Class: Sample

A biological sample used in structural biology experiments

classDiagram class Sample click Sample href "../Sample/" NamedThing <|-- Sample click NamedThing href "../NamedThing/" Sample : anatomy Sample --> "0..1" OntologyTerm : anatomy click OntologyTerm href "../OntologyTerm/" Sample : biophysical_properties Sample --> "*" BiophysicalProperty : biophysical_properties click BiophysicalProperty href "../BiophysicalProperty/" Sample : buffer_composition Sample --> "0..1" BufferComposition : buffer_composition click BufferComposition href "../BufferComposition/" Sample : cell_type Sample --> "0..1" OntologyTerm : cell_type click OntologyTerm href "../OntologyTerm/" Sample : concentration Sample : concentration_unit Sample --> "0..1" ConcentrationUnitEnum : concentration_unit click ConcentrationUnitEnum href "../ConcentrationUnitEnum/" Sample : conformational_ensemble Sample --> "0..1" ConformationalEnsemble : conformational_ensemble click ConformationalEnsemble href "../ConformationalEnsemble/" Sample : database_cross_references Sample --> "*" DatabaseCrossReference : database_cross_references click DatabaseCrossReference href "../DatabaseCrossReference/" Sample : description Sample : evolutionary_conservation Sample --> "0..1" EvolutionaryConservation : evolutionary_conservation click EvolutionaryConservation href "../EvolutionaryConservation/" Sample : functional_sites Sample --> "*" FunctionalSite : functional_sites click FunctionalSite href "../FunctionalSite/" Sample : id Sample : ligand_interactions Sample --> "*" LigandInteraction : ligand_interactions click LigandInteraction href "../LigandInteraction/" Sample : molecular_composition Sample --> "0..1" MolecularComposition : molecular_composition click MolecularComposition href "../MolecularComposition/" Sample : molecular_weight Sample : mutation_effects Sample --> "*" MutationEffect : mutation_effects click MutationEffect href "../MutationEffect/" Sample : organism Sample --> "0..1" OntologyTerm : organism click OntologyTerm href "../OntologyTerm/" Sample : parent_sample_id Sample --> "0..1" Sample : parent_sample_id click Sample href "../Sample/" Sample : preparation_method Sample : protein_interactions Sample --> "*" ProteinProteinInteraction : protein_interactions click ProteinProteinInteraction href "../ProteinProteinInteraction/" Sample : ptm_annotations Sample --> "*" PostTranslationalModification : ptm_annotations click PostTranslationalModification href "../PostTranslationalModification/" Sample : purity_percentage Sample : quality_metrics Sample : sample_code Sample : sample_type Sample --> "1" SampleTypeEnum : sample_type click SampleTypeEnum href "../SampleTypeEnum/" Sample : storage_conditions Sample --> "0..1" StorageConditions : storage_conditions click StorageConditions href "../StorageConditions/" Sample : structural_features Sample --> "*" StructuralFeature : structural_features click StructuralFeature href "../StructuralFeature/" Sample : title

Inheritance

NamedThing
- Sample

Slots

Name	Cardinality and Range	Description	Inheritance
sample_code	1 String	Human-friendly laboratory identifier or facility code for the sample (e	direct
sample_type	1 SampleTypeEnum	Type of biological sample	direct
molecular_composition	0..1 MolecularComposition	Description of molecular composition including sequences, modifications, liga...	direct
molecular_weight	0..1 Float	Molecular weight in kDa	direct
concentration	0..1 Float	Sample concentration in mg/mL or µM	direct
concentration_unit	0..1 ConcentrationUnitEnum	Unit of concentration measurement	direct
buffer_composition	0..1 BufferComposition	Buffer composition including pH, salts, additives	direct
preparation_method	0..1 String	Method used to prepare the sample	direct
storage_conditions	0..1 StorageConditions	Storage conditions for the sample	direct
organism	0..1 OntologyTerm	Source organism for the sample (e	direct
anatomy	0..1 OntologyTerm	Anatomical part or tissue (e	direct
cell_type	0..1 OntologyTerm	Cell type if applicable (e	direct
parent_sample_id	0..1 Sample	Reference to parent sample for derivation tracking	direct
purity_percentage	0..1 Float	Sample purity as percentage	direct
quality_metrics	0..1 String	Quality control metrics for the sample	direct
functional_sites	* FunctionalSite	Functional site annotations for proteins in the sample	direct
structural_features	* StructuralFeature	Structural feature annotations	direct
protein_interactions	* ProteinProteinInteraction	Protein-protein interaction annotations	direct
ligand_interactions	* LigandInteraction	Small molecule interaction annotations	direct
mutation_effects	* MutationEffect	Effects of mutations present in the sample	direct
ptm_annotations	* PostTranslationalModification	Post-translational modification annotations	direct
biophysical_properties	* BiophysicalProperty	Measured or predicted biophysical properties	direct
evolutionary_conservation	0..1 EvolutionaryConservation	Evolutionary conservation data	direct
conformational_ensemble	0..1 ConformationalEnsemble	Conformational states and dynamics	direct
database_cross_references	* DatabaseCrossReference	Cross-references to external databases	direct
id	1 Uriorcurie	Globally unique identifier as an IRI or CURIE for machine processing and exte...	NamedThing
title	0..1 String		NamedThing
description	0..1 String		NamedThing

Usages

used by	used in	type	used
Study	samples	range	Sample
Sample	parent_sample_id	range	Sample

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Sample
description: A biological sample used in structural biology experiments
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  sample_code:
    name: sample_code
    description: Human-friendly laboratory identifier or facility code for the sample
      (e.g., 'ALS-12.3.1-SAMPLE-001', 'LAB-PROT-2024-01'). Used for local reference
      and tracking within laboratory workflows.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    required: true
  sample_type:
    name: sample_type
    description: Type of biological sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: SampleTypeEnum
    required: true
  molecular_composition:
    name: molecular_composition
    description: Description of molecular composition including sequences, modifications,
      ligands
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: MolecularComposition
  molecular_weight:
    name: molecular_weight
    description: Molecular weight in kDa
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: float
    unit:
      ucum_code: kDa
  concentration:
    name: concentration
    description: Sample concentration in mg/mL or µM
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: float
  concentration_unit:
    name: concentration_unit
    description: Unit of concentration measurement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: ConcentrationUnitEnum
  buffer_composition:
    name: buffer_composition
    description: Buffer composition including pH, salts, additives
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: BufferComposition
  preparation_method:
    name: preparation_method
    description: Method used to prepare the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
  storage_conditions:
    name: storage_conditions
    description: Storage conditions for the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: StorageConditions
  organism:
    name: organism
    description: Source organism for the sample (e.g., NCBITaxon:3702 for Arabidopsis
      thaliana)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: OntologyTerm
  anatomy:
    name: anatomy
    description: Anatomical part or tissue (e.g., UBERON:0008945 for leaf)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: OntologyTerm
  cell_type:
    name: cell_type
    description: Cell type if applicable (e.g., CL:0000057 for fibroblast)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: OntologyTerm
  parent_sample_id:
    name: parent_sample_id
    description: Reference to parent sample for derivation tracking
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: Sample
  purity_percentage:
    name: purity_percentage
    description: Sample purity as percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: float
    minimum_value: 0
    maximum_value: 100
  quality_metrics:
    name: quality_metrics
    description: Quality control metrics for the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - ExperimentRun
  functional_sites:
    name: functional_sites
    description: Functional site annotations for proteins in the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: FunctionalSite
    multivalued: true
    inlined: true
    inlined_as_list: true
  structural_features:
    name: structural_features
    description: Structural feature annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: StructuralFeature
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_interactions:
    name: protein_interactions
    description: Protein-protein interaction annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ProteinProteinInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  ligand_interactions:
    name: ligand_interactions
    description: Small molecule interaction annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  mutation_effects:
    name: mutation_effects
    description: Effects of mutations present in the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: MutationEffect
    multivalued: true
    inlined: true
    inlined_as_list: true
  ptm_annotations:
    name: ptm_annotations
    description: Post-translational modification annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: PostTranslationalModification
    multivalued: true
    inlined: true
    inlined_as_list: true
  biophysical_properties:
    name: biophysical_properties
    description: Measured or predicted biophysical properties
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: BiophysicalProperty
    multivalued: true
    inlined: true
    inlined_as_list: true
  evolutionary_conservation:
    name: evolutionary_conservation
    description: Evolutionary conservation data
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: EvolutionaryConservation
    inlined: true
  conformational_ensemble:
    name: conformational_ensemble
    description: Conformational states and dynamics
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ConformationalEnsemble
    inlined: true
  database_cross_references:
    name: database_cross_references
    description: Cross-references to external databases
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Sample
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: Sample
description: A biological sample used in structural biology experiments
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  sample_code:
    name: sample_code
    description: Human-friendly laboratory identifier or facility code for the sample
      (e.g., 'ALS-12.3.1-SAMPLE-001', 'LAB-PROT-2024-01'). Used for local reference
      and tracking within laboratory workflows.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sample_code
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
  sample_type:
    name: sample_type
    description: Type of biological sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sample_type
    owner: Sample
    domain_of:
    - Sample
    range: SampleTypeEnum
    required: true
  molecular_composition:
    name: molecular_composition
    description: Description of molecular composition including sequences, modifications,
      ligands
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: molecular_composition
    owner: Sample
    domain_of:
    - Sample
    range: MolecularComposition
  molecular_weight:
    name: molecular_weight
    description: Molecular weight in kDa
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: molecular_weight
    owner: Sample
    domain_of:
    - Sample
    range: float
    unit:
      ucum_code: kDa
  concentration:
    name: concentration
    description: Sample concentration in mg/mL or µM
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: concentration
    owner: Sample
    domain_of:
    - Sample
    range: float
  concentration_unit:
    name: concentration_unit
    description: Unit of concentration measurement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: concentration_unit
    owner: Sample
    domain_of:
    - Sample
    range: ConcentrationUnitEnum
  buffer_composition:
    name: buffer_composition
    description: Buffer composition including pH, salts, additives
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: buffer_composition
    owner: Sample
    domain_of:
    - Sample
    range: BufferComposition
  preparation_method:
    name: preparation_method
    description: Method used to prepare the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: preparation_method
    owner: Sample
    domain_of:
    - Sample
    range: string
  storage_conditions:
    name: storage_conditions
    description: Storage conditions for the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: storage_conditions
    owner: Sample
    domain_of:
    - Sample
    range: StorageConditions
  organism:
    name: organism
    description: Source organism for the sample (e.g., NCBITaxon:3702 for Arabidopsis
      thaliana)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: organism
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: OntologyTerm
  anatomy:
    name: anatomy
    description: Anatomical part or tissue (e.g., UBERON:0008945 for leaf)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: anatomy
    owner: Sample
    domain_of:
    - Sample
    range: OntologyTerm
  cell_type:
    name: cell_type
    description: Cell type if applicable (e.g., CL:0000057 for fibroblast)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cell_type
    owner: Sample
    domain_of:
    - Sample
    range: OntologyTerm
  parent_sample_id:
    name: parent_sample_id
    description: Reference to parent sample for derivation tracking
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: parent_sample_id
    owner: Sample
    domain_of:
    - Sample
    range: Sample
  purity_percentage:
    name: purity_percentage
    description: Sample purity as percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: purity_percentage
    owner: Sample
    domain_of:
    - Sample
    range: float
    minimum_value: 0
    maximum_value: 100
  quality_metrics:
    name: quality_metrics
    description: Quality control metrics for the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: quality_metrics
    owner: Sample
    domain_of:
    - Sample
    - ExperimentRun
    range: string
  functional_sites:
    name: functional_sites
    description: Functional site annotations for proteins in the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: functional_sites
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: FunctionalSite
    multivalued: true
    inlined: true
    inlined_as_list: true
  structural_features:
    name: structural_features
    description: Structural feature annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: structural_features
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: StructuralFeature
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_interactions:
    name: protein_interactions
    description: Protein-protein interaction annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: protein_interactions
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ProteinProteinInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  ligand_interactions:
    name: ligand_interactions
    description: Small molecule interaction annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ligand_interactions
    owner: Sample
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  mutation_effects:
    name: mutation_effects
    description: Effects of mutations present in the sample
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: mutation_effects
    owner: Sample
    domain_of:
    - Sample
    range: MutationEffect
    multivalued: true
    inlined: true
    inlined_as_list: true
  ptm_annotations:
    name: ptm_annotations
    description: Post-translational modification annotations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ptm_annotations
    owner: Sample
    domain_of:
    - Sample
    range: PostTranslationalModification
    multivalued: true
    inlined: true
    inlined_as_list: true
  biophysical_properties:
    name: biophysical_properties
    description: Measured or predicted biophysical properties
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: biophysical_properties
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: BiophysicalProperty
    multivalued: true
    inlined: true
    inlined_as_list: true
  evolutionary_conservation:
    name: evolutionary_conservation
    description: Evolutionary conservation data
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: evolutionary_conservation
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: EvolutionaryConservation
    inlined: true
  conformational_ensemble:
    name: conformational_ensemble
    description: Conformational states and dynamics
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: conformational_ensemble
    owner: Sample
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ConformationalEnsemble
    inlined: true
  database_cross_references:
    name: database_cross_references
    description: Cross-references to external databases
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: database_cross_references
    owner: Sample
    domain_of:
    - Sample
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: Sample
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: Sample
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: Sample
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string