Class: Dataset

Root container holding flat entity collections and association tables. Follows relational database design patterns for structural biology data.

URI: lambdaber:Dataset

classDiagram class Dataset click Dataset href "../Dataset/" NamedThing <|-- Dataset click NamedThing href "../NamedThing/" Dataset : data_files Dataset --> "*" DataFile : data_files click DataFile href "../DataFile/" Dataset : description Dataset : experiment_instrument_associations Dataset --> "*" ExperimentInstrumentAssociation : experiment_instrument_associations click ExperimentInstrumentAssociation href "../ExperimentInstrumentAssociation/" Dataset : experiment_runs Dataset --> "*" ExperimentRun : experiment_runs click ExperimentRun href "../ExperimentRun/" Dataset : experiment_sample_associations Dataset --> "*" ExperimentSampleAssociation : experiment_sample_associations click ExperimentSampleAssociation href "../ExperimentSampleAssociation/" Dataset : id Dataset : images Dataset --> "*" Image : images click Image href "../Image/" Dataset : instruments Dataset --> "*" Instrument : instruments click Instrument href "../Instrument/" Dataset : keywords Dataset : protein_constructs Dataset --> "*" ProteinConstruct : protein_constructs click ProteinConstruct href "../ProteinConstruct/" Dataset : sample_preparations Dataset --> "*" SamplePreparation : sample_preparations click SamplePreparation href "../SamplePreparation/" Dataset : samples Dataset --> "*" Sample : samples click Sample href "../Sample/" Dataset : studies Dataset --> "*" Study : studies click Study href "../Study/" Dataset : study_experiment_associations Dataset --> "*" StudyExperimentAssociation : study_experiment_associations click StudyExperimentAssociation href "../StudyExperimentAssociation/" Dataset : study_sample_associations Dataset --> "*" StudySampleAssociation : study_sample_associations click StudySampleAssociation href "../StudySampleAssociation/" Dataset : study_workflow_associations Dataset --> "*" StudyWorkflowAssociation : study_workflow_associations click StudyWorkflowAssociation href "../StudyWorkflowAssociation/" Dataset : title Dataset : workflow_experiment_associations Dataset --> "*" WorkflowExperimentAssociation : workflow_experiment_associations click WorkflowExperimentAssociation href "../WorkflowExperimentAssociation/" Dataset : workflow_input_associations Dataset --> "*" WorkflowInputAssociation : workflow_input_associations click WorkflowInputAssociation href "../WorkflowInputAssociation/" Dataset : workflow_output_associations Dataset --> "*" WorkflowOutputAssociation : workflow_output_associations click WorkflowOutputAssociation href "../WorkflowOutputAssociation/" Dataset : workflow_runs Dataset --> "*" WorkflowRun : workflow_runs click WorkflowRun href "../WorkflowRun/"

Inheritance

NamedThing
- Dataset

Slots

Name	Cardinality and Range	Description	Inheritance
keywords	* String	Keywords or tags describing the dataset for search and categorization	direct
studies	* Study	All studies in this dataset	direct
instruments	* Instrument	All instruments used across studies	direct
protein_constructs	* ProteinConstruct	All protein constructs	direct
samples	* Sample	All samples across all studies	direct
sample_preparations	* SamplePreparation	All sample preparations	direct
experiment_runs	* ExperimentRun	All experiment runs (data collection sessions)	direct
workflow_runs	* WorkflowRun	All workflow runs (computational processing)	direct
data_files	* DataFile	All data files	direct
images	* Image	All images	direct
study_sample_associations	* StudySampleAssociation	Links between studies and samples (M:N)	direct
study_experiment_associations	* StudyExperimentAssociation	Links between studies and experiments (M:N)	direct
study_workflow_associations	* StudyWorkflowAssociation	Links between studies and workflows (M:N)	direct
experiment_sample_associations	* ExperimentSampleAssociation	Links between experiments and samples (M:N with role)	direct
experiment_instrument_associations	* ExperimentInstrumentAssociation	Links between experiments and instruments (M:N)	direct
workflow_experiment_associations	* WorkflowExperimentAssociation	Links between workflows and source experiments (M:N)	direct
workflow_input_associations	* WorkflowInputAssociation	Links between workflows and input files	direct
workflow_output_associations	* WorkflowOutputAssociation	Links between workflows and output files	direct
id	1 Uriorcurie	Globally unique identifier as an IRI or CURIE for machine processing and exte...	NamedThing
title	0..1 String	A human-readable name or title for this entity	NamedThing
description	0..1 String	A detailed textual description of this entity	NamedThing

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Dataset
description: Root container holding flat entity collections and association tables.
  Follows relational database design patterns for structural biology data.
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  keywords:
    name: keywords
    description: Keywords or tags describing the dataset for search and categorization
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    - Study
    range: string
    multivalued: true
  studies:
    name: studies
    description: All studies in this dataset
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: Study
    multivalued: true
    inlined: true
    inlined_as_list: true
  instruments:
    name: instruments
    description: All instruments used across studies
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: Instrument
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_constructs:
    name: protein_constructs
    description: All protein constructs
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: ProteinConstruct
    multivalued: true
    inlined: true
    inlined_as_list: true
  samples:
    name: samples
    description: All samples across all studies
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: Sample
    multivalued: true
    inlined: true
    inlined_as_list: true
  sample_preparations:
    name: sample_preparations
    description: All sample preparations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: SamplePreparation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_runs:
    name: experiment_runs
    description: All experiment runs (data collection sessions)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: ExperimentRun
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_runs:
    name: workflow_runs
    description: All workflow runs (computational processing)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: WorkflowRun
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_files:
    name: data_files
    description: All data files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: DataFile
    multivalued: true
    inlined: true
    inlined_as_list: true
  images:
    name: images
    description: All images
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: Image
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_sample_associations:
    name: study_sample_associations
    description: Links between studies and samples (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: StudySampleAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_experiment_associations:
    name: study_experiment_associations
    description: Links between studies and experiments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: StudyExperimentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_workflow_associations:
    name: study_workflow_associations
    description: Links between studies and workflows (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: StudyWorkflowAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_sample_associations:
    name: experiment_sample_associations
    description: Links between experiments and samples (M:N with role)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: ExperimentSampleAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_instrument_associations:
    name: experiment_instrument_associations
    description: Links between experiments and instruments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: ExperimentInstrumentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_experiment_associations:
    name: workflow_experiment_associations
    description: Links between workflows and source experiments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: WorkflowExperimentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_input_associations:
    name: workflow_input_associations
    description: Links between workflows and input files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: WorkflowInputAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_output_associations:
    name: workflow_output_associations
    description: Links between workflows and output files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Dataset
    range: WorkflowOutputAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
tree_root: true

Induced

name: Dataset
description: Root container holding flat entity collections and association tables.
  Follows relational database design patterns for structural biology data.
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  keywords:
    name: keywords
    description: Keywords or tags describing the dataset for search and categorization
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: keywords
    owner: Dataset
    domain_of:
    - Dataset
    - Study
    range: string
    multivalued: true
  studies:
    name: studies
    description: All studies in this dataset
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: studies
    owner: Dataset
    domain_of:
    - Dataset
    range: Study
    multivalued: true
    inlined: true
    inlined_as_list: true
  instruments:
    name: instruments
    description: All instruments used across studies
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: instruments
    owner: Dataset
    domain_of:
    - Dataset
    range: Instrument
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_constructs:
    name: protein_constructs
    description: All protein constructs
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: protein_constructs
    owner: Dataset
    domain_of:
    - Dataset
    range: ProteinConstruct
    multivalued: true
    inlined: true
    inlined_as_list: true
  samples:
    name: samples
    description: All samples across all studies
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: samples
    owner: Dataset
    domain_of:
    - Dataset
    range: Sample
    multivalued: true
    inlined: true
    inlined_as_list: true
  sample_preparations:
    name: sample_preparations
    description: All sample preparations
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sample_preparations
    owner: Dataset
    domain_of:
    - Dataset
    range: SamplePreparation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_runs:
    name: experiment_runs
    description: All experiment runs (data collection sessions)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_runs
    owner: Dataset
    domain_of:
    - Dataset
    range: ExperimentRun
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_runs:
    name: workflow_runs
    description: All workflow runs (computational processing)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_runs
    owner: Dataset
    domain_of:
    - Dataset
    range: WorkflowRun
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_files:
    name: data_files
    description: All data files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: data_files
    owner: Dataset
    domain_of:
    - Dataset
    range: DataFile
    multivalued: true
    inlined: true
    inlined_as_list: true
  images:
    name: images
    description: All images
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: images
    owner: Dataset
    domain_of:
    - Dataset
    range: Image
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_sample_associations:
    name: study_sample_associations
    description: Links between studies and samples (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: study_sample_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: StudySampleAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_experiment_associations:
    name: study_experiment_associations
    description: Links between studies and experiments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: study_experiment_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: StudyExperimentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  study_workflow_associations:
    name: study_workflow_associations
    description: Links between studies and workflows (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: study_workflow_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: StudyWorkflowAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_sample_associations:
    name: experiment_sample_associations
    description: Links between experiments and samples (M:N with role)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_sample_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: ExperimentSampleAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  experiment_instrument_associations:
    name: experiment_instrument_associations
    description: Links between experiments and instruments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_instrument_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: ExperimentInstrumentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_experiment_associations:
    name: workflow_experiment_associations
    description: Links between workflows and source experiments (M:N)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_experiment_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: WorkflowExperimentAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_input_associations:
    name: workflow_input_associations
    description: Links between workflows and input files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_input_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: WorkflowInputAssociation
    multivalued: true
    inlined: true
    inlined_as_list: true
  workflow_output_associations:
    name: workflow_output_associations
    description: Links between workflows and output files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_output_associations
    owner: Dataset
    domain_of:
    - Dataset
    range: WorkflowOutputAssociation
    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: Dataset
    domain_of:
    - NamedThing
    - Attribute
    range: uriorcurie
    required: true
  title:
    name: title
    description: A human-readable name or title for this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: Dataset
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A detailed textual description of this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: Dataset
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string
tree_root: true