SchemaDefinition
name: Sample
description: LinkML schema for electron microscopy sample and author-related metadata, broadly following the EMDB standard with some additions.
id: https://w3id.org/oscem-schemas/latest/sample
imports: linkml:types
imports: ./custom_types
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  prefix prefix: linkml
  prefix reference: https://w3id.org/linkml/
prefixes:
  prefix prefix: sample
  prefix reference: https://w3id.org/oscem-schemas/latest/sample
prefixes:
  prefix prefix: types
  prefix reference: https://w3id.org/oscem-schemas/latest/custom_types
default prefix: sample
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: sample.yaml
source file date: 2025-12-05T16:03:40
source file size: 9873
generation date: 2025-12-05T16:06:27

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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: Sample
domain of: Sample
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
owner: Sample
domain of: Sample
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: Grid
domain of: Grid
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
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://example.org/UNKNOWN/qudt/hasUnit
slot uri: http://example.org/UNKNOWN/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://example.org/UNKNOWN/qudt/hasQuantityKind
slot uri: http://example.org/UNKNOWN/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: Sample_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
is a: name
domain: Sample
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesname
alias: name
owner: Sample
domain of: Sample
is usage slot: true
usage slot name: name
range: string
required: true

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SlotDefinition
name: Grid_manufacturer
definition uri: https://w3id.org/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: Grid
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmanufacturer
alias: manufacturer
owner: Grid
domain of: Grid
is usage slot: true
usage slot name: manufacturer
range: string

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

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

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

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

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

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

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

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

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

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

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

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

SlotDefinition
name: SampleMolecular_overall_molecule
definition uri: https://w3id.org/oscem-schemas/latest/sampleoverall_molecule
description: Description of the overall molecule
from schema: https://w3id.org/oscem-schemas/latest/sample
is a: Sample_overall_molecule
domain: SampleMolecular
slot uri: https://w3id.org/oscem-schemas/latest/sampleoverall_molecule
alias: overall_molecule
owner: SampleMolecular
domain of: SampleMolecular
is usage slot: true
usage slot name: overall_molecule
range: OverallMolecule
required: true
inlined: true
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://example.org/UNKNOWN/qudt/hasUnit
is a: unit
domain: QuantityValue
slot uri: http://example.org/UNKNOWN/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://example.org/UNKNOWN/qudt/hasQuantityKind
is a: value
domain: QuantityValue
slot uri: http://example.org/UNKNOWN/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

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

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

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

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

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

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

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

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://example.org/UNKNOWN/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