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Class: XRayPreparation

X-ray crystallography specific preparation

URI: lambdaber:XRayPreparation

classDiagram class XRayPreparation click XRayPreparation href "../XRayPreparation/" TechniqueSpecificPreparation <|-- XRayPreparation click TechniqueSpecificPreparation href "../TechniqueSpecificPreparation/" XRayPreparation : additives XRayPreparation : cryoprotectant XRayPreparation : cryoprotectant_concentration XRayPreparation : crystal_notes XRayPreparation : crystal_size_um XRayPreparation : crystallization_conditions XRayPreparation : crystallization_method XRayPreparation --> "0..1" CrystallizationMethodEnum : crystallization_method click CrystallizationMethodEnum href "../CrystallizationMethodEnum/" XRayPreparation : description XRayPreparation : drop_ratio_protein_to_reservoir XRayPreparation : drop_volume_nl XRayPreparation : flash_cooling_method XRayPreparation : initial_hit_condition XRayPreparation : mounting_method XRayPreparation : optimization_strategy XRayPreparation : optimized_condition XRayPreparation : protein_buffer XRayPreparation : protein_concentration_mg_per_ml XRayPreparation : reservoir_volume_ul XRayPreparation : screen_name XRayPreparation : seed_stock_dilution XRayPreparation : seeding_type XRayPreparation : soak_compound XRayPreparation : soak_conditions XRayPreparation : temperature_c

Inheritance

Slots

Name Cardinality and Range Description Inheritance
protein_concentration_mg_per_ml 0..1
Float		 Protein concentration for crystallization in mg/mL direct
protein_buffer 0..1
String		 Buffer composition for protein solution direct
additives 0..1
String		 Additives mixed with protein before crystallization direct
crystallization_method 0..1
CrystallizationMethodEnum		 Method used for crystallization direct
screen_name 0..1
String		 Name of crystallization screen used direct
temperature_c 0..1
Float		 Crystallization temperature in Celsius direct
drop_ratio_protein_to_reservoir 0..1
String		 Ratio of protein to reservoir solution in drop (e direct
drop_volume_nl 0..1
Float		 Total drop volume in nanoliters direct
reservoir_volume_ul 0..1
Float		 Reservoir volume in microliters direct
seeding_type 0..1
String		 Type of seeding used (micro, macro, streak) direct
seed_stock_dilution 0..1
String		 Dilution factor for seed stock direct
initial_hit_condition 0..1
String		 Description of initial crystallization hit condition direct
optimization_strategy 0..1
String		 Strategy used to optimize crystals direct
optimized_condition 0..1
String		 Final optimized crystallization condition direct
crystallization_conditions 0..1
String		 Detailed crystallization conditions direct
crystal_size_um 0..1
String		 Crystal dimensions in micrometers direct
cryoprotectant 0..1
String		 Cryoprotectant used direct
cryoprotectant_concentration 0..1
Float		 Cryoprotectant concentration percentage direct
soak_compound 0..1
String		 Compound used for soaking (ligand, heavy atom) direct
soak_conditions 0..1
String		 Conditions for crystal soaking direct
mounting_method 0..1
String		 Crystal mounting method direct
flash_cooling_method 0..1
String		 Flash cooling protocol direct
crystal_notes 0..1
String		 Additional notes about crystal quality and handling direct
description 0..1
String		 AttributeGroup

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:XRayPreparation
native lambdaber:XRayPreparation

LinkML Source

Direct

name: XRayPreparation
description: X-ray crystallography specific preparation
from_schema: https://w3id.org/lambda-ber-schema/
is_a: TechniqueSpecificPreparation
attributes:
  protein_concentration_mg_per_ml:
    name: protein_concentration_mg_per_ml
    description: Protein concentration for crystallization in mg/mL
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: float
  protein_buffer:
    name: protein_buffer
    description: Buffer composition for protein solution
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  additives:
    name: additives
    description: Additives mixed with protein before crystallization
    from_schema: https://w3id.org/lambda-ber-schema/
    domain_of:
    - BufferComposition
    - XRayPreparation
  crystallization_method:
    name: crystallization_method
    description: Method used for crystallization
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: CrystallizationMethodEnum
  screen_name:
    name: screen_name
    description: Name of crystallization screen used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  temperature_c:
    name: temperature_c
    description: Crystallization temperature in Celsius
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: float
  drop_ratio_protein_to_reservoir:
    name: drop_ratio_protein_to_reservoir
    description: Ratio of protein to reservoir solution in drop (e.g., 1:1, 2:1)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  drop_volume_nl:
    name: drop_volume_nl
    description: Total drop volume in nanoliters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: float
  reservoir_volume_ul:
    name: reservoir_volume_ul
    description: Reservoir volume in microliters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: float
  seeding_type:
    name: seeding_type
    description: Type of seeding used (micro, macro, streak)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  seed_stock_dilution:
    name: seed_stock_dilution
    description: Dilution factor for seed stock
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  initial_hit_condition:
    name: initial_hit_condition
    description: Description of initial crystallization hit condition
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  optimization_strategy:
    name: optimization_strategy
    description: Strategy used to optimize crystals
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  optimized_condition:
    name: optimized_condition
    description: Final optimized crystallization condition
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  crystallization_conditions:
    name: crystallization_conditions
    description: Detailed crystallization conditions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  crystal_size_um:
    name: crystal_size_um
    description: Crystal dimensions in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  cryoprotectant:
    name: cryoprotectant
    description: Cryoprotectant used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: string
  cryoprotectant_concentration:
    name: cryoprotectant_concentration
    description: Cryoprotectant concentration percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
    range: float
  soak_compound:
    name: soak_compound
    description: Compound used for soaking (ligand, heavy atom)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  soak_conditions:
    name: soak_conditions
    description: Conditions for crystal soaking
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  mounting_method:
    name: mounting_method
    description: Crystal mounting method
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  flash_cooling_method:
    name: flash_cooling_method
    description: Flash cooling protocol
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation
  crystal_notes:
    name: crystal_notes
    description: Additional notes about crystal quality and handling
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - XRayPreparation

Induced

name: XRayPreparation
description: X-ray crystallography specific preparation
from_schema: https://w3id.org/lambda-ber-schema/
is_a: TechniqueSpecificPreparation
attributes:
  protein_concentration_mg_per_ml:
    name: protein_concentration_mg_per_ml
    description: Protein concentration for crystallization in mg/mL
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: protein_concentration_mg_per_ml
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: float
  protein_buffer:
    name: protein_buffer
    description: Buffer composition for protein solution
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: protein_buffer
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  additives:
    name: additives
    description: Additives mixed with protein before crystallization
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: additives
    owner: XRayPreparation
    domain_of:
    - BufferComposition
    - XRayPreparation
    range: string
  crystallization_method:
    name: crystallization_method
    description: Method used for crystallization
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: crystallization_method
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: CrystallizationMethodEnum
  screen_name:
    name: screen_name
    description: Name of crystallization screen used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: screen_name
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  temperature_c:
    name: temperature_c
    description: Crystallization temperature in Celsius
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: temperature_c
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: float
  drop_ratio_protein_to_reservoir:
    name: drop_ratio_protein_to_reservoir
    description: Ratio of protein to reservoir solution in drop (e.g., 1:1, 2:1)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: drop_ratio_protein_to_reservoir
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  drop_volume_nl:
    name: drop_volume_nl
    description: Total drop volume in nanoliters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: drop_volume_nl
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: float
  reservoir_volume_ul:
    name: reservoir_volume_ul
    description: Reservoir volume in microliters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: reservoir_volume_ul
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: float
  seeding_type:
    name: seeding_type
    description: Type of seeding used (micro, macro, streak)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: seeding_type
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  seed_stock_dilution:
    name: seed_stock_dilution
    description: Dilution factor for seed stock
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: seed_stock_dilution
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  initial_hit_condition:
    name: initial_hit_condition
    description: Description of initial crystallization hit condition
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: initial_hit_condition
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  optimization_strategy:
    name: optimization_strategy
    description: Strategy used to optimize crystals
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: optimization_strategy
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  optimized_condition:
    name: optimized_condition
    description: Final optimized crystallization condition
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: optimized_condition
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  crystallization_conditions:
    name: crystallization_conditions
    description: Detailed crystallization conditions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: crystallization_conditions
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  crystal_size_um:
    name: crystal_size_um
    description: Crystal dimensions in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: crystal_size_um
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  cryoprotectant:
    name: cryoprotectant
    description: Cryoprotectant used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cryoprotectant
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  cryoprotectant_concentration:
    name: cryoprotectant_concentration
    description: Cryoprotectant concentration percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cryoprotectant_concentration
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: float
  soak_compound:
    name: soak_compound
    description: Compound used for soaking (ligand, heavy atom)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: soak_compound
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  soak_conditions:
    name: soak_conditions
    description: Conditions for crystal soaking
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: soak_conditions
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  mounting_method:
    name: mounting_method
    description: Crystal mounting method
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: mounting_method
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  flash_cooling_method:
    name: flash_cooling_method
    description: Flash cooling protocol
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: flash_cooling_method
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  crystal_notes:
    name: crystal_notes
    description: Additional notes about crystal quality and handling
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: crystal_notes
    owner: XRayPreparation
    domain_of:
    - XRayPreparation
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: description
    owner: XRayPreparation
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string