepretreatment_type
description: Type of pretreatment of the grid, i.e., glow discharge
from schema: https://w3id.org/osc-em/sample
is a: pretreatment_type
domain: Grid
slot uri: https://w3id.org/osc-em/samplepretreatment_type
alias: pretreatment_type
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: pretreatment_type
range: string

SlotDefinition
name: Grid_pretreatment_time
definition uri: https://w3id.org/osc-em/samplepretreatment_time
description: Length of time of the pretreatment in s
from schema: https://w3id.org/osc-em/sample
is a: pretreatment_time
domain: Grid
slot uri: https://w3id.org/osc-em/samplepretreatment_time
alias: pretreatment_time
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: pretreatment_time
range: QuantitySI
inlined: true

SlotDefinition
name: Grid_pretreatment_pressure
definition uri: https://w3id.org/osc-em/samplepretreatment_pressure
description: Pressure of the chamber during pretreatment, in Pa
from schema: https://w3id.org/osc-em/sample
is a: pretreatment_pressure
domain: Grid
slot uri: https://w3id.org/osc-em/samplepretreatment_pressure
alias: pretreatment_pressure
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: pretreatment_pressure
range: QuantitySI
inlined: true

SlotDefinition
name: Grid_pretreatment_atmosphere
definition uri: https://w3id.org/osc-em/samplepretreatment_atmosphere
description: Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.
from schema: https://w3id.org/osc-em/sample
is a: pretreatment_atmosphere
domain: Grid
slot uri: https://w3id.org/osc-em/samplepretreatment_atmosphere
alias: pretreatment_atmosphere
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: pretreatment_atmosphere
range: string

SlotDefinition
name: SampleMolecular_name
definition uri: https://w3id.org/osc-em/custom_typesname
description: The name of the item
from schema: https://w3id.org/osc-em/custom_types
is a: Sample_name
domain: SampleMolecular
slot uri: https://w3id.org/osc-em/custom_typesname
alias: name
owner: SampleMolecular
domain of: SampleMolecular
is usage slot: true
usage slot name: name
range: string

SlotDefinition
name: SampleMolecular_description
definition uri: https://w3id.org/osc-em/custom_typesdescription
description: The description of the item
from schema: https://w3id.org/osc-em/custom_types
is a: Sample_description
domain: SampleMolecular
slot uri: https://w3id.org/osc-em/custom_typesdescription
alias: description
owner: SampleMolecular
domain of: SampleMolecular
is usage slot: true
usage slot name: description
range: string

SlotDefinition
name: SampleMolecular_overall_molecule
definition uri: https://w3id.org/osc-em/sampleoverall_molecule
description: Description of the overall molecule
from schema: https://w3id.org/osc-em/sample
is a: Sample_overall_molecule
domain: SampleMolecular
slot uri: https://w3id.org/osc-em/sampleoverall_molecule
alias: overall_molecule
owner: SampleMolecular
domain of: SampleMolecular
is usage slot: true
usage slot name: overall_molecule
range: OverallMolecule
required: true
inlined: true

SlotDefinition
name: TiltAngle_minimal
definition uri: https://w3id.org/osc-em/custom_typesminimal
description: Minimal value of a given dataset property
from schema: https://w3id.org/osc-em/custom_types
is a: minimal
domain: TiltAngle
slot uri: https://w3id.org/osc-em/custom_typesminimal
alias: minimal
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: minimal
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: TiltAngle_maximal
definition uri: https://w3id.org/osc-em/custom_typesmaximal
description: Maximal value of a given dataset property
from schema: https://w3id.org/osc-em/custom_types
is a: maximal
domain: TiltAngle
slot uri: https://w3id.org/osc-em/custom_typesmaximal
alias: maximal
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: maximal
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: TiltAngle_increment
definition uri: https://w3id.org/osc-em/custom_typesincrement
description: Increment between elements of a series
from schema: https://w3id.org/osc-em/custom_types
is a: increment
domain: TiltAngle
slot uri: https://w3id.org/osc-em/custom_typesincrement
alias: increment
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: increment
range: QuantitySI
required: true
inlined: true

SlotDefinition
name: AcquisitionTomo_tilt_axis_angle
definition uri: https://w3id.org/osc-em/tomography/tilt_axis_angle
description: The tilt axis angle of a tomography series
from schema: https://w3id.org/osc-em/tomography
is a: tilt_axis_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/osc-em/tomography/tilt_axis_angle
alias: tilt_axis_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
is usage slot: true
usage slot name: tilt_axis_angle
range: float
required: true

SlotDefinition
name: AcquisitionTomo_tilt_angle
definition uri: https://w3id.org/osc-em/tomography/tilt_angle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/osc-em/tomography
is a: tilt_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/osc-em/tomography/tilt_angle
alias: tilt_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
is usage slot: true
usage slot name: tilt_angle
range: TiltAngle
required: true
inlined: true

SlotDefinition
name: AcquisitionSubTomo_technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Subtomogram averaging
from schema: https://w3id.org/osc-em/acquisition
is a: Acquisition_technique
domain: AcquisitionSubTomo
slot uri: https://w3id.org/osc-em/acquisitiontechnique
alias: technique
owner: AcquisitionSubTomo
domain of: AcquisitionSubTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: subtomo

SlotDefinition
name: AcquisitionEnvTomo_technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Environmental tomography
from schema: https://w3id.org/osc-em/acquisition
is a: Acquisition_technique
domain: AcquisitionEnvTomo
slot uri: https://w3id.org/osc-em/acquisitiontechnique
alias: technique
owner: AcquisitionEnvTomo
domain of: AcquisitionEnvTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: env_tomo

SlotDefinition
name: AcquisitionCelTomo_technique
definition uri: https://w3id.org/osc-em/acquisitiontechnique
description: Cellular tomography
from schema: https://w3id.org/osc-em/acquisition
is a: Acquisition_technique
domain: AcquisitionCelTomo
slot uri: https://w3id.org/osc-em/acquisitiontechnique
alias: technique
owner: AcquisitionCelTomo
domain of: AcquisitionCelTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: cellular_tomo

SlotDefinition
name: Organizational_authors
definition uri: https://w3id.org/osc-em/organizational/authors
description: List of authors associated with the project
from schema: https://w3id.org/osc-em/organizational
is a: authors
domain: Organizational
slot uri: https://w3id.org/osc-em/organizational/authors
alias: authors
owner: Organizational
domain of: Organizational
is usage slot: true
usage slot name: authors
range: Author
required: true
multivalued: true
inlined: true

SlotDefinition
name: Organizational_funder
definition uri: https://w3id.org/osc-em/organizational/funder
description: funding organization/person.
from schema: https://w3id.org/osc-em/organizational
is a: funder
domain: Organizational
slot uri: https://w3id.org/osc-em/organizational/funder
alias: funder
owner: Organizational
domain of: Organizational
is usage slot: true
usage slot name: funder
range: Funder
multivalued: true
inlined: true

SlotDefinition
name: Author_family_name
definition uri: https://w3id.org/osc-em/organizational/family_name
description: last name
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/familyName
is a: family_name
domain: Author
slot uri: http://schema.org/familyName
alias: family_name
owner: Author
domain of: Author
is usage slot: true
usage slot name: family_name
range: string
required: true

SlotDefinition
name: Author_given_name
definition uri: https://w3id.org/osc-em/organizational/given_name
description: first name
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/givenName
is a: given_name
domain: Author
slot uri: http://schema.org/givenName
alias: given_name
owner: Author
domain of: Author
is usage slot: true
usage slot name: given_name
range: string
required: true

SlotDefinition
name: Author_email
definition uri: https://w3id.org/osc-em/organizational/email
description: email
from schema: https://w3id.org/osc-em/organizational
mappings: http://schema.org/email
is a: email
domain: Author
slot uri: http://schema.org/email
alias: email
owner: Author
domain of: Author
is usage slot: true
usage slot name: email
range: string
required: true
pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$

SlotDefinition
name: Author_orcid
definition uri: https://w3id.org/osc-em/organizational/orcid
description: ORCID of the author, a type of unique identifier
from schema: https://w3id.org/osc-em/organizational
is a: orcid
domain: Author
slot uri: https://w3id.org/osc-em/organizational/orcid
alias: orcid
owner: Author
domain of: Author
is usage slot: true
usage slot name: orcid
range: string

SlotDefinition
name: Author_country
definition uri: https://w3id.org/osc-em/organizational/country
description: Country of the institution
from schema: https://w3id.org/osc-em/organizational
is a: country
domain: Author
slot uri: https://w3id.org/osc-em/organizational/country
alias: country
owner: Author
domain of: Author
is usage slot: true
usage slot name: country
range: string

SlotDefinition
name: Author_type_org
definition uri: https://w3id.org/osc-em/organizational/type_org
description: Type of organization, academic, commercial, governmental, etc.
from schema: https://w3id.org/osc-em/organizational
is a: type_org
domain: Author
slot uri: https://w3id.org/osc-em/organizational/type_org
alias: type_org
owner: Author
domain of: Author
is usage slot: true
usage slot name: type_org
range: OrganizationTypeEnum
required: true

SlotDefinition
name: Author_name_org
definition uri: https://w3id.org/osc-em/organizational/name_org
description: Name of the organization
from schema: https://w3id.org/osc-em/organizational
is a: name_org
domain: Author
slot uri: https://w3id.org/osc-em/organizational/name_org
alias: name_org
owner: Author
domain of: Author
is usage slot: true
usage slot name: name_org
range: string

SlotDefinition
name: EMDatasetBase_acquisition
definition uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: acquisition
domain: EMDatasetBase
slot uri: https://w3id.org/osc-em/OSCEM_schemasacquisition
alias: acquisition
owner: EMDatasetBase
domain of: EMDatasetBase
is usage slot: true
usage slot name: acquisition
range: Any
inlined: true

SlotDefinition
name: EMDatasetBase_instrument
definition uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: instrument
domain: EMDatasetBase
slot uri: https://w3id.org/osc-em/OSCEM_schemasinstrument
alias: instrument
owner: EMDatasetBase
domain of: EMDatasetBase
is usage slot: true
usage slot name: instrument
range: Any
inlined: true

SlotDefinition
name: EMDatasetBase_sample
definition uri: https://w3id.org/osc-em/OSCEM_schemassample
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: sample
domain: EMDatasetBase
slot uri: https://w3id.org/osc-em/OSCEM_schemassample
alias: sample
owner: EMDatasetBase
domain of: EMDatasetBase
is usage slot: true
usage slot name: sample
range: Any
inlined: true

SlotDefinition
name: EMDatasetBase_organizational
definition uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
from schema: https://w3id.org/osc-em/oscem-emdataset
is a: organizational
domain: EMDatasetBase
slot uri: https://w3id.org/osc-em/OSCEM_schemasorganizational
alias: organizational
owner: EMDatasetBase
domain of: EMDatasetBase
is usage slot: true
usage slot name: organizational
range: Any
inlined: true

SlotDefinition
name: QuantityValue_unit
definition uri: https://w3id.org/osc-em/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/osc-em/custom_types
mappings: http://qudt.org/schema/qudt/hasUnit
is a: unit
domain: QuantityValue
slot uri: http://qudt.org/schema/qudt/hasUnit
alias: unit
owner: QuantityValue
domain of: QuantityValue
is usage slot: true
usage slot name: unit
range: string
required: true

SlotDefinition
name: QuantityValue_value
definition uri: https://w3id.org/osc-em/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/osc-em/custom_types
mappings: http://qudt.org/schema/qudt/hasQuantityKind
is a: value
domain: QuantityValue
slot uri: http://qudt.org/schema/qudt/hasQuantityKind
alias: value
owner: QuantityValue
domain of: QuantityValue
is usage slot: true
usage slot name: value
range: float
required: true

SlotDefinition
name: Descriptor_descriptor_name
definition uri: https://w3id.org/osc-em/custom_typesdescriptor_name
description: Name defining the descriptor
from schema: https://w3id.org/osc-em/custom_types
is a: descriptor_name
domain: Descriptor
slot uri: https://w3id.org/osc-em/custom_typesdescriptor_name
alias: descriptor_name
owner: Descriptor
domain of: Descriptor
is usage slot: true
usage slot name: descriptor_name
range: string
required: true

SlotDefinition
name: Descriptor_descriptor_thing
definition uri: https://w3id.org/osc-em/custom_typesdescriptor_thing
description: Description of the descriptor
from schema: https://w3id.org/osc-em/custom_types
is a: descriptor_thing
domain: Descriptor
slot uri: https://w3id.org/osc-em/custom_typesdescriptor_thing
alias: descriptor_thing
owner: Descriptor
domain of: Descriptor
is usage slot: true
usage slot name: descriptor_thing
range: Any
inlined: true

ClassDefinition
name: EMDatasetTomo
definition uri: https://w3id.org/osc-em/oscem-schemas-subtomo/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
slots: EMDatasetTomo_acquisition
slots: EMDatasetTomo_instrument
slots: EMDatasetTomo_sample
slots: EMDatasetTomo_organizational
class uri: https://w3id.org/osc-em/oscem-schemas-subtomo/EMDatasetTomo
tree root: true

ClassDefinition
name: Acquisition
definition uri: https://w3id.org/osc-em/acquisitionAcquisition
description: General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
from schema: https://w3id.org/osc-em/acquisition
slots: Acquisition_technique
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
class uri: https://w3id.org/osc-em/acquisitionAcquisition

ClassDefinition
name: AcquisitionSpa
definition uri: https://w3id.org/osc-em/acquisitionAcquisitionSpa
from schema: https://w3id.org/osc-em/acquisition
is a: Acquisition
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionSpa_technique
class uri: https://w3id.org/osc-em/acquisitionAcquisitionSpa

ClassDefinition
name: EnergyFilter
definition uri: https://w3id.org/osc-em/acquisitionEnergyFilter
description: A device used to filter for electrons with specific energy.
from schema: https://w3id.org/osc-em/acquisition
slots: EnergyFilter_used
slots: EnergyFilter_model
slots: EnergyFilter_width_energy_filter
class uri: https://w3id.org/osc-em/acquisitionEnergyFilter

ClassDefinition
name: SpecialistOptics
definition uri: https://w3id.org/osc-em/acquisitionSpecialistOptics
description: Optional optics used to correct for instrument limitations.
from schema: https://w3id.org/osc-em/acquisition
slots: phaseplate
slots: spherical_aberration_corrector
slots: chromatic_aberration_corrector
class uri: https://w3id.org/osc-em/acquisitionSpecialistOptics

ClassDefinition
name: Phaseplate
definition uri: https://w3id.org/osc-em/acquisitionPhaseplate
description: Used to modulate the phase of the electron wave.
from schema: https://w3id.org/osc-em/acquisition
slots: Phaseplate_used
slots: Phaseplate_instrument_type
class uri: https://w3id.org/osc-em/acquisitionPhaseplate

ClassDefinition
name: SphericalAberrationCorrector
definition uri: https://w3id.org/osc-em/acquisitionSphericalAberrationCorrector
description: Special device used to correct instrument inherent spherical aberration.
from schema: https://w3id.org/osc-em/acquisition
slots: SphericalAberrationCorrector_used
slots: SphericalAberrationCorrector_instrument_type
class uri: https://w3id.org/osc-em/acquisitionSphericalAberrationCorrector

ClassDefinition
name: ChromaticAberrationCorrector
definition uri: https://w3id.org/osc-em/acquisitionChromaticAberrationCorrector
description: Special device used to correct instrument inherent chromatic aberration.
from schema: https://w3id.org/osc-em/acquisition
slots: ChromaticAberrationCorrector_used
slots: ChromaticAberrationCorrector_instrument_type
class uri: https://w3id.org/osc-em/acquisitionChromaticAberrationCorrector

ClassDefinition
name: Detector
definition uri: https://w3id.org/osc-em/acquisitionDetector
description: Class representing a detector
from schema: https://w3id.org/osc-em/acquisition
slots: name
slots: mode
slots: dispersion
slots: collection_angle
class uri: https://w3id.org/osc-em/acquisitionDetector

ClassDefinition
name: Instrument
definition uri: https://w3id.org/osc-em/instrumentInstrument
description: Instrument values, mostly constant across a data collection.
from schema: https://w3id.org/osc-em/instrument
slots: Instrument_microscope
slots: Instrument_illumination
slots: Instrument_imaging
slots: Instrument_electron_source
slots: Instrument_acceleration_voltage
slots: Instrument_c2_aperture
slots: Instrument_cs
slots: Instrument_operating_mode
slots: Instrument_beam_convergence
class uri: https://w3id.org/osc-em/instrumentInstrument

ClassDefinition
name: Microscope
definition uri: https://w3id.org/osc-em/instrumentMicroscope
description: Microscope information
from schema: https://w3id.org/osc-em/instrument
mappings: schema:Microscope
slots: Microscope_model
slots: Microscope_manufacturer
class uri: http://schema.org/Microscope

ClassDefinition
name: Sample
definition uri: https://w3id.org/osc-em/sampleSample
description: Unifying class to describe the full sample.
from schema: https://w3id.org/osc-em/sample
slots: Sample_name
slots: Sample_description
slots: Sample_overall_molecule
slots: Sample_molecule
slots: Sample_ligands
slots: Sample_specimen
slots: Sample_grid
class uri: https://w3id.org/osc-em/sampleSample

ClassDefinition
name: OverallMolecule
definition uri: https://w3id.org/osc-em/sampleOverallMolecule
description: Description of the overall molecule
from schema: https://w3id.org/osc-em/sample
slots: OverallMolecule_molecular_overall_type
slots: OverallMolecule_name_sample
slots: OverallMolecule_source
slots: OverallMolecule_molecular_weight
slots: OverallMolecule_assembly
class uri: https://w3id.org/osc-em/sampleOverallMolecule

ClassDefinition
name: Molecule
definition uri: https://w3id.org/osc-em/sampleMolecule
description: More detailed information about individual molecules.
from schema: https://w3id.org/osc-em/sample
slots: Molecule_name_mol
slots: Molecule_molecular_type
slots: Molecule_molecular_class
slots: Molecule_sequence
slots: Molecule_natural_source
slots: Molecule_taxonomy_id_source
slots: Molecule_expression_system
slots: Molecule_taxonomy_id_expression
slots: Molecule_gene_name
class uri: https://w3id.org/osc-em/sampleMolecule

ClassDefinition
name: Ligand
definition uri: https://w3id.org/osc-em/sampleLigand
description: Information on ligands if present.
from schema: https://w3id.org/osc-em/sample
slots: Ligand_present
slots: smiles
slots: reference
class uri: https://w3id.org/osc-em/sampleLigand

ClassDefinition
name: Specimen
definition uri: https://w3id.org/osc-em/sampleSpecimen
description: Description of specimen handling.
from schema: https://w3id.org/osc-em/sample
slots: Specimen_buffer
slots: Specimen_concentration
slots: Specimen_ph
slots: Specimen_vitrification
slots: Specimen_vitrification_cryogen
slots: Specimen_humidity
slots: Specimen_temperature
slots: Specimen_staining
slots: Specimen_embedding
slots: Specimen_shadowing
class uri: https://w3id.org/osc-em/sampleSpecimen

ClassDefinition
name: Grid
definition uri: https://w3id.org/osc-em/sampleGrid
description: Details on the grid used in the experiment.
from schema: https://w3id.org/osc-em/sample
slots: Grid_manufacturer
slots: Grid_material
slots: Grid_mesh
slots: Grid_film_support
slots: Grid_film_material
slots: Grid_film_topology
slots: Grid_film_thickness
slots: Grid_pretreatment_type
slots: Grid_pretreatment_time
slots: Grid_pretreatment_pressure
slots: Grid_pretreatment_atmosphere
class uri: https://w3id.org/osc-em/sampleGrid

ClassDefinition
name: SampleMolecular
definition uri: https://w3id.org/osc-em/sampleSampleMolecular
from schema: https://w3id.org/osc-em/sample
is a: Sample
slots: Sample_molecule
slots: Sample_ligands
slots: Sample_specimen
slots: Sample_grid
slots: SampleMolecular_name
slots: SampleMolecular_description
slots: SampleMolecular_overall_molecule
class uri: https://w3id.org/osc-em/sampleSampleMolecular

ClassDefinition
name: TiltAngle
definition uri: https://w3id.org/osc-em/tomography/TiltAngle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/osc-em/tomography
is a: Series
slots: TiltAngle_minimal
slots: TiltAngle_maximal
slots: TiltAngle_increment
class uri: https://w3id.org/osc-em/tomography/TiltAngle

ClassDefinition
name: AcquisitionTomo
definition uri: https://w3id.org/osc-em/tomography/AcquisitionTomo
from schema: https://w3id.org/osc-em/tomography
is a: Acquisition
slots: Acquisition_technique
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
class uri: https://w3id.org/osc-em/tomography/AcquisitionTomo

ClassDefinition
name: AcquisitionSubTomo
definition uri: https://w3id.org/osc-em/tomography/AcquisitionSubTomo
from schema: https://w3id.org/osc-em/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionSubTomo_technique
class uri: https://w3id.org/osc-em/tomography/AcquisitionSubTomo

ClassDefinition
name: AcquisitionEnvTomo
definition uri: https://w3id.org/osc-em/tomography/AcquisitionEnvTomo
from schema: https://w3id.org/osc-em/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionEnvTomo_technique
class uri: https://w3id.org/osc-em/tomography/AcquisitionEnvTomo

ClassDefinition
name: AcquisitionCelTomo
definition uri: https://w3id.org/osc-em/tomography/AcquisitionCelTomo
from schema: https://w3id.org/osc-em/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionCelTomo_technique
class uri: https://w3id.org/osc-em/tomography/AcquisitionCelTomo

ClassDefinition
name: Organizational
definition uri: https://w3id.org/osc-em/organizational/Organizational
description: Overarching category for authors and grants
from schema: https://w3id.org/osc-em/organizational
slots: grants
slots: Organizational_authors
slots: Organizational_funder
class uri: https://w3id.org/osc-em/organizational/Organizational

ClassDefinition
name: Person
definition uri: https://w3id.org/osc-em/organizational/Person
description: personal information
from schema: https://w3id.org/osc-em/organizational
mappings: schema:Person
slots: family_name
slots: given_name
slots: job_title
slots: email
slots: telephone
class uri: http://schema.org/Person

ClassDefinition
name: Author
definition uri: https://w3id.org/osc-em/organizational/Author
description: Details on the person performing the experiment.
from schema: https://w3id.org/osc-em/organizational
is a: Person
slots: job_title
slots: telephone
slots: Author_orcid
slots: Author_country
slots: role
slots: Author_name_org
slots: Author_type_org
slots: Author_family_name
slots: Author_given_name
slots: Author_email
class uri: https://w3id.org/osc-em/organizational/Author

ClassDefinition
name: Grant
definition uri: https://w3id.org/osc-em/organizational/Grant
description: Grant
from schema: https://w3id.org/osc-em/organizational
mappings: schema:Grant
slots: grant_name
slots: start_date
slots: end_date
slots: budget
slots: project_id
slots: country
class uri: http://schema.org/Grant

ClassDefinition
name: Funder
definition uri: https://w3id.org/osc-em/organizational/Funder
description: Description of the project funding
from schema: https://w3id.org/osc-em/organizational
slots: funder_name
slots: type_org
slots: country
class uri: https://w3id.org/osc-em/organizational/Funder

ClassDefinition
name: EMDatasetBase
definition uri: https://w3id.org/osc-em/OSCEM_schemasEMDatasetBase
description: OSC-EM Metadata for a dataset
from schema: https://w3id.org/osc-em/oscem-emdataset
abstract: true
slots: EMDatasetBase_acquisition
slots: EMDatasetBase_instrument
slots: EMDatasetBase_sample
slots: EMDatasetBase_organizational
class uri: https://w3id.org/osc-em/OSCEM_schemasEMDatasetBase

ClassDefinition
name: Any
definition uri: https://w3id.org/osc-em/custom_typesAny
description: Any type, used as the base for type-narrowing.
from schema: https://w3id.org/osc-em/custom_types
mappings: linkml:Any
class uri: https://w3id.org/linkml/Any

ClassDefinition
name: Range
definition uri: https://w3id.org/osc-em/custom_typesRange
description: A range constructed from min and max
from schema: https://w3id.org/osc-em/custom_types
slots: minimal
slots: maximal
class uri: https://w3id.org/osc-em/custom_typesRange

ClassDefinition
name: Series
definition uri: https://w3id.org/osc-em/custom_typesSeries
description: A series of numbers constructed from min, max, and increment
from schema: https://w3id.org/osc-em/custom_types
is a: Range
slots: minimal
slots: maximal
slots: increment
class uri: https://w3id.org/osc-em/custom_typesSeries

ClassDefinition
name: ImageSize
definition uri: https://w3id.org/osc-em/custom_typesImageSize
description: size of a 2D image (in integer units)
from schema: https://w3id.org/osc-em/custom_types
slots: height
slots: width
class uri: https://w3id.org/osc-em/custom_typesImageSize

ClassDefinition
name: BoundingBox2D
definition uri: https://w3id.org/osc-em/custom_typesBoundingBox2D
description: an axis-aligned 2D bounding box (float units)
from schema: https://w3id.org/osc-em/custom_types
slots: x_min
slots: x_max
slots: y_min
slots: y_max
class uri: https://w3id.org/osc-em/custom_typesBoundingBox2D

ClassDefinition
name: QuantityValue
definition uri: https://w3id.org/osc-em/custom_typesQuantityValue
description: if a value has a unit, it should be given as a unit value pair.
from schema: https://w3id.org/osc-em/custom_types
mappings: qudt:quantityValue
slots: QuantityValue_unit
slots: QuantityValue_value
class uri: http://qudt.org/schema/qudt/quantityValue

ClassDefinition
name: QuantitySI
definition uri: https://w3id.org/osc-em/custom_typesQuantitySI
description: unit value extended to have two additional fields si_value and si_unit
from schema: https://w3id.org/osc-em/custom_types
is a: QuantityValue
slots: QuantityValue_unit
slots: QuantityValue_value
slots: valueSI
slots: unitSI
class uri: https://w3id.org/osc-em/custom_typesQuantitySI

ClassDefinition
name: Descriptor
definition uri: https://w3id.org/osc-em/custom_typesDescriptor
description: List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
from schema: https://w3id.org/osc-em/custom_types
abstract: true
slots: Descriptor_descriptor_name
slots: Descriptor_descriptor_thing
class uri: https://w3id.org/osc-em/custom_typesDescriptor

ClassDefinition
name: Descriptors
definition uri: https://w3id.org/osc-em/custom_typesDescriptors
from schema: https://w3id.org/osc-em/custom_types
is a: Descriptor
slots: Descriptor_descriptor_name
slots: Descriptor_descriptor_thing
class uri: https://w3id.org/osc-em/custom_typesDescriptors