oscem-schemas-cellular-tomo
type: SchemaDefinition
name: CellularTomography
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/oscem-schemas/latest/cellular_tomo
imports: linkml:types
imports: ./acquisition
imports: ./instrument
imports: ./sample_cellular_tomo_lab
imports: ./tomography
imports: ./organizational
imports: ./emdataset
imports: custom_types
imports: sample_environmental
imports: acquisition
license: CC-BY
prefixes:
  prefix prefix: linkml
  prefix reference: https://w3id.org/linkml/
default prefix: https://w3id.org/oscem-schemas/latest/cellular_tomo/
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_cellular_tomo.yaml
source file date: 2025-12-05T16:03:40
source file size: 1146
generation date: 2025-12-05T16:04:47

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/oscem-schemas/latest/acquisitionAcquisitionTechnique
from schema: https://w3id.org/oscem-schemas/latest/acquisition
permissible values:
  text: spa
permissible values:
  text: subtomo
permissible values:
  text: env_tomo
permissible values:
  text: cellular_tomo

name: OrganizationTypeEnum
definition uri: https://w3id.org/oscem-schemas/latest/organizational/OrganizationTypeEnum
description: Allowed values for authors organizations.
from schema: https://w3id.org/oscem-schemas/latest/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

name: FreezingMethodEnum
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleFreezingMethodEnum
description: Allowed freezing options.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
permissible values:
  text: plunge_freezing
  description: Typically used for smaller and thinner samples in both SPA and tomography.
permissible values:
  text: high_pressure_freezing
  description: Usually used for larger organic complexes, such as organoids or even tissue samples.

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

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

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

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

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

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

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

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

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

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

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

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

SlotDefinition
name: detectors
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
owner: Acquisition
domain of: Acquisition
range: Detector
multivalued: true
inlined: true
inlined as list: true

SlotDefinition
name: used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionimage_size
description: The size of the image in pixels, height and width given.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimage_size
owner: Acquisition
domain of: Acquisition
range: ImageSize
inlined: true
inlined as list: true

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

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

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

SlotDefinition
name: frames_per_movie
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionframes_per_movie
owner: Acquisition
domain of: Acquisition
range: integer

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

SlotDefinition
name: images_generated
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimages_generated
owner: Acquisition
domain of: Acquisition
range: integer

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

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

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

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

SlotDefinition
name: instrument_type
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionspherical_aberration_corrector
description: Specialist device to correct for spherical aberration of the microscope lenses
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionspherical_aberration_corrector
owner: SpecialistOptics
domain of: SpecialistOptics
range: SphericalAberrationCorrector
inlined: true
inlined as list: true

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

SlotDefinition
name: beamshift
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: beamtilt
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtilt
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: imageshift
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimageshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: beamtiltgroups
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtiltgroups
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: gainref_flip_rotate
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiongainref_flip_rotate
owner: Acquisition
domain of: Acquisition
range: string

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

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

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

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

SlotDefinition
name: microscope
definition uri: https://w3id.org/oscem-schemas/latest/instrumentmicroscope
description: Microscope information
from schema: https://w3id.org/oscem-schemas/latest/instrument
slot uri: https://w3id.org/oscem-schemas/latest/instrumentmicroscope
owner: Instrument
domain of: Instrument
range: Microscope
inlined: true
inlined as list: true

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

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

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

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

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

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

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

SlotDefinition
name: beam_convergence
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrument
slot uri: https://w3id.org/oscem-schemas/latest/instrumentbeam_convergence
owner: Instrument
domain of: Instrument
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: temperature_growth
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomotemperature_growth
description: Temperature of the sample; in K.
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomotemperature_growth
owner: GrowthCondition
domain of: GrowthCondition
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: atmosphere_growth
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomoatmosphere_growth
description: What was the atmosphere the sample was in, elaborate on any special gases present etc.
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomoatmosphere_growth
owner: GrowthCondition
domain of: GrowthCondition
range: string

SlotDefinition
name: media
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomomedia
description: What growth media was used
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomomedia
owner: GrowthCondition
domain of: GrowthCondition
range: string

SlotDefinition
name: growth_location
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomogrowth_location
description: In/on what kind of surface/container the cells were grown; i.e. directly on a grid
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomogrowth_location
owner: GrowthCondition
domain of: GrowthCondition
range: string

SlotDefinition
name: cell_cycle
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomocell_cycle
description: What was the targeted cell cycle state, if any
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomocell_cycle
owner: GrowthCondition
domain of: GrowthCondition
range: string

SlotDefinition
name: treatment
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomotreatment
description: Were there any special treatment conditions; such as addition of certain chemicals etc
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomotreatment
owner: GrowthCondition
domain of: GrowthCondition
range: string

SlotDefinition
name: growth_condition
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomogrowth_condition
description: How the specimen was grown
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slot uri: https://w3id.org/oscem-schemas/latest/cellular_tomogrowth_condition
owner: SampleCell
domain of: SampleCell
range: GrowthCondition
inlined: true
inlined as list: true

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

SlotDefinition
name: tilt_angle
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/tomography
slot uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
range: TiltAngle
inlined: true
inlined as list: true

SlotDefinition
name: family_name
definition uri: https://w3id.org/oscem-schemas/latest/organizational/family_name
description: last name
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/given_name
description: first name
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/job_title
description: job title
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/email
description: email
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/telephone
description: work phone
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/person
description: person
from schema: https://w3id.org/oscem-schemas/latest/organizational
mappings: http://schema.org/Person
slot uri: http://schema.org/Person
range: Person
inlined: true
inlined as list: true

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

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

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

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

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

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

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

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

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

SlotDefinition
name: budget
definition uri: https://w3id.org/oscem-schemas/latest/organizational/budget
description: budget
from schema: https://w3id.org/oscem-schemas/latest/organizational
slot uri: https://w3id.org/oscem-schemas/latest/organizational/budget
owner: Grant
domain of: Grant
range: QuantityValue
inlined: true
inlined as list: true

SlotDefinition
name: project_id
definition uri: https://w3id.org/oscem-schemas/latest/organizational/project_id
description: project id
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/grants
description: List of grants associated with the project
from schema: https://w3id.org/oscem-schemas/latest/organizational
slot uri: https://w3id.org/oscem-schemas/latest/organizational/grants
owner: Organizational
domain of: Organizational
range: Grant
multivalued: true
inlined: true
inlined as list: true

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

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

SlotDefinition
name: acquisition
definition uri: https://w3id.org/oscem-schemas/latest/acquisition
from schema: https://w3id.org/oscem-schemas/latest/emdataset
slot uri: https://w3id.org/oscem-schemas/latest/acquisition
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: instrument
definition uri: https://w3id.org/oscem-schemas/latest/instrument
from schema: https://w3id.org/oscem-schemas/latest/emdataset
slot uri: https://w3id.org/oscem-schemas/latest/instrument
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: sample
definition uri: https://w3id.org/oscem-schemas/latest/sample
from schema: https://w3id.org/oscem-schemas/latest/emdataset
slot uri: https://w3id.org/oscem-schemas/latest/sample
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: organizational
definition uri: https://w3id.org/oscem-schemas/latest/organizational
from schema: https://w3id.org/oscem-schemas/latest/emdataset
slot uri: https://w3id.org/oscem-schemas/latest/organizational
owner: EMDatasetBase
domain of: EMDatasetBase
range: Any
inlined: true
inlined as list: true

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

SlotDefinition
name: description
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescription
description: The description of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescription
range: string

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

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

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

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

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

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

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

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

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

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

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

SlotDefinition
name: unit
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/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/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptors
range: Descriptors
multivalued: true
inlined: true
inlined as list: true

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

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

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

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

SlotDefinition
name: organism
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganism
description: the organism(s) present in your sample, if not perfectly defined try to asses as close as possible.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganism
owner: SpecimenEnv
domain of: SpecimenEnv
range: string
multivalued: true

SlotDefinition
name: tissue
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampletissue
description: if the sample is a tissue sample please indicate what type of tissue.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampletissue
owner: SpecimenEnv
domain of: SpecimenEnv
range: string

SlotDefinition
name: source_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplesource_env
description: where is this sample from? i.e. Hospital
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplesource_env
owner: SpecimenEnv
domain of: SpecimenEnv
range: string

SlotDefinition
name: location
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplelocation
description: the geographical location of your source, optimally in a geographic coordinate system.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplelocation
owner: SpecimenEnv
domain of: SpecimenEnv
range: string

SlotDefinition
name: collection_date
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplecollection_date
description: When the sample was collected
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplecollection_date
owner: SpecimenEnv
domain of: SpecimenEnv
range: date

SlotDefinition
name: handling
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplehandling
description: What was done to the sample, please give an overview of relevant treatments.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplehandling
owner: SpecimenEnv
domain of: SpecimenEnv
range: string

SlotDefinition
name: cryogen_sample_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplecryogen_sample_env
description: the cryogen used to freeze the sample, i.e. ethane
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplecryogen_sample_env
owner: Freezing
domain of: Freezing
range: string

SlotDefinition
name: method
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplemethod
description: freezing method - such as plunge freezing, high pressure freezing etc.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplemethod
owner: Freezing
domain of: Freezing
range: FreezingMethodEnum

SlotDefinition
name: blotting
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleblotting
description: whether blotting was performed.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleblotting
owner: Freezing
domain of: Freezing
range: boolean

SlotDefinition
name: humidity_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplehumidity_env
description: humidity of the atmosphere right before/ during freezing; in %.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplehumidity_env
owner: Freezing
domain of: Freezing
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: temperature_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampletemperature_env
description: temperature of the sample right before freezing; in K.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampletemperature_env
owner: Freezing
domain of: Freezing
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: atmosphere
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleatmosphere
description: What was the atmosphere the sample was in right before freezing, elaborate on any special gases present etc.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleatmosphere
owner: Freezing
domain of: Freezing
range: string

SlotDefinition
name: details
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampledetails
description: Any further comments on the freezing process go here.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampledetails
owner: Freezing
domain of: Freezing
range: string

SlotDefinition
name: freezing
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplefreezing
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplefreezing
owner: SampleEnv
domain of: SampleEnv
range: Freezing
inlined: true
inlined as list: true

SlotDefinition
name: thinning
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplethinning
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplethinning
owner: SampleEnv
domain of: SampleEnv
range: Thinning
inlined: true
inlined as list: true

SlotDefinition
name: method_thin
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplemethod_thin
description: The thinning method used, such as FIB milling.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplemethod_thin
owner: Thinning
domain of: Thinning
range: string

SlotDefinition
name: instrument_thin
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleinstrument_thin
description: Instrument used for thinning the sample
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleinstrument_thin
owner: Thinning
domain of: Thinning
range: string

SlotDefinition
name: ion_source
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleion_source
description: what ion source was used?
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleion_source
owner: Thinning
domain of: Thinning
range: string

SlotDefinition
name: target_thickness
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampletarget_thickness
description: What was the target thickness of the lamella; in nm.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampletarget_thickness
owner: Thinning
domain of: Thinning
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: lift_out
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplelift_out
description: whether a lift out was performed
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplelift_out
owner: Thinning
domain of: Thinning
range: boolean

SlotDefinition
name: tomogram_features
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampletomogram_features
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampletomogram_features
owner: SampleEnv
domain of: SampleEnv
range: TomogramFeatures
inlined: true
inlined as list: true

SlotDefinition
name: cellular_features
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplecellular_features
description: What type of cellular features are present in your tomograms?
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplecellular_features
owner: TomogramFeatures
domain of: TomogramFeatures
range: string

SlotDefinition
name: organelles
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganelles
description: What organelles; if any; are present?
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganelles
owner: TomogramFeatures
domain of: TomogramFeatures
range: string
multivalued: true

SlotDefinition
name: main_target
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplemain_target
description: What was the main biological target of your research for this tomogram?
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplemain_target
owner: TomogramFeatures
domain of: TomogramFeatures
range: string

SlotDefinition
name: details_tomo
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampledetails_tomo
description: If you have any further comments on your tomograms please leave them here
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampledetails_tomo
owner: TomogramFeatures
domain of: TomogramFeatures
range: string

SlotDefinition
name: specimen_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplespecimen_env
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplespecimen_env
owner: SampleEnv
domain of: SampleEnv
range: SpecimenEnv
inlined: true
inlined as list: true

SlotDefinition
name: EMDatasetCell_acquisition
definition uri: https://w3id.org/oscem-schemas/latest/acquisition
description: Describe the data acquisition parameters
from schema: https://w3id.org/oscem-schemas/latest/emdataset
is a: acquisition
domain: EMDatasetCell
slot uri: https://w3id.org/oscem-schemas/latest/acquisition
alias: acquisition
owner: EMDatasetCell
domain of: EMDatasetCell
is usage slot: true
usage slot name: acquisition
range: AcquisitionCelTomo
required: true
inlined: true
inlined as list: true

SlotDefinition
name: EMDatasetCell_instrument
definition uri: https://w3id.org/oscem-schemas/latest/instrument
description: Describe the instrument used to acquire the data
from schema: https://w3id.org/oscem-schemas/latest/emdataset
is a: instrument
domain: EMDatasetCell
slot uri: https://w3id.org/oscem-schemas/latest/instrument
alias: instrument
owner: EMDatasetCell
domain of: EMDatasetCell
is usage slot: true
usage slot name: instrument
range: Instrument
required: true
inlined: true
inlined as list: true

SlotDefinition
name: EMDatasetCell_sample
definition uri: https://w3id.org/oscem-schemas/latest/sample
description: Sample information
from schema: https://w3id.org/oscem-schemas/latest/emdataset
is a: sample
domain: EMDatasetCell
slot uri: https://w3id.org/oscem-schemas/latest/sample
alias: sample
owner: EMDatasetCell
domain of: EMDatasetCell
is usage slot: true
usage slot name: sample
range: SampleCell
inlined: true
inlined as list: true

SlotDefinition
name: EMDatasetCell_organizational
definition uri: https://w3id.org/oscem-schemas/latest/organizational
description: Information on authors and grants
from schema: https://w3id.org/oscem-schemas/latest/emdataset
is a: organizational
domain: EMDatasetCell
slot uri: https://w3id.org/oscem-schemas/latest/organizational
alias: organizational
owner: EMDatasetCell
domain of: EMDatasetCell
is usage slot: true
usage slot name: organizational
range: Organizational
inlined: true
inlined as list: true

SlotDefinition
name: Acquisition_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Specifies which Acquisition subschema/class is in use.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: technique
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitiondetectors
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: detectors
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
alias: detectors
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: detectors
range: Detector
required: true
multivalued: true
inlined: true
inlined as list: true

SlotDefinition
name: Acquisition_date_time
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondate_time
description: Time and date of the data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: date_time
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionbinning_camera
description: Level of binning on the images applied during data collection
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: binning_camera
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

SlotDefinition
name: Acquisition_pixel_size
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionpixel_size
description: Pixel size, in Angstrom
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: pixel_size
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

SlotDefinition
name: AcquisitionSpa_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Single particle acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition_technique
domain: AcquisitionSpa
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: model
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionwidth_energy_filter
description: Width of the energy filter used.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: width_energy_filter
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

SlotDefinition
name: Phaseplate_used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: Phaseplate
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitioninstrument_type
description: Type of phaseplate
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: Phaseplate
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrumentmicroscope
description: Microscope information
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: microscope
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/instrumentmicroscope
alias: microscope
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: microscope
range: Microscope
required: true
inlined: true
inlined as list: true

SlotDefinition
name: Instrument_illumination
definition uri: https://w3id.org/oscem-schemas/latest/instrumentillumination
description: Mode of illumination used during data collection
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: illumination
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrumentimaging
description: Mode of imaging used during data collection
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: imaging
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrumentelectron_source
description: Type of electron source used in the microscope, such as FEG
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: electron_source
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrumentacceleration_voltage
description: Voltage used for the electron acceleration, in kV
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: acceleration_voltage
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

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

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

SlotDefinition
name: Instrument_operating_mode
definition uri: https://w3id.org/oscem-schemas/latest/instrumentoperating_mode
description: Operating mode of the microscope, i.e. "TEM", "STEM"
from schema: https://w3id.org/oscem-schemas/latest/instrument
is a: operating_mode
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/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/oscem-schemas/latest/instrument
is a: beam_convergence
domain: Instrument
slot uri: https://w3id.org/oscem-schemas/latest/instrumentbeam_convergence
alias: beam_convergence
owner: Instrument
domain of: Instrument
is usage slot: true
usage slot name: beam_convergence
range: QuantitySI
inlined: true
inlined as list: true

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

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

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

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

SlotDefinition
name: AcquisitionTomo_tilt_axis_angle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_axis_angle
description: The tilt axis angle of a tomography series
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: tilt_axis_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/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/oscem-schemas/latest/tomography
is a: tilt_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

SlotDefinition
name: AcquisitionSubTomo_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Subtomogram averaging
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition_technique
domain: AcquisitionSubTomo
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitiontechnique
description: Environmental tomography
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition_technique
domain: AcquisitionEnvTomo
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitiontechnique
description: Cellular tomography
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition_technique
domain: AcquisitionCelTomo
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/authors
description: List of authors associated with the project
from schema: https://w3id.org/oscem-schemas/latest/organizational
is a: authors
domain: Organizational
slot uri: https://w3id.org/oscem-schemas/latest/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
inlined as list: true

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

SlotDefinition
name: Author_family_name
definition uri: https://w3id.org/oscem-schemas/latest/organizational/family_name
description: last name
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/given_name
description: first name
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/email
description: email
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/orcid
description: ORCID of the author, a type of unique identifier
from schema: https://w3id.org/oscem-schemas/latest/organizational
is a: orcid
domain: Author
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/country
description: Country of the institution
from schema: https://w3id.org/oscem-schemas/latest/organizational
is a: country
domain: Author
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/type_org
description: Type of organization, academic, commercial, governmental, etc.
from schema: https://w3id.org/oscem-schemas/latest/organizational
is a: type_org
domain: Author
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/name_org
description: Name of the organization
from schema: https://w3id.org/oscem-schemas/latest/organizational
is a: name_org
domain: Author
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisition
from schema: https://w3id.org/oscem-schemas/latest/emdataset
is a: acquisition
domain: EMDatasetBase
slot uri: https://w3id.org/oscem-schemas/latest/acquisition
alias: acquisition
owner: EMDatasetBase
domain of: EMDatasetBase
is usage slot: true
usage slot name: acquisition
range: Any
inlined: true
inlined as list: true

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

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

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

SlotDefinition
name: QuantityValue_unit
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesdescriptor_name
description: Name defining the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: descriptor_name
domain: Descriptor
slot uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesdescriptor_thing
description: Description of the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: descriptor_thing
domain: Descriptor
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_thing
alias: descriptor_thing
owner: Descriptor
domain of: Descriptor
is usage slot: true
usage slot name: descriptor_thing
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: SampleEnv_specimen_env
definition uri: https://w3id.org/oscem-schemas/latest/environmental_samplespecimen_env
from schema: https://w3id.org/oscem-schemas/latest/sample-env
is a: specimen_env
domain: SampleEnv
slot uri: https://w3id.org/oscem-schemas/latest/environmental_samplespecimen_env
alias: specimen_env
owner: SampleEnv
domain of: SampleEnv
is usage slot: true
usage slot name: specimen_env
range: SpecimenEnv
required: true
inlined: true
inlined as list: true

SlotDefinition
name: SpecimenEnv_organism
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganism
description: the organism(s) present in your sample, if not perfectly defined try to asses as close as possible.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
is a: organism
domain: SpecimenEnv
slot uri: https://w3id.org/oscem-schemas/latest/environmental_sampleorganism
alias: organism
owner: SpecimenEnv
domain of: SpecimenEnv
is usage slot: true
usage slot name: organism
range: string
required: true
multivalued: true

ClassDefinition
name: EMDatasetCell
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomo/EMDatasetCell
description: Cryo electron tomography dataset of a cellular sample, lab grown
from schema: https://w3id.org/oscem-schemas/latest/cellular_tomo
is a: EMDatasetBase
slots: EMDatasetCell_acquisition
slots: EMDatasetCell_instrument
slots: EMDatasetCell_sample
slots: EMDatasetCell_organizational
class uri: https://w3id.org/oscem-schemas/latest/cellular_tomo/EMDatasetCell
tree root: true

ClassDefinition
name: Acquisition
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionAcquisition

ClassDefinition
name: AcquisitionSpa
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisitionSpa
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/acquisitionAcquisitionSpa

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

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

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

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

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

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

ClassDefinition
name: Instrument
definition uri: https://w3id.org/oscem-schemas/latest/instrumentInstrument
description: Instrument values, mostly constant across a data collection.
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/instrumentInstrument

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

ClassDefinition
name: SampleCell
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomoSampleCell
description: Unifying class to describe the full sample with growth conditions
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
is a: SampleEnv
slots: SampleEnv_specimen_env
slots: freezing
slots: thinning
slots: tomogram_features
slots: growth_condition
class uri: https://w3id.org/oscem-schemas/latest/cellular_tomoSampleCell

ClassDefinition
name: GrowthCondition
definition uri: https://w3id.org/oscem-schemas/latest/cellular_tomoGrowthCondition
description: How the cells were grown
from schema: https://w3id.org/oscem-schemas/latest/sample-cellular-tomo-lab
slots: media
slots: growth_location
slots: cell_cycle
slots: treatment
slots: atmosphere_growth
slots: temperature_growth
class uri: https://w3id.org/oscem-schemas/latest/cellular_tomoGrowthCondition

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

ClassDefinition
name: AcquisitionTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionTomo
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/tomography/AcquisitionTomo

ClassDefinition
name: AcquisitionSubTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionSubTomo
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/tomography/AcquisitionSubTomo

ClassDefinition
name: AcquisitionEnvTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionEnvTomo
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/tomography/AcquisitionEnvTomo

ClassDefinition
name: AcquisitionCelTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionCelTomo
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/tomography/AcquisitionCelTomo

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

ClassDefinition
name: Person
definition uri: https://w3id.org/oscem-schemas/latest/organizational/Person
description: personal information
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/Author
description: Details on the person performing the experiment.
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/organizational/Author

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

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

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

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

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

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

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

ClassDefinition
name: QuantityValue
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesQuantityValue
description: if a value has a unit, it should be given as a unit value pair.
from schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_typesQuantitySI
description: unit value extended to have two additional fields si_value and si_unit
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: QuantityValue
slots: QuantityValue_unit
slots: QuantityValue_value
slots: valueSI
slots: unitSI
class uri: https://w3id.org/oscem-schemas/latest/custom_typesQuantitySI

ClassDefinition
name: Descriptor
definition uri: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/custom_types
abstract: true
slots: Descriptor_descriptor_name
slots: Descriptor_descriptor_thing
class uri: https://w3id.org/oscem-schemas/latest/custom_typesDescriptor

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

ClassDefinition
name: SampleEnv
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleSampleEnv
description: Unifying class to describe the full sample.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slots: SampleEnv_specimen_env
slots: freezing
slots: thinning
slots: tomogram_features
class uri: https://w3id.org/oscem-schemas/latest/environmental_sampleSampleEnv

ClassDefinition
name: SpecimenEnv
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleSpecimenEnv
description: base information on the acquisition and treatment of the sample itself.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slots: SpecimenEnv_organism
slots: tissue
slots: source_env
slots: location
slots: collection_date
slots: handling
class uri: https://w3id.org/oscem-schemas/latest/environmental_sampleSpecimenEnv

ClassDefinition
name: Freezing
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleFreezing
description: how the sample was frozen.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slots: cryogen_sample_env
slots: method
slots: blotting
slots: humidity_env
slots: temperature_env
slots: atmosphere
slots: details
class uri: https://w3id.org/oscem-schemas/latest/environmental_sampleFreezing

ClassDefinition
name: Thinning
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleThinning
description: how the frozen sample was thinned by i.e. FiB-milling
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slots: method_thin
slots: instrument_thin
slots: ion_source
slots: target_thickness
slots: lift_out
class uri: https://w3id.org/oscem-schemas/latest/environmental_sampleThinning

ClassDefinition
name: TomogramFeatures
definition uri: https://w3id.org/oscem-schemas/latest/environmental_sampleTomogramFeatures
description: what was the target of the tomograms, and what area of a cell do they cover.
from schema: https://w3id.org/oscem-schemas/latest/sample-env
slots: cellular_features
slots: organelles
slots: main_target
slots: details_tomo
class uri: https://w3id.org/oscem-schemas/latest/environmental_sampleTomogramFeatures